22145 - User contributions [en]

22145 Immunological Bioinformatics Course Programme January 2021

2024-03-20T14:49:26Z

WikiSysop: /* 2021 Course Schedule Overview */

= COURSE PLAN FOR 2021 =

==EXAM==

The pdf with the exam will be uploaded here on Friday January 22nd, 13 - 15hs



'''Guidelines'''

* The exam will be made available at the wiki at 13.00hs. Upload a '''pdf''' with your answers '''no later than 15.00hs on DTU inside''' written exam assignment.
* You must connect at Zoom 5 minutes before the exam, and have the '''camera turned ON during the whole exam'''. Failing to meet this requirement will invalidate the exam.
* This is an '''individual exam'''. Remember sharing or copying answers is not allowed and will be severely punished according to DTU rules and code-of-honor.

==Information for Course Participants==

'''Course Format'''
* NEWS! Due to new restrictions on Covid19 this course will be completely conducted online and all classes will be recorded and uploaded
* Due to group work on some classes, it will be mandatory that you are connected and work online on the allocated time for those
* This will be needed for the entire first day, the question and answer sessions, and the final exam
* Classes will be a mixture of lectures, group work and individual exercises
* Most of the group work will consist of computer exercises, where students are required to use their laptops
* General Question and Answer will be live and uploaded after the session
* Specif Question and Answers for exercise-lectures will be held on Piazza, where you need to create an user
* All learning resources will be available through DTU inside or this site
* Expected time usage: [https://www.dtu.dk/english/Education/Course-base 1 ECTS point equals approx. 28 hours], this translates to an expected time usage of ~10 hours/day for a 5 ECTS 3-week course

'''Course Resources'''
* [http://teaching.healthtech.dtu.dk/22145/index.php/22145_-_Immunological_Bioinformatics Official course website]
* [https://kurser.dtu.dk/course/22145 Official course description]
* [https://dtudk.zoom.us/meeting/register/u5Ypc-iupjIuGtzs8eF0RlM5xijlcFdwQaQq ZOOM link for live classes(registration with DTU mail needed)]
* [https://piazza.com/dtu.dk/fall2020/22145 Piazza link for Q&A on exercises]
* IMPORTANT: Please note, that the below course programme can be subject to changes or updates. Make sure to reload the page, to get the newest version of the programme.

'''Course Teachers'''
* [CB] [https://www.dtu.dk/english/service/phonebook/Person?id=142840&cpid=263035&tab=2&qt=dtupublicationquery Carolina Barra]
* [PM] [https://www.dtu.dk/english/service/phonebook/person?id=34983&cpid=257128&tab=2&qt=dtupublicationquery Paolo Marcatili]
* [MN] [https://www.dtu.dk/english/service/phonebook/person?id=5973&cpid=214020&tab=1&qt=dtupublicationquery Morten Nielsen]
* [BR] [https://www.dtu.dk/english/service/phonebook/person?id=104623&cpid=257289&tab=3&qt=dtuprojectquery Birkir Reynisson]
* [HP] [https://www.dtu.dk/service/telefonbog/person?id=88645&cpid=262443&tab=3&qt=dtuprojectquery Helle Rus Povlsen]
* [MV] [https://www.dtu.dk/english/service/phonebook/Person?id=129355&cpid=257376&tab=2&qt=dtuprojectquery Milena Vujovic]
* [AM] [https://www.dtu.dk/english/service/phonebook/Person?id=124312&cpid=274573&tab=3&qt=dtuprojectquery Alessandro Montemurro]

'''General Daily Schedule'''

* 09.00 - 12.00 Lectures
* 12.00 - 13.00 Lunch
* 13.00 - 13.30 Live sessions Q&A
* 13.30 - 17.00 Exercises

'''Location'''

* NOTE: This edition of the course will be completely online

'''Profiles of Invited Speakers for Mini Symposium'''
* Clinical perspective: [https://research.ku.dk/search/?pure=en%2Fpersons%2F458748 MD, PhD, Clinical Associate Professor Marco Donia, Center for Cancer Immune Therapy (CCIT) and Unit for Experimental Cancer Treatment (EFEK), Herlev-Gentofte Hospital and University of Copenhagen]
* Molecular Biology perspective: [https://www.dtu.dk/service/telefonbog/person?id=102741&cpid=&tab=2&qt=dtupublicationquery PhD, Adjunkt Professor Sunil Kumar Saini, Section for Experimental and Translational Immunology, Department of Health Technology, Technical University of Denmark]
* Biomedical Industry perspective: upon confirmation.
* Bioinformatics Industry perspective: [https://www.vaccibody.com/management/ PhD, Head of Bioinformatics Monika Sekelja, Vaccibody A/S]

==2021 Course Schedule Overview==

{| class="wikitable" style="font-size:75%;"
|+ Teaching Day 1-8
!
! Monday Jan. 4th
! Tuesday Jan. 5th
! Wednesday Jan. 6th
! Thursday Jan. 7th
! Friday Jan. 8th
! Monday Jan. 11th
! Tuesday Jan. 12th
! Wednesday Jan. 13th
|-
! Topic
! Introduction and Basic Immunology
! T-Cell Epitopes
! Antigen Processing and Presentation, HLA Clustering, and Vaccine Design
! Protein Structure of B-/T-Cell Receptors and B-Cell Epitopes
! Immunopeptidomics, T-Cell Repertoires and the IEDB
! Antibody Humanization and T-Cell Interaction Models
! De-Immunization and Chimeric Antigen Receptor (CAR) Immunotherapy
! Mini-symposium on Immunoinformatics by Invited Speakers
|-
! 09.00 - 09.30
| [http://www.cbs.dtu.dk/courses/27685.imm/presentations/Carol/Course_Introduction_2021.pdf Course Introduction] '''Live on Zoom''' Recording: [http://www.cbs.dtu.dk/courses/27685.imm/recordings/22145_2021/Introduction_IB.mp4 MP4] [CB]
| Lecture: Prediction of MHC peptide binding Part 1 [MN]. Session materials: [http://www.cbs.dtu.dk/courses/27685.imm/presentations/MHCbinding_2020_part1.pdf Slides [PDF]]. Recording: [http://www.cbs.dtu.dk/courses/27685.imm/recordings/MHC_part1.mp4 [MP4]], Logo handout: [http://www.cbs.dtu.dk/courses/27685.imm/presentations/Ex_Logo.pdf [PDF]], [http://www.cbs.dtu.dk/courses/27685.imm/presentations/Ex_Logo_ans.pdf Answer Logo handout] Logo handout Recording [http://www.cbs.dtu.dk/courses/27685.imm/recordings/Ex_Logo.mp4 [MP4]].
| Lecture: MHC motif deconvolution - Identifying sequence motifs in large scale ligand data sets [MN]. Session materials: [http://www.cbs.dtu.dk/courses/27685.imm/presentations/MHCMotifDecon_2021.pdf Slides [PDF]]. Recording: [http://www.cbs.dtu.dk/courses/27685.imm/recordings/MHCMotifDecon_2021.mp4 [MP4]].
| Lecture: [https://teaching.healthtech.dtu.dk/material/22145/pdf/Antibody_structure.pdf TCR and BCR structure]. Recording: [https://youtu.be/HP-zcAugLkk Antibody Modelling] [PM]
[https://youtu.be/8dzwdlKTUXI Solution]
| Lecture: [http://www.cbs.dtu.dk/courses/27685.imm/presentations/Carol/Immunopeptidomics_2021.pdf Immunopeptidomics] '''Live on Zoom''' Recording: [http://www.cbs.dtu.dk/courses/27685.imm/recordings/22145_2021/Immunopeptidomics_CB.mp4 MP4] [CB]
| Lecture: [https://teaching.healthtech.dtu.dk/22145/images/e/ec/Humanization_2021_notabhu_reduced.pdf Antibody Humanization] [https://youtu.be/WXMrdDSHA6M Video] [PM]
| Lecture: Protein Drug Deimmunization '''Live on Zoom''' [http://www.cbs.dtu.dk/courses/27685.imm/deimmune_Presentation/2021_01_12_Deimmunization_22145.pdf pdf] [http://www.cbs.dtu.dk/courses/27685.imm/deimmune_Presentation/2021_01_12_DeimmunePresentation.mp4 mp4] [BR]
| Talk 1: '''Cancer immunotherapy in the clinic.''' Marco Donia '''Live!''' [http://www.cbs.dtu.dk/courses/27685.imm/recordings/22145_2021/Talk1_MarcoDonia.mp4 video]
|-
! 09.30 - 10.15
| [[Micro_Project_on_Basic_Immunology|Micro project group work]] '''Live on Zoom''' [CB]
| Lecture: Prediction of MHC peptide binding part 2 [MN]. Session materials: [http://www.cbs.dtu.dk/courses/27685.imm/presentations/MHCbinding_2020_part2.pdf Slides [PDF]]. Recording: [http://www.cbs.dtu.dk/courses/27685.imm/recordings/MHC_part2.mp4 [MP4]]. NN handout [http://www.cbs.dtu.dk/courses/27685.imm/presentations/NN_handout.pdf [PDF]]. NN handout Recording [http://www.cbs.dtu.dk/courses/27685.imm/recordings/Ex_NN.mp4 [MP4]].
| Lecture: What defines a T cell epitope? Is there any thing beyond MHC binding? [MN] Session materials: [http://www.cbs.dtu.dk/courses/27685.imm/presentations/Processing_Tcell_2018.pdf Slides [PDF]]. Recording: [http://www.cbs.dtu.dk/courses/27685.imm/recordings/Processing_Tcell_2018.mp4 [MP4]].
| Exercise: [[Antibody Structure Prediction and Analysis]] Recording: [https://youtu.be/5t7aUkXVuwk Exercise] [PM]
| Exercise files: [https://teaching.healthtech.dtu.dk/material/22145/pdf/Peptides-HD-DR2b.txt Peptides] [https://teaching.healthtech.dtu.dk/material/22145/pdf/Alleles-HD-DR2b.txt Alleles_list] Answers: [http://www.cbs.dtu.dk/courses/27685.imm/presentations/Carol/Exercise_guidelines_answers.pdf Answers]'''Live on Zoom''' [CB]
| Exercise: [[Antibody Humanization]] [PM]
| Exercise: [[Protein Drug Deimmunization]] [BR]
| Talk 2: '''SARS-CoV-2 full genome profiling for T cell immunity and immunodominance in COVID-19 infection.''' Sunil Kumar Saini '''Live!''' [http://www.cbs.dtu.dk/courses/27685.imm/recordings/22145_2021/Talk2_SunilSaini.mp4 video]
|-
! 10.15 - 10.30
! Break
! Break
! Break
! Break
! Break
! Break
! Break
! Break
|-
! 10.30 - 11.15
| [[Micro_Project_on_Basic_Immunology|Micro project group work]] '''Live on Zoom''' [CB]
| Lecture: Prediction of MHC peptide binding part 3 [MN]. Session materials: [http://www.cbs.dtu.dk/courses/27685.imm/presentations/MHCbinding_2020_part3.pdf Slides [PDF]]. Recording: [http://www.cbs.dtu.dk/courses/27685.imm/recordings/MHC_part3.mp4 [MP4]].
| Lecture: Selecting the one in a million. Strategies for selecting peptide subsets, and vaccine design [MN]. Session materials: [http://www.cbs.dtu.dk/courses/27685.imm/presentations/Vaccine_design_2019.pdf Slides [PDF]]. Recording: [http://www.cbs.dtu.dk/courses/27685.imm/recordings/Vaccine_design_2019.mp4 [MP4]].
| Lecture: [https://teaching.healthtech.dtu.dk/material/22145/pdf/Linear_epitope_prediction.pdf Linear B-cell epitope prediction]. Recording: [https://youtu.be/Ukk5XJfuh6k] [PM]
| Lecture: T-Cell Receptor Repertoires '''Live on Zoom''' [http://www.cbs.dtu.dk/courses/27685.imm/presentations/Carol/20210108MV_Tcell_receptor_repertoires_updated.pdf Slides] Recording: [[http://www.cbs.dtu.dk/courses/27685.imm/recordings/22145_2021/20210108MV_Tcell_receptor_repertoires.mp4 [MP4]] [MV]
| Lecture: Single cell technologies for T-cell epitopes [http://www.cbs.dtu.dk/courses/27685.imm/presentations/Carol/single_cell_general.pdf Single Cell] and [http://www.cbs.dtu.dk/courses/27685.imm/presentations/Carol/nettcr_project.pdf NetTCR Project] [http://www.cbs.dtu.dk/courses/27685.imm/recordings/22145_2021/Single_cell.mp4 video]'''Live on Zoom''' [HP]
| Lecture: [https://teaching.healthtech.dtu.dk/36685/images/8/87/Deimmunisation.pptx.pdf Humanization and deimmunization for cancer T cell therapy molecules] [http://www.cbs.dtu.dk/courses/27685.imm/recordings/22145_2021/Deimmunisation_CART-cells.mp4 video] [PM]
| Talk 3: '''The utilization of bioinformatics to guide drug design.''' Monika Sekelja '''Live!''' [http://www.cbs.dtu.dk/courses/27685.imm/recordings/22145_2021/Talk3_MonikaSekelja.mp4 video]
|-
! 11.15 - 12.00
| [[Micro_Project_on_Basic_Immunology|Micro project group work]] '''Live on Zoom''' [CB]
| Lecture: [http://www.cbs.dtu.dk/courses/ILRI_workshop/presentations/Performance_measure.pdf Performance measures] [MN]. Recording: [http://www.cbs.dtu.dk/courses/22125/recordings/Performance_measure.mp4 [MP4]].
| Lecture: Selecting the one in a million. Strategies for selecting peptide subsets, and vaccine design [MN] cont.
| Lecture: [https://teaching.healthtech.dtu.dk/material/22145/pdf/Conformational_epitope_prediction.pdf Conformational B-cell epitope prediction]. Recording: [https://youtu.be/xg8Wf4rNsqw][PM]
| Lecture: The Immune Epitope Database & Tools '''Live on Zoom''' [http://www.cbs.dtu.dk/courses/27685.imm/presentations/Carol/2021_01_08_IEDB.pdf PDF] [http://www.cbs.dtu.dk/courses/27685.imm/recordings/2021_01_08_IEDB_Presentation.mp4 mp4] [BR]
| Lecture: [http://www.cbs.dtu.dk/courses/27685.imm/presentations/Carol/netTCR_interactions_2021.pdf Modelling TCRpMHC interactions] [http://www.cbs.dtu.dk/courses/27685.imm/recordings/22145_2021/NetTCR_video.mp4 video]'''Live on Zoom''' [AM]
| Lecture: [https://teaching.healthtech.dtu.dk/36685/images/8/87/Deimmunisation.pptx.pdf Humanization and deimmunization for cancer T cell therapy molecules] [PM]
| Talk 4: TBC Live!
|-
! 12.00 - 13.00
! Lunch Break
! Lunch Break
! Lunch Break
! Lunch Break
! Lunch Break
! Lunch Break
! Lunch Break
! Lunch Break
|-
! 13.00 - 13.30
| '''Live:''' Q&A Session [CB]
| '''Live:''' Quiz: [https://kursusquiz.dtu.dk/quiz/solochallenge/398/holding/571?lang=en MHC binding]. Q&A Session [MN]. Recordings: [http://www.cbs.dtu.dk/courses/27685.imm//recordings/QA_2021-01-05_1.mp4 R1 [MP4]]. [http://www.cbs.dtu.dk/courses/27685.imm//recordings/QA_2021-01-05_2.mp4 R2 [MP4]]. [http://www.cbs.dtu.dk/courses/27685.imm//recordings/QA_2021-01-05_3.mp4 R3 [MP4]].
| '''Live:''' Exercise recap [MN]. Quiz: [https://kursusquiz.dtu.dk/quiz/solochallenge/400/holding/578?lang=en MHC processing, epitope discovery and vaccine design]. Q&A Session [MN]. Recordings: [http://www.cbs.dtu.dk/courses/27685.imm//recordings/QA_2021-01-06.mp4 R1 [MP4]].
| '''Live:''' Exercise recap [MN] Recordings: [http://www.cbs.dtu.dk/courses/27685.imm//recordings/QA_2021-01-07.mp4 R1 [MP4]].
| '''Live:''' Exercise recap Recordings: [http://www.cbs.dtu.dk/courses/27685.imm//recordings/22145_2021/PM_live_recap_exercises_Ab_TCRs.mp4 [MP4]] [PM]
| '''Live:''' Exercise recap [http://www.cbs.dtu.dk/courses/27685.imm/recordings/22145_2021/Live_exercise_recap_immunopeptidomics_IEDB_CB_BR.mp4 video] [CB] and [BR]
| '''Live:''' Exercise recap [http://www.cbs.dtu.dk/courses/27685.imm/recordings/22145_2021/HP_exercise_recap_single_cell_netTCR.mp4 video] [HP]
| '''Live:''' Exercise recap [PM]
|-
! 13.30 - 17.00
| [[Micro_Project_on_Basic_Immunology|Micro project group work]] '''Live on Zoom''' [http://www.cbs.dtu.dk/courses/27685.imm/recordings/22145_2021/Group_Presentations_day1part1.mp4 Presentations_part1] [http://www.cbs.dtu.dk/courses/27685.imm/recordings/22145_2021/Group_Presentations_day1part2.mp4 Presentations_part2] [CB]
| Exercise:[http://www.cbs.dtu.dk/courses/27685.imm/exercise_MHC_bind/exercise_2019.php Prediction of MHC:peptide binding using PSSM and ANN]
[http://www.cbs.dtu.dk/courses/27685.imm/exercise_MHC_bind/exercise_2019_ans.php Answers: Prediction of MHC:peptide binding using PSSM and ANN]
| Exercise: [http://www.cbs.dtu.dk/courses/27685.imm/exercise_HCVVaccine/exercise_HCVVaccine_2021.php Development of vaccines against HCV] [MN] [http://www.cbs.dtu.dk/courses/27685.imm/exercise_HCVVaccine/exercise_HCVVaccine_2021_ans.php Answers]
| Exercise: [http://www.cbs.dtu.dk/courses/27485.imm/epitope_2014.php B cell epitope predictions] [PM]
| Exercise: [https://teaching.healthtech.dtu.dk/22145/index.php/T-Cell_Receptor_Repertoires#Retrieve_and_Upload_Repertoire_data T-Cell Receptor Repertoires] [MV] [https://teaching.healthtech.dtu.dk/material/22145/ljess/repertoire_analysis.html Suggested answers] Exercise: [[IEDB]] [BR]
| Exercise: [[Single cell technologies for T-cell epitopes]] [HP]
| Exercise: [https://teaching.healthtech.dtu.dk/36685/index.php/Exercise_on_CAR_T-cell_humanisation_and_de-immunisation CAR T-cell humanisation and de-immunisation] [PM]
| '''Live on Zoom''' [http://www.cbs.dtu.dk/courses/27685.imm/presentations/Carol/project_and_exam.pdf Introduction to project and exam] [CB]
|- style="vertical-align: top;" |
! Learning Resources
|
Required
* Paper: [https://onlinelibrary.wiley.com/doi/abs/10.1002/bies.201900200 Peptide Presentation to T Cells: Solving the Immunogenic Puzzle]
* Video: [https://www.youtube.com/watch?v=K09xzIQ8zsg Tumour immunology and immunotherapy]
* Video: [https://www.youtube.com/watch?v=vponeaNiewE Decoding cancer immunology: Hunting hidden tumours]
Optional
* Video: [https://www.youtube.com/watch?v=fSEFXl2XQpc Back to Basics]
|
Required
* Book: [https://teaching.healthtech.dtu.dk/material/22145/pdf/Lund_et_al_immunological_bioinformatics_2005_chapter_3.pdf Immuno. Bioinfo. Ch. 3]
* Book: [https://teaching.healthtech.dtu.dk/material/22145/pdf/Lund_et_al_immunological_bioinformatics_2005_chapter_4.pdf Immuno. Bioinfo. Ch. 4]
* Paper: [http://bioinformatics.oxfordjournals.org/cgi/reprint/23/24/3265 Modeling the adaptive immune system: predictions and simulations]
* Paper: [https://www.annualreviews.org/doi/pdf/10.1146/annurev-biodatasci-021920-100259 Immunoinformatics: Predicting Peptide–MHC Binding]
Optional
* Paper: [https://www.mcponline.org/content/18/12/2459.long NNAlign_MA; MHC Peptidome Deconvolution for Accurate MHC Binding Motif Characterization and Improved T-cell Epitope Predictions]
* Paper: [https://pubs.acs.org/doi/10.1021/acs.jproteome.9b00874 Improved Prediction of MHC II Antigen Presentation through Integration and Motif Deconvolution of Mass Spectrometry MHC Eluted Ligand Data]
|
Required
* Book: [https://teaching.healthtech.dtu.dk/material/22145/pdf/Lund_et_al_immunological_bioinformatics_2005_chapter_13.pdf Immuno. Bioinfo. Ch. 13]
* Book: [https://teaching.healthtech.dtu.dk/material/22145/pdf/Lund_et_al_immunological_bioinformatics_2005_chapter_14.pdf Immuno. Bioinfo. Ch. 14]
* Paper: [https://www.annualreviews.org/doi/10.1146/annurev-immunol-082119-124838 T Cell Epitope Predictions]
Optional
* Paper: [https://www.ncbi.nlm.nih.gov/pubmed/23097419 Simultaneous alignment and clustering of peptide data using a Gibbs sampling approach]
* Paper: [http://www.jimmunol.org/content/178/12/7890.long A Quantitative Analysis of the Variables Affecting the Repertoire of T Cell Specificities Recognized after Vaccinia Virus Infection]
* Paper: [https://www.ncbi.nlm.nih.gov/pubmed/24760079 Identification and HLA-tetramer-validation of human CD4+ and CD8+ T cell responses against HCMV proteins IE1 and IE2]
|
* [https://teaching.healthtech.dtu.dk/material/22145/pdf/Immunological_bioinformatics_Quiz_1_2019.pdf Mini Quiz]
* [https://teaching.healthtech.dtu.dk/material/22145/pdf/Pymol-edu-license-2021.txt Pymol license]

Required
* None
Optional
* Paper: [https://academic.oup.com/nar/article/3787843 BepiPred 2.0]
* Paper: [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531324/ B-cell epitope prediction]
* Video: [http://www.youtube.com/watch?v=Z36dUduOk1Y Simplified B-cell walkthrough] (Nice and easy understandable explanation of B-cells)
* Resource: [https://pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/ PDB 101: Introduction to PDB Data]
|

* Rstudio: [https://rstudio.com/products/rstudio/download/ Get it] [https://datascienceplus.com/introduction-to-rstudio/ Quick guide] [https://teaching.healthtech.dtu.dk/22145/index.php/Getting_started_with_RStudio_Cloud,_R_and_rmarkdown Getting started]

Required
* Video: [https://www.youtube.com/watch?v=Na-Zc-xWCLE Immunology wars: A billion antibodies]
* Video: [https://www.youtube.com/watch?v=JJmqt40Z3mM Antibody (BCR) and TCR Diversity]
* Video: [https://www.youtube.com/watch?v=h9mqsllg1Cs Antibody Somatic (VDJ) Recombination I]
* Video: [https://www.youtube.com/watch?v=_D2x-dhh6Pg Antibody Somatic (VDJ) Recombination II]
* Book: [https://cn.inside.dtu.dk/cnnet/filesharing/download/8df4dfc2-e023-43b8-a2cd-1a00e1e902bc Kuby Ch. 7: The Organization and Expression of Lymphocyte Receptor Genes]
* Paper: [https://www.ncbi.nlm.nih.gov/pubmed/25300482 The immune epitope database (IEDB) 3.0.]
Optional
* None
|
Required
* Paper: [https://www.biorxiv.org/content/early/2018/10/02/433706 NetTCR: sequence-based prediction of TCR binding to peptide-MHC complexes using convolutional neural networks]
* Paper: [https://www.nature.com/articles/nbt.4303 T cell receptor fingerprinting enables in-depth characterization of the interactions governing recognition of peptide–MHC complexes]
* Paper: [https://www.nature.com/articles/s41598-019-50932-4 TCRpMHCmodels: Structural modelling of TCR-pMHC class I complexes]
* Paper: [https://www.sciencedirect.com/science/article/pii/S0161589017306211 Identification of the cognate peptide-MHC target of T cell receptors using molecular modeling and force field scoring]
* Tech report: [https://teaching.healthtech.dtu.dk/material/22145/ljess/10x_AN047_IP_A_New_Way_of_Exploring_Immunity_Digital.pdf A New Way of Exploring Immunity – Linking Highly Multiplexed Antigen Recognition to Immune Repertoire and Phenotype]
Optional
* None
|
Required
* None
Optional
* Paper: [https://www.ncbi.nlm.nih.gov/pubmed/27322891 Design and engineering of deimmunized biotherapeutics]
|
|}

==Project Period and Exam==

=== Project ===

'''Wednesday January 13th - Wednesday January 20nd - Project Work'''

Please note the following (***time has been updated***):
* The deadline for uploading the final project Poster presentation (i.e. ''not'' a report) to [https://www.inside.dtu.dk/ DTU inside] will be '''Wednesday January 20nd at 11.59AM'''
* It is a prerequisite for the exam to complete this assignment and as such, ''failure to meet the deadline will result in a failed exam''
* Furthermore and very important - Each group member is responsible for ''all'' aspects of the group work and subsequent presentation

'''Groups and Projects 2021'''

* Groups will be preset based on educational diversity

* [https://cn.inside.dtu.dk/cnnet/filesharing/download/950b168e-0786-4b7e-85bd-1389e9a61869 The groups list for 2021]

=== Exam Schedule ===

* General exam format will consist on 2 parts ([https://kurser.dtu.dk/course/22145 course learning objectives]):

Oral presentation of the poster project ~10 minutes for all group presentation + 5 minutes for questions (15 minutes total)
Date: January 21st 2021 (specific times per group to be announced)

Written exam ~20 questions 2hs, all conducted online on DTU Inside
Date: January 22st 2021

* Individual grades will be given after the finalization of the course

Single cell technologies for T-cell epitopes

2024-03-20T14:46:49Z

WikiSysop: Created page with "'''It is the intention with the following exercises, that you discuss and solve the following tasks and questions in your groups, so talk to each other for mutual benefit''' = Introduction = The purpose of this exercise is to get a feeling with T-cell CDR3 sequence data and to try to make predictions on which sequences will bind a specific peptide. We will here use to approaches for predictions: a naive 'database look-up' approach and a neural network approach. With th..."

'''It is the intention with the following exercises, that you discuss and solve the following tasks and questions in your groups, so talk to each other for mutual benefit'''

= Introduction =

The purpose of this exercise is to get a feeling with T-cell CDR3 sequence data and to try to make predictions on which sequences will bind a specific peptide. We will here use to approaches for predictions: a naive 'database look-up' approach and a neural network approach. With the naive approach we have a set of CDR3 sequences where we know the corresponding epitopes. We can compare our query CDR3 sequences with the validated set and compute a similarity score. We could then make the assumption that a high similarity score can be used to infer the epitope for the query CDR3 sequence. However, if this approach solved the problem of pairing CDR3 sequences and epitopes, we wouldn't still be doing this research. The pairing is simply more complicated than that. Therefore, we instead utilize neural networks which lets us model non-linear relations. In the exercise we present to you our in-house model, netTCR. Other models exist out there, but we can only speak for our own.

In this exercise, you will be working with curated T-cell epitopes from the IEDB and single cell immune profiling data sets from 10x Genomics. The peptides <code>GILGFVFTL</code>, <code>GLCTLVAML</code> and <code>NLVPMVATV</code> in conjugation with <code>HLA-A*02:01</code> are heavily studied and many <code>TCR-CDR3b</code> sequences annotated as binders exist in the IEDB. Here, we will create a database of annotated binders using the IEDB and then use single cell data to compare the similarity between <code>TCR-CDR3b</code> sequences annotated as binders and non-binders.

= Theoretical questions =

Discuss the following ''10 quick ones'' with your group to make sure, that you are on track:

* '''Q1:''' Where in the cell are MHC Class I molecules found?
* '''Q2:''' Do all human cells express MHC Class I molecules?
* '''Q3:''' How many HLA class I molecules do each person have?
* '''Q4:''' Which T-cells interact with MHC Class I?
* '''Q5:''' Where do the peptides that bind MHC Class I come from?
* '''Q6:''' Does MHC class I distinguish between self and non-self?
* '''Q7:''' Explain the difference between a peptide and an epitope in context with MHC Class I presentation
* '''Q8:''' How do virus peptides end up on being presented by MHC Class I?
* '''Q9:''' In cancer, there is no influx of foreign proteins, explain how cancer epitopes arise
* '''Q10:''' Briefly explain why understanding all three components of the TCRpMHC system is so extremely important in context with vaccinology
* '''Q11:''' What are the source proteins for the peptides <code>GILGFVFTL</code>, <code>GLCTLVAML</code> and <code>NLVPMVATV</code>?

= Setup your Google Colab Notebook =

Access the notebooks using a Google Drive account. Notebooks can be found [https://drive.google.com/drive/folders/18360Nkt6oKFVDfBVvO1tp33z8VnWTCSG?usp=sharing here]. You need the notebooks to complete the exercise. The notebooks contain code blocks that you will not be held accountable for. To code is not a prerequisite for this course, but you are encouraged to try to understand what is going on. All you need to do is upload data, run the notebooks, and download data.

= Retrieve Data =

== IEDB Data ==

# Go to the [https://www.iedb.org/ Immune Epitope Database and Analysis Resource], which your worked with on day 2 of the course
# In the '''Epitope''' box, select ''Linear Epitope'' enter the sequence of one of the aforementioned peptides
# In the '''Assay''' box, tick ''Positive Assays Only'' and ''T Cell Assays''
# In the '''MHC Restriction''' box, click ''Find''
## Click the blue plus sign next to ''MHC molecule''
## Click the blue plus sign next to ''Class I''
## Click the blue plus sign next to ''Human''
## Click the blue plus sign next to ''HLA-A''
## Click ''HLA-A*02:01''
## Click ''Apply''
# Click ''Search''
# On the left of the results page find the '''Receptor''' box and tick ''Has receptor sequence'', set '''type''' to ''TCRab'' and '''Chain''' to ''beta''
# Scroll down and click ''Search''
# Now, click the '''Receptors''' tab
# Verify, that you are on the '''T Cell Receptors''' tab
# Click ''Export Results'' and select ''Export to CSV file''

== 10x Genomics Single Cell T-Cell Data ==

''You may need to register to download the data in this section, if prompted, simply do so.''

# Go to the [https://support.10xgenomics.com/single-cell-vdj/datasets 10x Genomics Single Cell Immune Profiling Datasets]
# Find the '''Application Note - A New way of Exploring Immunity''' section
# Under '''Cell Ranger 3.0.2''' click '''CD8+ T cells of Healthy Donor X''' link (Choose an X in the range 1-4)
# This will take you to the page for the CD8+ T cells of Healthy Donor X
# Scroll down to the '''Output Files''' section
# Click the '''binarized matrix CSV''' link to download the '''vdj v1 hs aggregated donorX binarized matrix''' data set

= Prepare and analyse the data =

From the previous exercise steps you should now have the following two files:

tcell_receptor_table_export_1578653238.csv
vdj_v1_hs_aggregated_donor1_binarized_matrix.csv

Verify, that this is the case, note that <code>1578653238</code> is a download id and therefore will not be the same. Also, depending on which donor you choose <code>donor1</code> will be different.

Go to [https://colab.research.google.com/drive/1aNgFI8jmf_SYl9PRfYVl19gFoNnGBDcV?usp=sharing this colab notebook]

This notebook will create eight files:

# Two database files (based on the IEDB data) containing CDR3 alpha and beta sequences, respectively.
# Three "binder" query files (based on the 10x annotated binders) containing CDR3 alpha, beta, and alpha+beta sequences, respectively.
# Three "non-binder" query files (based on the 10x annotated non-binders) containing CDR3 alpha, beta, and alpha+beta sequences, respectively.

== Create Sequence Logos ==

This is also part of the colab notebook.

* '''Q15:''' Look at and interpret the logos
* '''Q16:''' It seems that for both logos, the first and last three positions are quite conserved. Yet, we know that one logo represents a set of non-binders and the other a set of binders, so why can we not see the specificity for the target peptide?

'''Go to this [https://docs.google.com/spreadsheets/d/1lqsEby0AuK8UmpgGBDUECM3kZvgi5CibHkJ0LSa78YE/edit?usp=sharing Google Sheet] and enter the stated values, which you can find in your above analysis. The first line is filled in for reference.''' (Note, the database/query files we create are based on a sampling, so do not despair if you do not get the same means and standard deviations)

= Naive database look-up approach =

== Calculate Similarity Scores using the MAIT-match server ==

The MAIT-match server calculates a similarity metric between two amino acid sequences based on the method proposed by [https://arxiv.org/abs/1205.6031 Shen ''et al.'']. If two sequences are highly similar, then the score will be close to 1 and if they are highly dissimilar, then the score will be close to 0.

From the above exercise step, you need 6 of the 8 files and you will have to make several runs/queries. For each query you will need:

# Database: an IEDB file (either alpha or beta)
# A query: a 10x genomics data set (either alpha or beta) (either positive or negative binders)

Make sure you query both 10x alpha files against the single IEDB alpha file and query both 10x beta files against the single IEDB beta file. You should end up with 4 files that I recommend you give these names:

# mait.cdr3a.pos.tsv
# mait.cdr3a.neg.tsv
# mait.cdr3b.pos.tsv
# mait.cdr3b.neg.tsv

The task ahead is to use the [http://www.cbs.dtu.dk/services/MAIT_Match/ MAIT Match Server] to calculate similarity scores between the known IEDB binders and the annotated 10x binders/non-binders, to see if 10x annotated binders are more similar to the IEDB binders, compared to 10x non-binders.

# Go to the [http://www.cbs.dtu.dk/services/MAIT_Match/ MAIT Match Server]
# Click the ''Choose file'' button under the first submission window and select the query file (10x data)
# Click the ''Choose file'' button under the second submission window and select the database file (IEDB data)
# Click ''Submit''

Once the server is done:

# Open a text editor (Mac: TextEdit, windows: Notepad)
# Copy / paste the resulting output
# Delete everything ''before'' <code>Res Sequence MAIT_hit Score</code>, so that the first line in the file is <code>Res Sequence MAIT_hit Score</code>
# Delete everything ''after'' the last line of scores, e.g. <code>Best ASSKARSLGNRGNEQF ASSKGGTRGNEQF 0.8460</code>
# Name file according to schema above
# Repeat the above steps

== Evaluate Similarity Scores ==

From the previous exercise steps you should now have the following four files:

# mait.cdr3a.pos.tsv
# mait.cdr3a.neg.tsv
# mait.cdr3b.pos.tsv
# mait.cdr3b.neg.tsv

Go to [https://colab.research.google.com/drive/1TRkvF831K12r2p30ag4QkyW7vK1SAkr9?usp=sharing this colab notebook]

= The netTCR server =

The [https://services.healthtech.dtu.dk/service.php?NetTCR-2.0 netTCR Server] NetTCR server predicts binding probability between a T-cell receptor CDR3 protein sequence and a MHC-I peptide binding to HLA-A*02:01. In this part we want to compare the ability of the netTCR server to assign scores versus that of the MAIT-match server.

# Go to the [https://services.healthtech.dtu.dk/service.php?NetTCR-2.0 netTCR Server]
# Click the '''Upload''' file button and select a query file you created previously
# In the drop-down menu '''Select peptides''', click the arrow down and select the target peptide your query file is based on
# Click the green '''Submit''' button
# Repeat the above such that you have predictions for alpha, beta and alpha+beta for both the positive and negative set.

When the predictions are completed:
# Copy the results to a text editor and save files with meaningful names
# Upoad the results to this [https://colab.research.google.com/drive/1uyx3MSDTunvkrl8me8a41e-0Sj4lzzOv?usp=sharing notebook]

Meaningful filenames:
# nettcr.cdr3a.pos.tsv
# nettcr.cdr3a.neg.tsv
# nettcr.cdr3b.pos.tsv
# nettcr.cdr3b.neg.tsv
# nettcr.cdr3ab.pos.tsv
# nettcr.cdr3ab.neg.tsv

= Advanced =

If you reach this point and there is still time left for exercises, then

* Redo the above analysis for another target peptide and re-enter the values you find in the google sheet
* From your sequence logos, you can see the clear conservation of the first and last 3 positions, adjust your above analysis to account for this

= Exercise Summary =

A student who has met the objectives of this exercise will be able to:

# Extract peptide and allele specific T-cell epitopes from the IEDB
# Extract single cell immune profiling data from 10x genomics
# Upload data to RStudio cloud
# Create an analysis using rmarkdown and pre-specified code
# Calculate sequence similarity metrics using the [http://www.cbs.dtu.dk/services/MAIT_Match/ MAIT Match Server]
# Use similarity metrics to create a TCR-CDR3b database
# Use similarity metrics to query a TCR-CDR3b database
# Interpret score distributions for TCR-CDR3b sequences annotated as binders and non-binders

IEDB

2024-03-20T14:46:11Z

WikiSysop: Created page with " == Immune Epitope DataBase (IEDB) Exercises == ---- The Immune Epitope DataBase (IEDB) is a very useful resource for researchers of immunology and immunoinformatics. It is a highly organized database of epitopes(or more precisely: epitope assay results) that has a user friendly search interface. It is maintained by the La Jolla Institute for Allergy and Immunology and has a dedicated team of curators and bioinformatitians that have mined the immunological literature. T..."

== Immune Epitope DataBase (IEDB) Exercises ==
----

The Immune Epitope DataBase (IEDB) is a very useful resource for researchers of immunology and immunoinformatics. It is a highly organized database of epitopes(or more precisely: epitope assay results) that has a user friendly search interface. It is maintained by the La Jolla Institute for Allergy and Immunology and has a dedicated team of curators and bioinformatitians that have mined the immunological literature. The IEDB is up to date with the immunological literature (within its scope) and is therefore a good place to get an idea of what has been studied and to what extent. Aside from this, they provide prediction tools that can be very useful when no experimental evidence exists. Best of all, it's all free (for academics)!

Today we will focus on building experience in querying the IEDB, so that you may search for data in your own research. Start by going to the [http://www.IEDB.org IEDB home page].

== Sequence Query ==

The goal here is to introduce you to the basic functionalities of the IEDB.

In the home page search (center field on homepage), in the ’Epitope’ field, select ’Linear Epitope’, ’Exact
Match’ and enter in the text box: ’ASNENMETM’. Leave remaining parameters as default and select
’Search’ in the bottom of the page.

*'''Q1: How many epitopes do you find?'''
*'''Q2: From which antigen molecule do the epitopes come from? What about the antigen organism?'''

Under the ’Epitopes’ search tab, inspect the column ’# References’ and note that the output table is sorted
by this column. Click the column header names to change sorting order. Sort again by number of references and
click the ’Details’ number for the epitope with most references. This leads you to a summary page for said
epitope. Note the tabulated T Cell Assay Results.

*'''Q3: What is the number of positive results for the ’qualitative binding’ assay? How about for ’pathogen burden after challenge’?'''

Back on the top of the results page, click around the different tabs(’Epitopes’, ’Antigen’,’Assays’...) for
different vantage points of the results.

*'''Q4: How many entries are under the Assay tab?'''

The ’Assay’ tab result can be further divided by tabs right above the results table(’T Cell Assays’, ’B Cell
Assays’, ’MHC Ligand Assays’).

*'''Q5: How many ’MHC Ligand Assays’ have been performed on the epitopes in question?'''

Applied filters are shown under ’Current Filters’ at the top of the results page. Try removing the ’Positive
Assays Only’ filter by clicking the red ’X’ and pressing ’Search’ (Top Left). You have now included negative
results in your search.

*'''Q6: How many negative ’MHC Ligand Assays’ are added by doing this?'''

You can add the ’Positive Assays Only’ filter back by refining your search. On the left side of the results
page note the search fields(’Epitope’, ’Antigen’, ’Receptor’, ’Assay’...). Scroll down to the ’Assay’ field and
select ’Positive Assays Only’. Scroll back to the top and select click ’Search’.

*'''Q7: What is the ’MHC Ligand Assay’ count now? Does it match your initial count?'''

Finally, inspect the results under the ’Reference’ tab. Click the PMID column entry for any row. This is a
PubMed link to the reference. Back in the result table, sort the resulting references by the date by clicking
the ’Date’ column header.

*'''Q8: What is the time span of publications for the epitopes?'''

Broaden your search. In the ’Epitope’ search field on the left of the results page, change the ’Exact Match’
search to a BLAST search with a 70% sequence homology.

*'''Q9: How many Epitopes does your search yield?'''

'''Pro tip:''' Start with a broad initial search(e.g. all T Cell epitopes) from the home page and then add filters in
steps(in the search field on left of results page). This way you can get a feel for which filter is most restrictive(where
do you lose most epitopes). This is also helpful for debugging a wrong search.

==Neutralizing Ebola Antibodies==

The goal here is to get a clinically interesting dataset by a few clicks on the IEDB.

Starting from the home page search, in the field, select only ’Positive assays only’ and ’B cell assays’. Leave
rest of parameters on default and click 'Search'.

*'''Q10: This should return a large amount of epitopes, how many?'''

Start refining your search using the search fields on the left of the results page. In the ’Organism’ box of
the ’Antigen’ field search for ’Ebolavirus (ID:186538, ID:186539, ID:186540, ID:186541)’. You can also try searching for ’Ebolavirus’ in the
organism finder in the ’Antigen’ field. Click ’Search’ (Top Left) again to add this filter.

*'''Q11: How many Ebola virus epitopes do you see?'''

Further refine your search by looking for only Ebola epitopes reactive in human cells. In the ’Host’ search
field, select ’Human’ and click 'Search' again.

*'''Q12: How many Human reactive Ebola virus epitopes results do you see?'''

Now, let’s filter the ebola epitope set down to only epitopes that have been positively shown to result in
neutralization in a human host. In the ’Assay’ search field, select the ’B Cell Assay’ finder. In the assay
finder, expand the ’Biological Activity’ folder and click ’Neutralization’, ’Apply’ and then search to add this
last filter.

*'''Q13: How many epitopes remain?'''

You now have a highly filtered set of epitopes with clinical interest. In the results page, click the ’Assay’ tab,
find the entry ID ’3218080’ and click it. This is an example of a monoclonal antibody that has shown promise in
the treatment of Ebola in humans. Remember that you can export your search results to a .csv format for later
use.

'''Pro Tip 2:''' When you have your dataset of interest ready for export, note the filters you have applied at the
top of the results page so that you may recreate the dataset later. Also, the results tab you export from influences
what you get.

'''Pro Tip 3:''' You may encounter a ’Bad Request’ error in your browser when working on the IEDB website. Try
clearing your recent browser history (cookies and cached data).

==Population Coverage of a SARS-CoV2 Peptide Vaccine==

We have all been influenced by the coronavirus disease 2019 (COVID-19) pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Fortunately, vaccines have been developed and approved in record time. The currently approved mRNA vaccines of Pfizer and Moderna code for the SARS-CoV-2 Spike Protein, a viral fusion protein that is important for cell adhesion and the induction of protective immunity.

This and the next exercise will be reminiscent of the HCV vaccine development exercise, but we will work with tools from the IEDB and target the SARS-CoV2 spike protein. Here we want to investigate the importance of population coverage in rational peptide vaccine design. To this end, we will work with data from the IEDB and use the Population Coverage Analysis Tool.

From the IEDB home page, search for MHC I restricted T-cell Epitopes in humans from the SARS-Cov-2 Spike glycoprotein antigen.

*'''Q14: How many assay results do you find?'''

In the Antigens tab, select the immunome browser for a mapping of all assay results onto the spike glycoprotein. Observing the "Epitope Assay Counts" plots, we note that most of the protein sequence has been tested. Let us select an epitope subset that has been repeatedly tested with positive assay results(high response frequency). Export the immunome browser results, (and with excel/R/python/...) filter to only include 9-mer peptides, and sort on the lower confidence interval of the Response Frequency.

*'''Q15: What 9-mer has the highest, and most reliable Response Frequency?'''

We will select the top 10 peptides with the highest response frequency as our peptide vaccine candidates. Next we want to test the population coverage of these 10 peptides using the population coverage tool. Population Coverage requires not only the epitope sequences but also by which MHCs they are presented. I have prepared this dataset by predicting binding of the peptides(with NetMHCpan-4.1) to a set of prevalent MHCs and for each peptide, only list the MHCs that bind them strongly(rank<0.5). This data is available here: [http://www.cbs.dtu.dk/courses/27685.imm/presentations/Carol/IEDB_Ex/Epitopes_PopulationCoverageInput.csv PopulationCoverageInput]

To open the Population Coverage tool: on the IEDB home page, under "Analysis Resource" select "Epitope Analysis Tools" and then "Population Coverage".

Try computing coverage of the 10 peptides to the European population, selecting "Class I seperate" and entering the peptides using Choose File.

*'''Q16: What percentage of the European population does the set of peptides cover?'''

Select "View chart data in table format".

*'''Q17: What percentage of the european population has 0 epitope/HLA hits?'''

Select "View coverage of individual epitope in Europe"

*'''Q18: How many Epitopes have more than 60% coverage of the population, each?'''

Rerun the Population Coverage computation with only the epitopes that each have more than 60% coverage of the European population.

*'''Q19: What coverage do you reach for the European population?'''

Rerun the Population Coverage computation with the same subset, but for the Central African population

*'''Q20: What coverage do you reach for the Central African population?'''

Hopefully this exercise has solidified the idea that one aspect of rational vaccine design is the balancing act between population coverage and cost/complexity/number of peptides.

==Epitope Conservancy Analysis of a SARS-CoV2 Peptide Vaccine==

Another concern when designing a peptide vaccine is the divergence of pathogen strains. A peptide vaccine can achieve excellent population coverage for a single pathogen strain, but a few mutations can render it useless. Therefore we must be aware of the genotypic landscape of current pathogen strains to test the robustness of a vaccine.

Using our epitope set from the previous questions, we want to test the Epitope Conservancy against a recently compiled set of known SARS-CoV-2 mutations[Xu et. al. Sept. 2020: Variations in SARS-CoV-2 Spike Protein Cell Epitopes and Glycosylation Profiles During Global Transmission Course of COVID-19]. I have compiled SARS-CoV-2 Spike Protein sequence variants (from reference sequence: QHD43416.1), containing 16 frequent mutations in each country untill April 26, 2020. This Fasta File can be found here. [http://www.cbs.dtu.dk/courses/27685.imm/presentations/Carol/IEDB_Ex/SpikeProteinVariants.fasta SpikeProteinVariants]

To open the Epitope Concervancy tool: on the IEDB home page, under "Analysis Resource" select "Epitope Analysis Tools" and then "Epitope Conservancy Analysis".

We will use a larger set of peptides as input([http://www.cbs.dtu.dk/courses/27685.imm/presentations/Carol/IEDB_Ex/Epitopes_EpitopeConservancyInput.fasta EpitopeConservancyPeptides]). Input the peptide sequences and the spike protein variant sequences and select "Epitope linear sequence conservancy" and then submit.

*'''Q21: Which Epitope has the lowest number of protein sequence matches at 100%?'''

*'''Q22: Do you think pathogen coverage will be a problem for a vaccine containing these epitopes? Why?'''

The variants were gathered from www.GISAID.org, an organization devoted to sharing data on coronaviruses causing COVID-19. Their front page has a plot showing the number of data submissions: "hCoV-19 Data Sharing via GISAID".

*'''Q23: How many times more submissions have been made since April 26th, 2020 (variants in this exercise)?'''

This indicates that it might be worth repeating this analysis with a more up to date dataset. It could also be interesting to test if variants have emerged whose mutations eliminate epitopes.

----

You should now have a fairly good grasp of the IEDB. It is now your job to
come up with some research questions that you can phrase in the form of an IEDB query.

Done!

Protein Drug Deimmunization

2024-03-20T14:43:37Z

WikiSysop: Created page with "== Protein Drug Deimmunization - Exercise == ---- Over the past few decades, biologics have gone from being experimental treatment options to standard care. They are very targeted and useful molecules in health care, but they come with their own immunological challenges. If a biologic is recognized as foreign by the immune system, Anti-Drug Antibodies can be formed that neutralize the biologic and render it useless. Deimmunization provides a potential solution to this..."

== Protein Drug Deimmunization - Exercise ==

----

Over the past few decades, biologics have gone from being experimental treatment options to standard care. They
are very targeted and useful molecules in health care, but they come with their own immunological challenges.
If a biologic is recognized as foreign by the immune system, Anti-Drug Antibodies can be formed that neutralize
the biologic and render it useless. Deimmunization provides a potential solution to this challenge.

The general strategy of deimmunization is to target T-Cell epitopes with mutation, thereby reducing immunogenicity of the biologic. Epitopes can be identified experimentally, but in silico prediction makes the process more
economically tractable.

Here we will go through a short exercise on in silico deimmunization of human Erythropoietin (EPO). EPO
is a protein that signals for the production of red blood cells in response to hypoxia. It is used in treatment of
anemia, but is perhaps better known for its use in blood doping. We will use the [http://www.IEDB.org IEDB] to get epitope data on
EPO, [https://www.uniprot.org/ Uniprot] to get its sequence, and [http://www.IEDB.org IEDB] again for tools on CD4 epitope prediction and deimmunization.

The goal of today’s exercise is to get you acquainted with existing CD4 epitope prediction- and deimmunization-
tools. You will handle and process data and question some technical aspects of the tools and results.

== Data Gathering ==

Start by going to the [http://www.IEDB.org IEDB homepage] and find T Cell epitope results for human erythropoietin. If nothing comes up, try reformulating your query. It should result in 19 epitopes from a single reference. In this publication, EPO was tested for immunogenicity by testing 15-mers; overlapping by 10-mers, covering the entire sequence. Under the antigen tab, navigate to the immunome browser to get an overview of the results.

*'''Q1: Looking at the T-cell epitope response frequency profile of EPO, in what region/regions of the protein is immunogenicity mostly found?'''

*'''Q2: Again, looking at the response frequency profile, an irregular pattern is observed for the first 27 amino acids. In the table of results below, it becomes apparent that no epitope assays were performed on this region. Why do you think that is? Hint: EPO is an extracellular protein'''

Export the immunome browser results to a .csv file.

The answer to question 2 can be found on [https://www.uniprot.org/ Uniprot], where we will also get the sequence for human EPO. Go to [https://www.uniprot.org/ Uniprot] and search for Erythropoietin. Select the human entry and download the .fasta file with the EPO sequence (click 'format' tab at top of page and select fasta). On the Uniprot page for human EPO, you can learn that EPO is a glycoprotein.

*'''Q3: Can you find any other information on the EPO Uniprot site that could explain the irregular response frequency pattern in the N-terminal of EPO(as seen in Question 2)?'''

This N-terminal sequence will interfere with our prediction so remove the first 27 residues in your EPO fasta and save it as e.g. EPO-processed.fasta

== CD4 Epitope Prediction ==

To deimmunize the EPO protein we will use two prediction tools available on the IEDB: "CD4 T-cell immunogenicity prediction" and "Deimmunization". On the [http://www.IEDB.org IEDB home page], under "Analysis Resource" select "T Cell Epitope Prediction". You should see links to the two tools with a paragraph explaining how they work. Read this carefully!

To gain confidence in the validity of the predictors, let us plot together the predicted immunogenicity and the experimentally measured response frequency.

Using the "CD4 T-cell immunogenicity prediction" tool, upload your processed EPO fasta file and run the prediction with the following parameters, "Prediction method": "IEDB recommended (combined)" and "Select maximum percentile rank threshold":"Show all peptides". This will start a prediction on 15-mers, overlapping by 10-mers, from the EPO protein and output results from two prediction methods(and their combined score). This will take a few seconds and once done, save the resulting .csv file.

Now we have two .csv files to compare, one with experimental data and the other with predictions. Import these with your program of choice (Python, R, Excel,...) so that you can manipulate, compare and plot the data.

*'''Q4: Compare the "Mapped Postion" column in the experimental result table to the "Start" and "End" columns in the prediction result table. Why are they different? Create a new "Start_mod" column in the prediction table so that it aligns with the first value in the "Mapped Position" column.'''

*'''Q5: The two tables have a different number of peptides. Why do you think that is? Hint: look at newly created "Start_mod" column in the prediction result table. '''

Remove the row with peptides that are not shared between the tables.

Now, the prediction scores and the response frequency have different units, so to make them comparable, we must process them. In the prediction score table, the "Combined score" column shows the weighed score of two models. It has the unit of rank, which can be interpreted as "where does the prediction score rank among prediction scores of random peptides" i.e. it is a percentage of random peptides with lower prediction score. That means that a high rank indicates low predicted immunogenicity, which is the reverse of the response frequency. Create a new column (e.g. "Combined score mod") where the "Combined score" become comparable to response frequency.

*'''Q6: What mapping function would you use to make the "Combined score" fall in the same range(and directionality) as response frequency?'''

Now create a line plot and a scatter plot comparing "Combined score mod" with the "Response Freq." columns.

*'''Q7: Does the predicted immunogenicity align with the measured epitopes?'''

*'''Q8: What is the Pearson correlation coefficient between "Combined Score Mod" and "Response Freq."?'''

== Deimmunization ==

Now that we have some confidence in the prediction tools, let us deimmunize EPO.

Open the "Deimmunization" tool on the IEDB and input your processed EPO .fasta file. Run the program with default parameters. This will predict and present the most immunogenic peptides in the input sequence. Select the top 5 peptides, enter a job name and your e-mail to receive your results when they are ready. Start running the job.

This takes quite a lot longer than performing a CD4 epitope prediction of the full EPO sequence, despite the same CD4 epitope prediction tools being used.

*'''Q9: Why does a deimmunization prediction for just a few epitopes take longer than a CD4 epitope prediction for the full EPO sequence?'''

This takes quite a while so I have uploaded the results of the [http://www.cbs.dtu.dk/courses/27685.imm/exercise_deimmune/deimmunization_EPO.csv deimmunization]. Download the result and inspect. Sort the table based on drop in immunogenicity to find the most influential mutations. Have a look at the suggested amino acid substitutions.

*'''Q10: Using the BLOSUM substitution matrix as a guide, do you expect these top suggested mutations to be structurally/functionally conservative?'''

Select an influential mutation (perhaps even several) and create a new EPO .fasta file where you substitute the wild type variant with the less immunogenic mutant. Input this fasta into the CD4 epitope prediction tool and run the prediction with the same parameters as in the "CD4 Epitope Prediction" section. Download the results when ready.

Now, after going through the same processing steps as in the "CD4 Epitope Prediction" section, plot the predicted immunogenicity for your mutant together with the predicted immunogenicity of the wild type.

*'''Q11: Do you notice a drop in predicted immunogenicity?'''

You now have tools to improve biologics!

Done!

File:CDR mut.png

2024-03-20T14:42:42Z

WikiSysop:

Antibody Humanization

2024-03-20T14:42:09Z

WikiSysop: Created page with "'''Humanization of the anti-VEGF antibody''' VEGF (vascular endothelial growth factor) is a target in cancer therapies, being the protein responsible for vascularization of tumoral tissue. The murine anti-VEGF antibody has been proved to be effective in blocking VEGF, but it is immunogenic. The Bevacizumab is the commercial, humanized version of the antibody. Let’s reproduce its humanization. Anti-VEGF Humanization The sequence of the murine antibody is: >Light c..."

'''Humanization of the anti-VEGF antibody'''
VEGF (vascular endothelial growth factor) is a target in cancer therapies, being the protein responsible for vascularization of tumoral tissue.

The murine anti-VEGF antibody has been proved to be effective in blocking VEGF, but it is immunogenic. The Bevacizumab is the commercial, humanized version of the antibody. Let’s reproduce its humanization.

Anti-VEGF Humanization

The sequence of the murine antibody is:

>Light chain
DIQMTQTTSSLSASLGDRVIISCSASQDISNYLNWYQQKPDGTVKVLIYFTSSLHSGVPSRFSGSGSGTDYSLTISNLEPEDIATYYCQ
QYSTVPWTFGGGTKLEIKR

>Heavy Chain
EIQLVQSGPELKQPGETVRISCKASGYTFTNYGMNWVKQAPGKGLKWMGWINTYTGEPTYAADFKRRFTFSLETSASTAYLQISNLK
NDDTATYFCAKYPHYYGSSHWYFDVWGAGTTVTVSS

We will use 2 main tools to perform the humanisation: [[http://www.imgt.org/3Dstructure-DB/cgi/DomainGapAlign.cgi DomainGapAlign]] and PyMol.

The humanisation protocol will follow these steps:

#Identify the human germlines more similar to the murine antibody
#Graft the murine CDRs to the human germline acceptors (obtaining the CDR-grafted antibody)
#Identify all the possible backmutations (all the differences between the murine and CDR grafted antibody
#Build the structural model for the murine and CDR-grafted antibody
#Map the backmutations on the models
#Prioritise the backmutations based on their effect on the structure

Before you start, try to answer to these logical questions, that will help to understand better your task:

1) You don't need to identify the human D gene of the heavy chain that is more similar to the murine one. Why?

2) All backmutations are located in the framework region, not in the CDRs. Why?

3) If you apply all possible backmutations, which antibody would you obtain?

Let's start with our tasks!

'''Q1 - What are the mouse V and J gene for the light and heavy chain?'''

<div class="toccolours mw-collapsible mw-collapsed" style="width:400px; overflow:auto;">
<div style="font-weight:bold;line-height:1.6;">Answer</div>
<div class="mw-collapsible-content mw-collapsed">
Light chain: IGKV10-94 and IGKJ1

Heavy chain: IGHV9-3-1 and IGHJ1
</div></div>

Now we want to identify suitable acceptors, i.e. antibody genes of human origin, for the humanisation. We will again use DomainGapAlign, but this time will select human genes only in the input page

'''Q2 - What are the most similar human V and J gene for the light and heavy chain? What is the similarity?'''

<div class="toccolours mw-collapsible mw-collapsed" style="width:400px; overflow:auto;">
<div style="font-weight:bold;line-height:1.6;">Answer</div>
<div class="mw-collapsible-content mw-collapsed">
Light chain: IGKV1-33 (74.7%) and IGKJ4 (90.9%)

Heavy chain: IGHV7-4 (71.4%) and IGHJ3 (85.7%)
</div></div>

Write down the sequences of the 4 human genes. Keep all the pages open since we will need them later.

Proceed with the humanization using the most similar germlines and the CDR grafting method. In this case, you need to graft the complete mouse CDRs on the human genes. Use the CDR as defined in the DomainGapAlign alignment

'''Q3 - What is the sequence of the CDR-grafted heavy and light chains?'''

<div class="toccolours mw-collapsible mw-collapsed" >
<div style="font-weight:bold;line-height:1.6;">Answer</div>
<div class="mw-collapsible-content mw-collapsed">
>Heavy_CDR
QVQLVQSGSELKKPGASVKVSCKASGYTFTNYGMNWVRQAPGQGLEWMGWINTYTGEPTYAQGFTGRFVFSLDTSVSTAYLQISSLKA EDTAVYYCAKYPHYYGSSHWYFDVWGQGTMVTVSS

>light_CDR
DIQMTQSPSSLSASVGDRVTITCQASQDISNYLNWYQQKPGKAPKLLIYFTSNLETGVPSRFSGSGSGTDFTFTISSLQPEDIATYYCQQYSTVPWTFGGGTKVEIK
</div></div>

Look again at the DomainGapAlign results of the murine antibody on the human germlines. You can use it to identify all possible backmutations - remember that the CDR have been grafted, so they are now 100% murine!

'''Q4: How many possible backmutations are present in the light and heavy chain?'''

<div class="toccolours mw-collapsible mw-collapsed" style="width:400px; overflow:auto;">
<div style="font-weight:bold;line-height:1.6;">Answer</div>
<div class="mw-collapsible-content mw-collapsed">
light: 20 possible backmutations

heavy: 25 possible backmutations
</div></div>

Using [[http://www.cbs.dtu.dk/services/LYRA/ Lyra]], build the models of the murine and CDR-grafted antibody. Rename the two models as murine.pdb and CDR_grafted.pdb.
Open the two models in the same pymol session and align them: click on the "A" button of the murine molecule -> align -> to molecule (*CA) -> CDR_grafted

'''Q5: What is the RMS between the two models?'''

<div class="toccolours mw-collapsible mw-collapsed" style="width:400px; overflow:auto;">
<div style="font-weight:bold;line-height:1.6;">Answer</div>
<div class="mw-collapsible-content mw-collapsed">
Executive: RMS = 0.812 (217 to 217 atoms)
</div></div>

Now, if you display the sequence of the antibodies (small "S" button in the bottom-right part of the screen) they should also be aligned

'''Q6: What templates are used for the murine and CDR_grafted models? Are they the same? Does this affect the accuracy of the models?'''

<div class="toccolours mw-collapsible mw-collapsed" style="width:600px; overflow:auto;">
<div style="font-weight:bold;line-height:1.6;">Answer</div>
<div class="mw-collapsible-content mw-collapsed">
Murine: 1BJ1, 3KLH, 2F19

CDR_grafted: 1BJ1

Since 1BJ1 is used for both models, they might be similar just because they are "copied" from the same template, so the actual RMSD might be larger than it actually appears

</div></div>

'''Q7: in PyMol, identify a few (5 on the heavy, 5 on the light chain) of the possible backmutations in the light and heavy chain and color them red'''

this is a picture of the CDR_grafted model, with all the backmutations colored according to their Blosum90 score

[[File:CDR mut.png]]

The murine and DR_grafted antibody have approximately 80% sequence identity. This will likely result in a partial or complete loss of affinity of the CDR-grafted molecule towards its antigen. By introducing some back mutations, we aim at restoring the affinity. It is important to remember that the more back mutation we introduce, the more we move back towards the original murine antibody, thus increasing the potential immunogenicity of the antibody.

For today exercise, we will focus only on a specific region of the antibody: the FR2 of the light and heavy chain. This region is at the interface of the two chains, and it mediates the packing between them. Even a small difference in the packing may result in a large distortion of the overall ABS.

'''Q8: How many mutations do we observe in the FR2 of the light and heavy chain? '''

<div class="toccolours mw-collapsible mw-collapsed" style="width:400px; overflow:auto;">
<div style="font-weight:bold;line-height:1.6;">Answer</div>
<div class="mw-collapsible-content mw-collapsed">
3 on the heavy chain, 5 on the light chain
</div></div>

'''Q9: Which of these backmutations is more likely to have an impact on the structure? '''

<div class="toccolours mw-collapsible mw-collapsed" style="width:400px; overflow:auto;">
<div style="font-weight:bold;line-height:1.6;">Answer</div>
<div class="mw-collapsible-content mw-collapsed">

DGTV->GKAP : mutations to and from glycine, and mutation to and from proline can have a drastic impact on the structure

</div></div>

Antibody Structure Prediction and Analysis

2024-03-20T14:41:28Z

WikiSysop: Created page with " == Antibody modeling == Requirements: [https://pymol.org/2/ Pymol] Download the version for your OS, then use the license file provided by the teachers '''Modeling of CLL antibody''' From the [http://www.cbs.dtu.dk/courses/27485.imm/VDJ_Exercise/rearrangements.txt rearrangements file], select the SI35 light and heavy chains. Translate the nucleic acid sequences to protein sequences (use a service of your choice, e.g. expasy or virtual ribosome). Go to the [http..."

== Antibody modeling ==

Requirements:
[https://pymol.org/2/ Pymol]

Download the version for your OS, then use the license file provided by the teachers

'''Modeling of CLL antibody'''

From the [http://www.cbs.dtu.dk/courses/27485.imm/VDJ_Exercise/rearrangements.txt rearrangements file], select the SI35 light and heavy chains.
Translate the nucleic acid sequences to protein sequences (use a service of your choice, e.g. expasy or virtual ribosome).

Go to the [http://www.cbs.dtu.dk/services/LYRA/index.php Lyra] web page.<br>

''Lyra is a tool for predicting antibody and TCR structures. It is possible to use Lyra in automated or expert mode. ''

Insert the light and heavy chains in the proper text area and submit. After a few seconds you will arrive to the output page, where the alignment and all the templates are displayed.

'''Q1: what is the sequence similarity of the best H and L templates for the framework (FW)?'''

'''Q2: What is the light chain type? Is it the most common in humans? '''

Focus on the sequence alignment used to generate the model.

'''Q3: where are the differences between target and template located? Which are the most drastic that could affect the modeling process (e.g. G->W)?'''

''hint: you can use the Blosum62 matrix to estimate the expected effect of a substitution: the lower the number, the larger the expected impact''

'''Q4: Do the loops/CDR have the same length in target and template? What does it mean, in terms of expected accuracy?'''

Now, look at the templates automatically selected by Lyra to build the final model

'''Q5: How many templates were used? Which is the region for which the template is more dissimilar to the target sequence?'''

Download the pdb file and open it with pymol. There is a small "S" bottom right, it shows/hides the sequence.
Show the whole protein as cartoon and color by chain. Select and color in red all the CDRs. (the selected residues appear as the "sele" item in the menu)

'''Q6: What is the general shape of the ABS: flat, a pocket, a mountain or a groove? '''

'''Q7: Which loop is the longest and protruding the most? Is this the most common case?'''

Use the [http://www.imgt.org/3Dstructure-DB/cgi/DomainGapAlign.cgi Domain Gap Align tool] identify the somatic mutations in the V and J regions. Show the mutations as sticks (main chain and side chain) and color them green

'''Q8: Which Mutations are located inside/near the CDRs? Which are the ones that are most likely to have an impact on the binding of the antibody?'''

Generate the electrostatic potentials of the Ig (action -> generate -> vacuum electrostatic -> protein contact potentials).

'''Q9: Identify the residues in the CDRs that mostly contribute to the charge distribution.'''<br>
''highlight them in the sequence and look for charged residues such as K, R, D, E ''

'''Q10: (optional) Mutate some residues in order to have a positive charge in the middle of the antigen binding site, then recalculate the electrostatic potentials'''

Finished!

Micro Project on Basic Immunology

2024-03-20T14:40:34Z

WikiSysop: Created page with "Make sure to read through all of this page ''before'' starting the micro-project == Background == Immunological bioinformatics is annotated as a [https://kurser.dtu.dk/course/22145 MSc/PhD eligible course], meaning that you will most likely be at the end of your studies when taking this course or you may be a PhD student. Today you will do active learning-work with a learning method called "Inquiry based learning", which is quite close to the way a researcher works, th..."

Make sure to read through all of this page ''before'' starting the micro-project

== Background ==

Immunological bioinformatics is annotated as a [https://kurser.dtu.dk/course/22145 MSc/PhD eligible course], meaning that you will most likely be at the end of your studies when taking this course or you may be a PhD student. Today you will do active learning-work with a learning method called "Inquiry based learning", which is quite close to the way a researcher works, therefore I have chosen this as the teaching method of the day.

Briefly, "Inquiry based learning" is based on a main question defining the topic and subsequently a series of investigative questions are generated. By working with and answering these questions, a deeper knowledge on the topic is obtained compared to simply sitting passively in on a classic lecture.

This course requires a working understanding of the bio-molecular mechanisms underlying human immunity to infection, so without further ado, the main question of today is:

<center>'''A one-immunity-gene-one-pathogen system is obviously not possible, so how is it that we as humans are able to respond to infections by pathogens that we have never been exposed to before?'''</center>

== Agenda ==

{| class="wikitable" style="font-size:100%;"
! Time
! Activity
|-
| 09.30 - 10.00

* '''Individually.''' Identify ''"10 things/questions that you need to learn more about to answer the main question"''
* Choose 1-2 of your questions to study further. Use the learning resources to guide your study.
* Draft a PowerPoint presentation listing the:
** 10 things you have identified
** Chosen 1-2 things to study further
** Begin the answer to the 1-2 things ''"It has something to do with.."''
** '''Upload a PDF''' of your list of 10 questions and your chosen answer to DTU Learn
|-
| 10.00-11.30

* '''In groups.''' Choose from the individual answers which are the most essential questions to be answered (1-2) and why?
* Answer those in deep using the learning resources and your expertise
* '''Upload a short presentation or video(10min)''' with a presentation of your group answer to DTU Learn. You might need to create a Zoom meetings to record.
|-
| 11.40-12.00
* '''In groups.'''What did you learn from the others' presentations? What can be improved?
* What have we learned today?
* What is the main conclusion of the answer to our main question?
|-
|}

== Suggested Learning Resources ==

Below here, you will find some suggested resources. You are free to use which ever materials you deem relevant, but please do remember, that the time is limited, so take care not to get side tracked!

* [https://armandoh.org/systems/immune-system/ Biology and Medicine Videos] by [http://unms.org.au/dr-armando-hasudungan-a-game-changer-in-medical-education/ Armando Hasudungan]
* [https://cn.inside.dtu.dk/cnnet/filesharing/download/8df4dfc2-e023-43b8-a2cd-1a00e1e902bc The Organization and Expression of Lymphocyte Receptor Genes]

== Remarks ==

* Make sure you state your "10 things" as questions
* For the final presentation, make sure to include references
* Do not include slides from other courses
* Do not reference a website, if you find a nice figure, trace it to its origin
* In general only reference official publications, i.e. scientific papers, books and reports
* The 10 minutes is sharp - you will be stopped, so keep time

22145 Immunological Bioinformatics Course Programme January 2021

2024-03-20T14:39:21Z

WikiSysop: /* 2021 Course Schedule Overview */

= COURSE PLAN FOR 2021 =

==EXAM==

The pdf with the exam will be uploaded here on Friday January 22nd, 13 - 15hs



'''Guidelines'''

* The exam will be made available at the wiki at 13.00hs. Upload a '''pdf''' with your answers '''no later than 15.00hs on DTU inside''' written exam assignment.
* You must connect at Zoom 5 minutes before the exam, and have the '''camera turned ON during the whole exam'''. Failing to meet this requirement will invalidate the exam.
* This is an '''individual exam'''. Remember sharing or copying answers is not allowed and will be severely punished according to DTU rules and code-of-honor.

==Information for Course Participants==

'''Course Format'''
* NEWS! Due to new restrictions on Covid19 this course will be completely conducted online and all classes will be recorded and uploaded
* Due to group work on some classes, it will be mandatory that you are connected and work online on the allocated time for those
* This will be needed for the entire first day, the question and answer sessions, and the final exam
* Classes will be a mixture of lectures, group work and individual exercises
* Most of the group work will consist of computer exercises, where students are required to use their laptops
* General Question and Answer will be live and uploaded after the session
* Specif Question and Answers for exercise-lectures will be held on Piazza, where you need to create an user
* All learning resources will be available through DTU inside or this site
* Expected time usage: [https://www.dtu.dk/english/Education/Course-base 1 ECTS point equals approx. 28 hours], this translates to an expected time usage of ~10 hours/day for a 5 ECTS 3-week course

'''Course Resources'''
* [http://teaching.healthtech.dtu.dk/22145/index.php/22145_-_Immunological_Bioinformatics Official course website]
* [https://kurser.dtu.dk/course/22145 Official course description]
* [https://dtudk.zoom.us/meeting/register/u5Ypc-iupjIuGtzs8eF0RlM5xijlcFdwQaQq ZOOM link for live classes(registration with DTU mail needed)]
* [https://piazza.com/dtu.dk/fall2020/22145 Piazza link for Q&A on exercises]
* IMPORTANT: Please note, that the below course programme can be subject to changes or updates. Make sure to reload the page, to get the newest version of the programme.

'''Course Teachers'''
* [CB] [https://www.dtu.dk/english/service/phonebook/Person?id=142840&cpid=263035&tab=2&qt=dtupublicationquery Carolina Barra]
* [PM] [https://www.dtu.dk/english/service/phonebook/person?id=34983&cpid=257128&tab=2&qt=dtupublicationquery Paolo Marcatili]
* [MN] [https://www.dtu.dk/english/service/phonebook/person?id=5973&cpid=214020&tab=1&qt=dtupublicationquery Morten Nielsen]
* [BR] [https://www.dtu.dk/english/service/phonebook/person?id=104623&cpid=257289&tab=3&qt=dtuprojectquery Birkir Reynisson]
* [HP] [https://www.dtu.dk/service/telefonbog/person?id=88645&cpid=262443&tab=3&qt=dtuprojectquery Helle Rus Povlsen]
* [MV] [https://www.dtu.dk/english/service/phonebook/Person?id=129355&cpid=257376&tab=2&qt=dtuprojectquery Milena Vujovic]
* [AM] [https://www.dtu.dk/english/service/phonebook/Person?id=124312&cpid=274573&tab=3&qt=dtuprojectquery Alessandro Montemurro]

'''General Daily Schedule'''

* 09.00 - 12.00 Lectures
* 12.00 - 13.00 Lunch
* 13.00 - 13.30 Live sessions Q&A
* 13.30 - 17.00 Exercises

'''Location'''

* NOTE: This edition of the course will be completely online

'''Profiles of Invited Speakers for Mini Symposium'''
* Clinical perspective: [https://research.ku.dk/search/?pure=en%2Fpersons%2F458748 MD, PhD, Clinical Associate Professor Marco Donia, Center for Cancer Immune Therapy (CCIT) and Unit for Experimental Cancer Treatment (EFEK), Herlev-Gentofte Hospital and University of Copenhagen]
* Molecular Biology perspective: [https://www.dtu.dk/service/telefonbog/person?id=102741&cpid=&tab=2&qt=dtupublicationquery PhD, Adjunkt Professor Sunil Kumar Saini, Section for Experimental and Translational Immunology, Department of Health Technology, Technical University of Denmark]
* Biomedical Industry perspective: upon confirmation.
* Bioinformatics Industry perspective: [https://www.vaccibody.com/management/ PhD, Head of Bioinformatics Monika Sekelja, Vaccibody A/S]

==2021 Course Schedule Overview==

{| class="wikitable" style="font-size:75%;"
|+ Teaching Day 1-8
!
! Monday Jan. 4th
! Tuesday Jan. 5th
! Wednesday Jan. 6th
! Thursday Jan. 7th
! Friday Jan. 8th
! Monday Jan. 11th
! Tuesday Jan. 12th
! Wednesday Jan. 13th
|-
! Topic
! Introduction and Basic Immunology
! T-Cell Epitopes
! Antigen Processing and Presentation, HLA Clustering, and Vaccine Design
! Protein Structure of B-/T-Cell Receptors and B-Cell Epitopes
! Immunopeptidomics, T-Cell Repertoires and the IEDB
! Antibody Humanization and T-Cell Interaction Models
! De-Immunization and Chimeric Antigen Receptor (CAR) Immunotherapy
! Mini-symposium on Immunoinformatics by Invited Speakers
|-
! 09.00 - 09.30
| [http://www.cbs.dtu.dk/courses/27685.imm/presentations/Carol/Course_Introduction_2021.pdf Course Introduction] '''Live on Zoom''' Recording: [http://www.cbs.dtu.dk/courses/27685.imm/recordings/22145_2021/Introduction_IB.mp4 MP4] [CB]
| Lecture: Prediction of MHC peptide binding Part 1 [MN]. Session materials: [http://www.cbs.dtu.dk/courses/27685.imm/presentations/MHCbinding_2020_part1.pdf Slides [PDF]]. Recording: [http://www.cbs.dtu.dk/courses/27685.imm/recordings/MHC_part1.mp4 [MP4]], Logo handout: [http://www.cbs.dtu.dk/courses/27685.imm/presentations/Ex_Logo.pdf [PDF]], [http://www.cbs.dtu.dk/courses/27685.imm/presentations/Ex_Logo_ans.pdf Answer Logo handout] Logo handout Recording [http://www.cbs.dtu.dk/courses/27685.imm/recordings/Ex_Logo.mp4 [MP4]].
| Lecture: MHC motif deconvolution - Identifying sequence motifs in large scale ligand data sets [MN]. Session materials: [http://www.cbs.dtu.dk/courses/27685.imm/presentations/MHCMotifDecon_2021.pdf Slides [PDF]]. Recording: [http://www.cbs.dtu.dk/courses/27685.imm/recordings/MHCMotifDecon_2021.mp4 [MP4]].
| Lecture: [https://teaching.healthtech.dtu.dk/material/22145/pdf/Antibody_structure.pdf TCR and BCR structure]. Recording: [https://youtu.be/HP-zcAugLkk Antibody Modelling] [PM]
[https://youtu.be/8dzwdlKTUXI Solution]
| Lecture: [http://www.cbs.dtu.dk/courses/27685.imm/presentations/Carol/Immunopeptidomics_2021.pdf Immunopeptidomics] '''Live on Zoom''' Recording: [http://www.cbs.dtu.dk/courses/27685.imm/recordings/22145_2021/Immunopeptidomics_CB.mp4 MP4] [CB]
| Lecture: [https://teaching.healthtech.dtu.dk/22145/images/e/ec/Humanization_2021_notabhu_reduced.pdf Antibody Humanization] [https://youtu.be/WXMrdDSHA6M Video] [PM]
| Lecture: Protein Drug Deimmunization '''Live on Zoom''' [http://www.cbs.dtu.dk/courses/27685.imm/deimmune_Presentation/2021_01_12_Deimmunization_22145.pdf pdf] [http://www.cbs.dtu.dk/courses/27685.imm/deimmune_Presentation/2021_01_12_DeimmunePresentation.mp4 mp4] [BR]
| Talk 1: '''Cancer immunotherapy in the clinic.''' Marco Donia '''Live!''' [http://www.cbs.dtu.dk/courses/27685.imm/recordings/22145_2021/Talk1_MarcoDonia.mp4 video]
|-
! 09.30 - 10.15
| [[Micro_Project_on_Basic_Immunology|Micro project group work]] '''Live on Zoom''' [CB]
| Lecture: Prediction of MHC peptide binding part 2 [MN]. Session materials: [http://www.cbs.dtu.dk/courses/27685.imm/presentations/MHCbinding_2020_part2.pdf Slides [PDF]]. Recording: [http://www.cbs.dtu.dk/courses/27685.imm/recordings/MHC_part2.mp4 [MP4]]. NN handout [http://www.cbs.dtu.dk/courses/27685.imm/presentations/NN_handout.pdf [PDF]]. NN handout Recording [http://www.cbs.dtu.dk/courses/27685.imm/recordings/Ex_NN.mp4 [MP4]].
| Lecture: What defines a T cell epitope? Is there any thing beyond MHC binding? [MN] Session materials: [http://www.cbs.dtu.dk/courses/27685.imm/presentations/Processing_Tcell_2018.pdf Slides [PDF]]. Recording: [http://www.cbs.dtu.dk/courses/27685.imm/recordings/Processing_Tcell_2018.mp4 [MP4]].
| Exercise: [[Antibody Structure Prediction and Analysis]] Recording: [https://youtu.be/5t7aUkXVuwk Exercise] [PM]
| Exercise files: [https://teaching.healthtech.dtu.dk/material/22145/pdf/Peptides-HD-DR2b.txt Peptides] [https://teaching.healthtech.dtu.dk/material/22145/pdf/Alleles-HD-DR2b.txt Alleles_list] Answers: [http://www.cbs.dtu.dk/courses/27685.imm/presentations/Carol/Exercise_guidelines_answers.pdf Answers]'''Live on Zoom''' [CB]
| Exercise: [[Antibody Humanization]] [PM]
| Exercise: [[Protein Drug Deimmunization]] [BR]
| Talk 2: '''SARS-CoV-2 full genome profiling for T cell immunity and immunodominance in COVID-19 infection.''' Sunil Kumar Saini '''Live!''' [http://www.cbs.dtu.dk/courses/27685.imm/recordings/22145_2021/Talk2_SunilSaini.mp4 video]
|-
! 10.15 - 10.30
! Break
! Break
! Break
! Break
! Break
! Break
! Break
! Break
|-
! 10.30 - 11.15
| [[Micro_Project_on_Basic_Immunology|Micro project group work]] '''Live on Zoom''' [CB]
| Lecture: Prediction of MHC peptide binding part 3 [MN]. Session materials: [http://www.cbs.dtu.dk/courses/27685.imm/presentations/MHCbinding_2020_part3.pdf Slides [PDF]]. Recording: [http://www.cbs.dtu.dk/courses/27685.imm/recordings/MHC_part3.mp4 [MP4]].
| Lecture: Selecting the one in a million. Strategies for selecting peptide subsets, and vaccine design [MN]. Session materials: [http://www.cbs.dtu.dk/courses/27685.imm/presentations/Vaccine_design_2019.pdf Slides [PDF]]. Recording: [http://www.cbs.dtu.dk/courses/27685.imm/recordings/Vaccine_design_2019.mp4 [MP4]].
| Lecture: [https://teaching.healthtech.dtu.dk/material/22145/pdf/Linear_epitope_prediction.pdf Linear B-cell epitope prediction]. Recording: [https://youtu.be/Ukk5XJfuh6k] [PM]
| Lecture: T-Cell Receptor Repertoires '''Live on Zoom''' [http://www.cbs.dtu.dk/courses/27685.imm/presentations/Carol/20210108MV_Tcell_receptor_repertoires_updated.pdf Slides] Recording: [[http://www.cbs.dtu.dk/courses/27685.imm/recordings/22145_2021/20210108MV_Tcell_receptor_repertoires.mp4 [MP4]] [MV]
| Lecture: Single cell technologies for T-cell epitopes [http://www.cbs.dtu.dk/courses/27685.imm/presentations/Carol/single_cell_general.pdf Single Cell] and [http://www.cbs.dtu.dk/courses/27685.imm/presentations/Carol/nettcr_project.pdf NetTCR Project] [http://www.cbs.dtu.dk/courses/27685.imm/recordings/22145_2021/Single_cell.mp4 video]'''Live on Zoom''' [HP]
| Lecture: [http://teaching.healthtech.dtu.dk/36685/images/8/87/Deimmunisation.pptx.pdf Humanization and deimmunization for cancer T cell therapy molecules] [http://www.cbs.dtu.dk/courses/27685.imm/recordings/22145_2021/Deimmunisation_CART-cells.mp4 video] [PM]
| Talk 3: '''The utilization of bioinformatics to guide drug design.''' Monika Sekelja '''Live!''' [http://www.cbs.dtu.dk/courses/27685.imm/recordings/22145_2021/Talk3_MonikaSekelja.mp4 video]
|-
! 11.15 - 12.00
| [[Micro_Project_on_Basic_Immunology|Micro project group work]] '''Live on Zoom''' [CB]
| Lecture: [http://www.cbs.dtu.dk/courses/ILRI_workshop/presentations/Performance_measure.pdf Performance measures] [MN]. Recording: [http://www.cbs.dtu.dk/courses/22125/recordings/Performance_measure.mp4 [MP4]].
| Lecture: Selecting the one in a million. Strategies for selecting peptide subsets, and vaccine design [MN] cont.
| Lecture: [https://teaching.healthtech.dtu.dk/material/22145/pdf/Conformational_epitope_prediction.pdf Conformational B-cell epitope prediction]. Recording: [https://youtu.be/xg8Wf4rNsqw][PM]
| Lecture: The Immune Epitope Database & Tools '''Live on Zoom''' [http://www.cbs.dtu.dk/courses/27685.imm/presentations/Carol/2021_01_08_IEDB.pdf PDF] [http://www.cbs.dtu.dk/courses/27685.imm/recordings/2021_01_08_IEDB_Presentation.mp4 mp4] [BR]
| Lecture: [http://www.cbs.dtu.dk/courses/27685.imm/presentations/Carol/netTCR_interactions_2021.pdf Modelling TCRpMHC interactions] [http://www.cbs.dtu.dk/courses/27685.imm/recordings/22145_2021/NetTCR_video.mp4 video]'''Live on Zoom''' [AM]
| Lecture: [http://teaching.healthtech.dtu.dk/36685/images/8/87/Deimmunisation.pptx.pdf Humanization and deimmunization for cancer T cell therapy molecules] [PM]
| Talk 4: TBC Live!
|-
! 12.00 - 13.00
! Lunch Break
! Lunch Break
! Lunch Break
! Lunch Break
! Lunch Break
! Lunch Break
! Lunch Break
! Lunch Break
|-
! 13.00 - 13.30
| '''Live:''' Q&A Session [CB]
| '''Live:''' Quiz: [https://kursusquiz.dtu.dk/quiz/solochallenge/398/holding/571?lang=en MHC binding]. Q&A Session [MN]. Recordings: [http://www.cbs.dtu.dk/courses/27685.imm//recordings/QA_2021-01-05_1.mp4 R1 [MP4]]. [http://www.cbs.dtu.dk/courses/27685.imm//recordings/QA_2021-01-05_2.mp4 R2 [MP4]]. [http://www.cbs.dtu.dk/courses/27685.imm//recordings/QA_2021-01-05_3.mp4 R3 [MP4]].
| '''Live:''' Exercise recap [MN]. Quiz: [https://kursusquiz.dtu.dk/quiz/solochallenge/400/holding/578?lang=en MHC processing, epitope discovery and vaccine design]. Q&A Session [MN]. Recordings: [http://www.cbs.dtu.dk/courses/27685.imm//recordings/QA_2021-01-06.mp4 R1 [MP4]].
| '''Live:''' Exercise recap [MN] Recordings: [http://www.cbs.dtu.dk/courses/27685.imm//recordings/QA_2021-01-07.mp4 R1 [MP4]].
| '''Live:''' Exercise recap Recordings: [http://www.cbs.dtu.dk/courses/27685.imm//recordings/22145_2021/PM_live_recap_exercises_Ab_TCRs.mp4 [MP4]] [PM]
| '''Live:''' Exercise recap [http://www.cbs.dtu.dk/courses/27685.imm/recordings/22145_2021/Live_exercise_recap_immunopeptidomics_IEDB_CB_BR.mp4 video] [CB] and [BR]
| '''Live:''' Exercise recap [http://www.cbs.dtu.dk/courses/27685.imm/recordings/22145_2021/HP_exercise_recap_single_cell_netTCR.mp4 video] [HP]
| '''Live:''' Exercise recap [PM]
|-
! 13.30 - 17.00
| [[Micro_Project_on_Basic_Immunology|Micro project group work]] '''Live on Zoom''' [http://www.cbs.dtu.dk/courses/27685.imm/recordings/22145_2021/Group_Presentations_day1part1.mp4 Presentations_part1] [http://www.cbs.dtu.dk/courses/27685.imm/recordings/22145_2021/Group_Presentations_day1part2.mp4 Presentations_part2] [CB]
| Exercise:[http://www.cbs.dtu.dk/courses/27685.imm/exercise_MHC_bind/exercise_2019.php Prediction of MHC:peptide binding using PSSM and ANN]
[http://www.cbs.dtu.dk/courses/27685.imm/exercise_MHC_bind/exercise_2019_ans.php Answers: Prediction of MHC:peptide binding using PSSM and ANN]
| Exercise: [http://www.cbs.dtu.dk/courses/27685.imm/exercise_HCVVaccine/exercise_HCVVaccine_2021.php Development of vaccines against HCV] [MN] [http://www.cbs.dtu.dk/courses/27685.imm/exercise_HCVVaccine/exercise_HCVVaccine_2021_ans.php Answers]
| Exercise: [http://www.cbs.dtu.dk/courses/27485.imm/epitope_2014.php B cell epitope predictions] [PM]
| Exercise: [https://teaching.healthtech.dtu.dk/22145/index.php/T-Cell_Receptor_Repertoires#Retrieve_and_Upload_Repertoire_data T-Cell Receptor Repertoires] [MV] [http://teaching.healthtech.dtu.dk/material/22145/ljess/repertoire_analysis.html Suggested answers] Exercise: [[IEDB]] [BR]
| Exercise: [[Single cell technologies for T-cell epitopes]] [HP]
| Exercise: [http://teaching.healthtech.dtu.dk/36685/index.php/Exercise_on_CAR_T-cell_humanisation_and_de-immunisation CAR T-cell humanisation and de-immunisation] [PM]
| '''Live on Zoom''' [http://www.cbs.dtu.dk/courses/27685.imm/presentations/Carol/project_and_exam.pdf Introduction to project and exam] [CB]
|- style="vertical-align: top;" |
! Learning Resources
|
Required
* Paper: [https://onlinelibrary.wiley.com/doi/abs/10.1002/bies.201900200 Peptide Presentation to T Cells: Solving the Immunogenic Puzzle]
* Video: [https://www.youtube.com/watch?v=K09xzIQ8zsg Tumour immunology and immunotherapy]
* Video: [https://www.youtube.com/watch?v=vponeaNiewE Decoding cancer immunology: Hunting hidden tumours]
Optional
* Video: [https://www.youtube.com/watch?v=fSEFXl2XQpc Back to Basics]
|
Required
* Book: [https://teaching.healthtech.dtu.dk/material/22145/pdf/Lund_et_al_immunological_bioinformatics_2005_chapter_3.pdf Immuno. Bioinfo. Ch. 3]
* Book: [https://teaching.healthtech.dtu.dk/material/22145/pdf/Lund_et_al_immunological_bioinformatics_2005_chapter_4.pdf Immuno. Bioinfo. Ch. 4]
* Paper: [http://bioinformatics.oxfordjournals.org/cgi/reprint/23/24/3265 Modeling the adaptive immune system: predictions and simulations]
* Paper: [https://www.annualreviews.org/doi/pdf/10.1146/annurev-biodatasci-021920-100259 Immunoinformatics: Predicting Peptide–MHC Binding]
Optional
* Paper: [https://www.mcponline.org/content/18/12/2459.long NNAlign_MA; MHC Peptidome Deconvolution for Accurate MHC Binding Motif Characterization and Improved T-cell Epitope Predictions]
* Paper: [https://pubs.acs.org/doi/10.1021/acs.jproteome.9b00874 Improved Prediction of MHC II Antigen Presentation through Integration and Motif Deconvolution of Mass Spectrometry MHC Eluted Ligand Data]
|
Required
* Book: [https://teaching.healthtech.dtu.dk/material/22145/pdf/Lund_et_al_immunological_bioinformatics_2005_chapter_13.pdf Immuno. Bioinfo. Ch. 13]
* Book: [https://teaching.healthtech.dtu.dk/material/22145/pdf/Lund_et_al_immunological_bioinformatics_2005_chapter_14.pdf Immuno. Bioinfo. Ch. 14]
* Paper: [https://www.annualreviews.org/doi/10.1146/annurev-immunol-082119-124838 T Cell Epitope Predictions]
Optional
* Paper: [https://www.ncbi.nlm.nih.gov/pubmed/23097419 Simultaneous alignment and clustering of peptide data using a Gibbs sampling approach]
* Paper: [http://www.jimmunol.org/content/178/12/7890.long A Quantitative Analysis of the Variables Affecting the Repertoire of T Cell Specificities Recognized after Vaccinia Virus Infection]
* Paper: [https://www.ncbi.nlm.nih.gov/pubmed/24760079 Identification and HLA-tetramer-validation of human CD4+ and CD8+ T cell responses against HCMV proteins IE1 and IE2]
|
* [https://teaching.healthtech.dtu.dk/material/22145/pdf/Immunological_bioinformatics_Quiz_1_2019.pdf Mini Quiz]
* [https://teaching.healthtech.dtu.dk/material/22145/pdf/Pymol-edu-license-2021.txt Pymol license]

Required
* None
Optional
* Paper: [https://academic.oup.com/nar/article/3787843 BepiPred 2.0]
* Paper: [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531324/ B-cell epitope prediction]
* Video: [http://www.youtube.com/watch?v=Z36dUduOk1Y Simplified B-cell walkthrough] (Nice and easy understandable explanation of B-cells)
* Resource: [https://pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/ PDB 101: Introduction to PDB Data]
|

* Rstudio: [https://rstudio.com/products/rstudio/download/ Get it] [https://datascienceplus.com/introduction-to-rstudio/ Quick guide] [https://teaching.healthtech.dtu.dk/22145/index.php/Getting_started_with_RStudio_Cloud,_R_and_rmarkdown Getting started]

Required
* Video: [https://www.youtube.com/watch?v=Na-Zc-xWCLE Immunology wars: A billion antibodies]
* Video: [https://www.youtube.com/watch?v=JJmqt40Z3mM Antibody (BCR) and TCR Diversity]
* Video: [https://www.youtube.com/watch?v=h9mqsllg1Cs Antibody Somatic (VDJ) Recombination I]
* Video: [https://www.youtube.com/watch?v=_D2x-dhh6Pg Antibody Somatic (VDJ) Recombination II]
* Book: [https://cn.inside.dtu.dk/cnnet/filesharing/download/8df4dfc2-e023-43b8-a2cd-1a00e1e902bc Kuby Ch. 7: The Organization and Expression of Lymphocyte Receptor Genes]
* Paper: [https://www.ncbi.nlm.nih.gov/pubmed/25300482 The immune epitope database (IEDB) 3.0.]
Optional
* None
|
Required
* Paper: [https://www.biorxiv.org/content/early/2018/10/02/433706 NetTCR: sequence-based prediction of TCR binding to peptide-MHC complexes using convolutional neural networks]
* Paper: [https://www.nature.com/articles/nbt.4303 T cell receptor fingerprinting enables in-depth characterization of the interactions governing recognition of peptide–MHC complexes]
* Paper: [https://www.nature.com/articles/s41598-019-50932-4 TCRpMHCmodels: Structural modelling of TCR-pMHC class I complexes]
* Paper: [https://www.sciencedirect.com/science/article/pii/S0161589017306211 Identification of the cognate peptide-MHC target of T cell receptors using molecular modeling and force field scoring]
* Tech report: [http://teaching.healthtech.dtu.dk/material/22145/ljess/10x_AN047_IP_A_New_Way_of_Exploring_Immunity_Digital.pdf A New Way of Exploring Immunity – Linking Highly Multiplexed Antigen Recognition to Immune Repertoire and Phenotype]
Optional
* None
|
Required
* None
Optional
* Paper: [https://www.ncbi.nlm.nih.gov/pubmed/27322891 Design and engineering of deimmunized biotherapeutics]
|
|}

==Project Period and Exam==

=== Project ===

'''Wednesday January 13th - Wednesday January 20nd - Project Work'''

Please note the following (***time has been updated***):
* The deadline for uploading the final project Poster presentation (i.e. ''not'' a report) to [https://www.inside.dtu.dk/ DTU inside] will be '''Wednesday January 20nd at 11.59AM'''
* It is a prerequisite for the exam to complete this assignment and as such, ''failure to meet the deadline will result in a failed exam''
* Furthermore and very important - Each group member is responsible for ''all'' aspects of the group work and subsequent presentation

'''Groups and Projects 2021'''

* Groups will be preset based on educational diversity

* [https://cn.inside.dtu.dk/cnnet/filesharing/download/950b168e-0786-4b7e-85bd-1389e9a61869 The groups list for 2021]

=== Exam Schedule ===

* General exam format will consist on 2 parts ([https://kurser.dtu.dk/course/22145 course learning objectives]):

Oral presentation of the poster project ~10 minutes for all group presentation + 5 minutes for questions (15 minutes total)
Date: January 21st 2021 (specific times per group to be announced)

Written exam ~20 questions 2hs, all conducted online on DTU Inside
Date: January 22st 2021

* Individual grades will be given after the finalization of the course

22145 Immunological Bioinformatics Course Programme January 2021

2024-03-20T14:36:32Z

WikiSysop: /* 2021 Course Schedule Overview */

= COURSE PLAN FOR 2021 =

==EXAM==

The pdf with the exam will be uploaded here on Friday January 22nd, 13 - 15hs



'''Guidelines'''

* The exam will be made available at the wiki at 13.00hs. Upload a '''pdf''' with your answers '''no later than 15.00hs on DTU inside''' written exam assignment.
* You must connect at Zoom 5 minutes before the exam, and have the '''camera turned ON during the whole exam'''. Failing to meet this requirement will invalidate the exam.
* This is an '''individual exam'''. Remember sharing or copying answers is not allowed and will be severely punished according to DTU rules and code-of-honor.

==Information for Course Participants==

'''Course Format'''
* NEWS! Due to new restrictions on Covid19 this course will be completely conducted online and all classes will be recorded and uploaded
* Due to group work on some classes, it will be mandatory that you are connected and work online on the allocated time for those
* This will be needed for the entire first day, the question and answer sessions, and the final exam
* Classes will be a mixture of lectures, group work and individual exercises
* Most of the group work will consist of computer exercises, where students are required to use their laptops
* General Question and Answer will be live and uploaded after the session
* Specif Question and Answers for exercise-lectures will be held on Piazza, where you need to create an user
* All learning resources will be available through DTU inside or this site
* Expected time usage: [https://www.dtu.dk/english/Education/Course-base 1 ECTS point equals approx. 28 hours], this translates to an expected time usage of ~10 hours/day for a 5 ECTS 3-week course

'''Course Resources'''
* [http://teaching.healthtech.dtu.dk/22145/index.php/22145_-_Immunological_Bioinformatics Official course website]
* [https://kurser.dtu.dk/course/22145 Official course description]
* [https://dtudk.zoom.us/meeting/register/u5Ypc-iupjIuGtzs8eF0RlM5xijlcFdwQaQq ZOOM link for live classes(registration with DTU mail needed)]
* [https://piazza.com/dtu.dk/fall2020/22145 Piazza link for Q&A on exercises]
* IMPORTANT: Please note, that the below course programme can be subject to changes or updates. Make sure to reload the page, to get the newest version of the programme.

'''Course Teachers'''
* [CB] [https://www.dtu.dk/english/service/phonebook/Person?id=142840&cpid=263035&tab=2&qt=dtupublicationquery Carolina Barra]
* [PM] [https://www.dtu.dk/english/service/phonebook/person?id=34983&cpid=257128&tab=2&qt=dtupublicationquery Paolo Marcatili]
* [MN] [https://www.dtu.dk/english/service/phonebook/person?id=5973&cpid=214020&tab=1&qt=dtupublicationquery Morten Nielsen]
* [BR] [https://www.dtu.dk/english/service/phonebook/person?id=104623&cpid=257289&tab=3&qt=dtuprojectquery Birkir Reynisson]
* [HP] [https://www.dtu.dk/service/telefonbog/person?id=88645&cpid=262443&tab=3&qt=dtuprojectquery Helle Rus Povlsen]
* [MV] [https://www.dtu.dk/english/service/phonebook/Person?id=129355&cpid=257376&tab=2&qt=dtuprojectquery Milena Vujovic]
* [AM] [https://www.dtu.dk/english/service/phonebook/Person?id=124312&cpid=274573&tab=3&qt=dtuprojectquery Alessandro Montemurro]

'''General Daily Schedule'''

* 09.00 - 12.00 Lectures
* 12.00 - 13.00 Lunch
* 13.00 - 13.30 Live sessions Q&A
* 13.30 - 17.00 Exercises

'''Location'''

* NOTE: This edition of the course will be completely online

'''Profiles of Invited Speakers for Mini Symposium'''
* Clinical perspective: [https://research.ku.dk/search/?pure=en%2Fpersons%2F458748 MD, PhD, Clinical Associate Professor Marco Donia, Center for Cancer Immune Therapy (CCIT) and Unit for Experimental Cancer Treatment (EFEK), Herlev-Gentofte Hospital and University of Copenhagen]
* Molecular Biology perspective: [https://www.dtu.dk/service/telefonbog/person?id=102741&cpid=&tab=2&qt=dtupublicationquery PhD, Adjunkt Professor Sunil Kumar Saini, Section for Experimental and Translational Immunology, Department of Health Technology, Technical University of Denmark]
* Biomedical Industry perspective: upon confirmation.
* Bioinformatics Industry perspective: [https://www.vaccibody.com/management/ PhD, Head of Bioinformatics Monika Sekelja, Vaccibody A/S]

==2021 Course Schedule Overview==

{| class="wikitable" style="font-size:75%;"
|+ Teaching Day 1-8
!
! Monday Jan. 4th
! Tuesday Jan. 5th
! Wednesday Jan. 6th
! Thursday Jan. 7th
! Friday Jan. 8th
! Monday Jan. 11th
! Tuesday Jan. 12th
! Wednesday Jan. 13th
|-
! Topic
! Introduction and Basic Immunology
! T-Cell Epitopes
! Antigen Processing and Presentation, HLA Clustering, and Vaccine Design
! Protein Structure of B-/T-Cell Receptors and B-Cell Epitopes
! Immunopeptidomics, T-Cell Repertoires and the IEDB
! Antibody Humanization and T-Cell Interaction Models
! De-Immunization and Chimeric Antigen Receptor (CAR) Immunotherapy
! Mini-symposium on Immunoinformatics by Invited Speakers
|-
! 09.00 - 09.30
| [http://www.cbs.dtu.dk/courses/27685.imm/presentations/Carol/Course_Introduction_2021.pdf Course Introduction] '''Live on Zoom''' Recording: [http://www.cbs.dtu.dk/courses/27685.imm/recordings/22145_2021/Introduction_IB.mp4 MP4] [CB]
| Lecture: Prediction of MHC peptide binding Part 1 [MN]. Session materials: [http://www.cbs.dtu.dk/courses/27685.imm/presentations/MHCbinding_2020_part1.pdf Slides [PDF]]. Recording: [http://www.cbs.dtu.dk/courses/27685.imm/recordings/MHC_part1.mp4 [MP4]], Logo handout: [http://www.cbs.dtu.dk/courses/27685.imm/presentations/Ex_Logo.pdf [PDF]], [http://www.cbs.dtu.dk/courses/27685.imm/presentations/Ex_Logo_ans.pdf Answer Logo handout] Logo handout Recording [http://www.cbs.dtu.dk/courses/27685.imm/recordings/Ex_Logo.mp4 [MP4]].
| Lecture: MHC motif deconvolution - Identifying sequence motifs in large scale ligand data sets [MN]. Session materials: [http://www.cbs.dtu.dk/courses/27685.imm/presentations/MHCMotifDecon_2021.pdf Slides [PDF]]. Recording: [http://www.cbs.dtu.dk/courses/27685.imm/recordings/MHCMotifDecon_2021.mp4 [MP4]].
| Lecture: [https://teaching.healthtech.dtu.dk/material/22145/pdf/Antibody_structure.pdf TCR and BCR structure]. Recording: [https://youtu.be/HP-zcAugLkk Antibody Modelling] [PM]
[https://youtu.be/8dzwdlKTUXI Solution]
| Lecture: [http://www.cbs.dtu.dk/courses/27685.imm/presentations/Carol/Immunopeptidomics_2021.pdf Immunopeptidomics] '''Live on Zoom''' Recording: [http://www.cbs.dtu.dk/courses/27685.imm/recordings/22145_2021/Immunopeptidomics_CB.mp4 MP4] [CB]
| Lecture: [https://teaching.healthtech.dtu.dk/22145/images/e/ec/Humanization_2021_notabhu_reduced.pdf Antibody Humanization] [https://youtu.be/WXMrdDSHA6M Video] [PM]
| Lecture: Protein Drug Deimmunization '''Live on Zoom''' [http://www.cbs.dtu.dk/courses/27685.imm/deimmune_Presentation/2021_01_12_Deimmunization_22145.pdf pdf] [http://www.cbs.dtu.dk/courses/27685.imm/deimmune_Presentation/2021_01_12_DeimmunePresentation.mp4 mp4] [BR]
| Talk 1: '''Cancer immunotherapy in the clinic.''' Marco Donia '''Live!''' [http://www.cbs.dtu.dk/courses/27685.imm/recordings/22145_2021/Talk1_MarcoDonia.mp4 video]
|-
! 09.30 - 10.15
| [[Micro_Project_on_Basic_Immunology|Micro project group work]] '''Live on Zoom''' [CB]
| Lecture: Prediction of MHC peptide binding part 2 [MN]. Session materials: [http://www.cbs.dtu.dk/courses/27685.imm/presentations/MHCbinding_2020_part2.pdf Slides [PDF]]. Recording: [http://www.cbs.dtu.dk/courses/27685.imm/recordings/MHC_part2.mp4 [MP4]]. NN handout [http://www.cbs.dtu.dk/courses/27685.imm/presentations/NN_handout.pdf [PDF]]. NN handout Recording [http://www.cbs.dtu.dk/courses/27685.imm/recordings/Ex_NN.mp4 [MP4]].
| Lecture: What defines a T cell epitope? Is there any thing beyond MHC binding? [MN] Session materials: [http://www.cbs.dtu.dk/courses/27685.imm/presentations/Processing_Tcell_2018.pdf Slides [PDF]]. Recording: [http://www.cbs.dtu.dk/courses/27685.imm/recordings/Processing_Tcell_2018.mp4 [MP4]].
| Exercise: [[Antibody Structure Prediction and Analysis]] Recording: [https://youtu.be/5t7aUkXVuwk Exercise] [PM]
| Exercise files: [[File: Peptides-HD-DR2b.txt|Peptides]] [[File: Alleles-HD-DR2b.txt |Alleles_list]] Answers: [http://www.cbs.dtu.dk/courses/27685.imm/presentations/Carol/Exercise_guidelines_answers.pdf Answers]'''Live on Zoom''' [CB]
| Exercise: [[Antibody Humanization]] [PM]
| Exercise: [[Protein Drug Deimmunization]] [BR]
| Talk 2: '''SARS-CoV-2 full genome profiling for T cell immunity and immunodominance in COVID-19 infection.''' Sunil Kumar Saini '''Live!''' [http://www.cbs.dtu.dk/courses/27685.imm/recordings/22145_2021/Talk2_SunilSaini.mp4 video]
|-
! 10.15 - 10.30
! Break
! Break
! Break
! Break
! Break
! Break
! Break
! Break
|-
! 10.30 - 11.15
| [[Micro_Project_on_Basic_Immunology|Micro project group work]] '''Live on Zoom''' [CB]
| Lecture: Prediction of MHC peptide binding part 3 [MN]. Session materials: [http://www.cbs.dtu.dk/courses/27685.imm/presentations/MHCbinding_2020_part3.pdf Slides [PDF]]. Recording: [http://www.cbs.dtu.dk/courses/27685.imm/recordings/MHC_part3.mp4 [MP4]].
| Lecture: Selecting the one in a million. Strategies for selecting peptide subsets, and vaccine design [MN]. Session materials: [http://www.cbs.dtu.dk/courses/27685.imm/presentations/Vaccine_design_2019.pdf Slides [PDF]]. Recording: [http://www.cbs.dtu.dk/courses/27685.imm/recordings/Vaccine_design_2019.mp4 [MP4]].
| Lecture: [https://teaching.healthtech.dtu.dk/material/22145/pdf/Linear_epitope_prediction.pdf Linear B-cell epitope prediction]. Recording: [https://youtu.be/Ukk5XJfuh6k] [PM]
| Lecture: T-Cell Receptor Repertoires '''Live on Zoom''' [http://www.cbs.dtu.dk/courses/27685.imm/presentations/Carol/20210108MV_Tcell_receptor_repertoires_updated.pdf Slides] Recording: [[http://www.cbs.dtu.dk/courses/27685.imm/recordings/22145_2021/20210108MV_Tcell_receptor_repertoires.mp4 [MP4]] [MV]
| Lecture: Single cell technologies for T-cell epitopes [http://www.cbs.dtu.dk/courses/27685.imm/presentations/Carol/single_cell_general.pdf Single Cell] and [http://www.cbs.dtu.dk/courses/27685.imm/presentations/Carol/nettcr_project.pdf NetTCR Project] [http://www.cbs.dtu.dk/courses/27685.imm/recordings/22145_2021/Single_cell.mp4 video]'''Live on Zoom''' [HP]
| Lecture: [http://teaching.healthtech.dtu.dk/36685/images/8/87/Deimmunisation.pptx.pdf Humanization and deimmunization for cancer T cell therapy molecules] [http://www.cbs.dtu.dk/courses/27685.imm/recordings/22145_2021/Deimmunisation_CART-cells.mp4 video] [PM]
| Talk 3: '''The utilization of bioinformatics to guide drug design.''' Monika Sekelja '''Live!''' [http://www.cbs.dtu.dk/courses/27685.imm/recordings/22145_2021/Talk3_MonikaSekelja.mp4 video]
|-
! 11.15 - 12.00
| [[Micro_Project_on_Basic_Immunology|Micro project group work]] '''Live on Zoom''' [CB]
| Lecture: [http://www.cbs.dtu.dk/courses/ILRI_workshop/presentations/Performance_measure.pdf Performance measures] [MN]. Recording: [http://www.cbs.dtu.dk/courses/22125/recordings/Performance_measure.mp4 [MP4]].
| Lecture: Selecting the one in a million. Strategies for selecting peptide subsets, and vaccine design [MN] cont.
| Lecture: [https://teaching.healthtech.dtu.dk/material/22145/pdf/Conformational_epitope_prediction.pdf Conformational B-cell epitope prediction]. Recording: [https://youtu.be/xg8Wf4rNsqw][PM]
| Lecture: The Immune Epitope Database & Tools '''Live on Zoom''' [http://www.cbs.dtu.dk/courses/27685.imm/presentations/Carol/2021_01_08_IEDB.pdf PDF] [http://www.cbs.dtu.dk/courses/27685.imm/recordings/2021_01_08_IEDB_Presentation.mp4 mp4] [BR]
| Lecture: [http://www.cbs.dtu.dk/courses/27685.imm/presentations/Carol/netTCR_interactions_2021.pdf Modelling TCRpMHC interactions] [http://www.cbs.dtu.dk/courses/27685.imm/recordings/22145_2021/NetTCR_video.mp4 video]'''Live on Zoom''' [AM]
| Lecture: [http://teaching.healthtech.dtu.dk/36685/images/8/87/Deimmunisation.pptx.pdf Humanization and deimmunization for cancer T cell therapy molecules] [PM]
| Talk 4: TBC Live!
|-
! 12.00 - 13.00
! Lunch Break
! Lunch Break
! Lunch Break
! Lunch Break
! Lunch Break
! Lunch Break
! Lunch Break
! Lunch Break
|-
! 13.00 - 13.30
| '''Live:''' Q&A Session [CB]
| '''Live:''' Quiz: [https://kursusquiz.dtu.dk/quiz/solochallenge/398/holding/571?lang=en MHC binding]. Q&A Session [MN]. Recordings: [http://www.cbs.dtu.dk/courses/27685.imm//recordings/QA_2021-01-05_1.mp4 R1 [MP4]]. [http://www.cbs.dtu.dk/courses/27685.imm//recordings/QA_2021-01-05_2.mp4 R2 [MP4]]. [http://www.cbs.dtu.dk/courses/27685.imm//recordings/QA_2021-01-05_3.mp4 R3 [MP4]].
| '''Live:''' Exercise recap [MN]. Quiz: [https://kursusquiz.dtu.dk/quiz/solochallenge/400/holding/578?lang=en MHC processing, epitope discovery and vaccine design]. Q&A Session [MN]. Recordings: [http://www.cbs.dtu.dk/courses/27685.imm//recordings/QA_2021-01-06.mp4 R1 [MP4]].
| '''Live:''' Exercise recap [MN] Recordings: [http://www.cbs.dtu.dk/courses/27685.imm//recordings/QA_2021-01-07.mp4 R1 [MP4]].
| '''Live:''' Exercise recap Recordings: [http://www.cbs.dtu.dk/courses/27685.imm//recordings/22145_2021/PM_live_recap_exercises_Ab_TCRs.mp4 [MP4]] [PM]
| '''Live:''' Exercise recap [http://www.cbs.dtu.dk/courses/27685.imm/recordings/22145_2021/Live_exercise_recap_immunopeptidomics_IEDB_CB_BR.mp4 video] [CB] and [BR]
| '''Live:''' Exercise recap [http://www.cbs.dtu.dk/courses/27685.imm/recordings/22145_2021/HP_exercise_recap_single_cell_netTCR.mp4 video] [HP]
| '''Live:''' Exercise recap [PM]
|-
! 13.30 - 17.00
| [[Micro_Project_on_Basic_Immunology|Micro project group work]] '''Live on Zoom''' [http://www.cbs.dtu.dk/courses/27685.imm/recordings/22145_2021/Group_Presentations_day1part1.mp4 Presentations_part1] [http://www.cbs.dtu.dk/courses/27685.imm/recordings/22145_2021/Group_Presentations_day1part2.mp4 Presentations_part2] [CB]
| Exercise:[http://www.cbs.dtu.dk/courses/27685.imm/exercise_MHC_bind/exercise_2019.php Prediction of MHC:peptide binding using PSSM and ANN]
[http://www.cbs.dtu.dk/courses/27685.imm/exercise_MHC_bind/exercise_2019_ans.php Answers: Prediction of MHC:peptide binding using PSSM and ANN]
| Exercise: [http://www.cbs.dtu.dk/courses/27685.imm/exercise_HCVVaccine/exercise_HCVVaccine_2021.php Development of vaccines against HCV] [MN] [http://www.cbs.dtu.dk/courses/27685.imm/exercise_HCVVaccine/exercise_HCVVaccine_2021_ans.php Answers]
| Exercise: [http://www.cbs.dtu.dk/courses/27485.imm/epitope_2014.php B cell epitope predictions] [PM]
| Exercise: [https://teaching.healthtech.dtu.dk/22145/index.php/T-Cell_Receptor_Repertoires#Retrieve_and_Upload_Repertoire_data T-Cell Receptor Repertoires] [MV] [http://teaching.healthtech.dtu.dk/material/22145/ljess/repertoire_analysis.html Suggested answers] Exercise: [[IEDB]] [BR]
| Exercise: [[Single cell technologies for T-cell epitopes]] [HP]
| Exercise: [http://teaching.healthtech.dtu.dk/36685/index.php/Exercise_on_CAR_T-cell_humanisation_and_de-immunisation CAR T-cell humanisation and de-immunisation] [PM]
| '''Live on Zoom''' [http://www.cbs.dtu.dk/courses/27685.imm/presentations/Carol/project_and_exam.pdf Introduction to project and exam] [CB]
|- style="vertical-align: top;" |
! Learning Resources
|
Required
* Paper: [https://onlinelibrary.wiley.com/doi/abs/10.1002/bies.201900200 Peptide Presentation to T Cells: Solving the Immunogenic Puzzle]
* Video: [https://www.youtube.com/watch?v=K09xzIQ8zsg Tumour immunology and immunotherapy]
* Video: [https://www.youtube.com/watch?v=vponeaNiewE Decoding cancer immunology: Hunting hidden tumours]
Optional
* Video: [https://www.youtube.com/watch?v=fSEFXl2XQpc Back to Basics]
|
Required
* Book: [https://teaching.healthtech.dtu.dk/material/22145/pdf/Lund_et_al_immunological_bioinformatics_2005_chapter_3.pdf Immuno. Bioinfo. Ch. 3]
* Book: [https://teaching.healthtech.dtu.dk/material/22145/pdf/Lund_et_al_immunological_bioinformatics_2005_chapter_4.pdf Immuno. Bioinfo. Ch. 4]
* Paper: [http://bioinformatics.oxfordjournals.org/cgi/reprint/23/24/3265 Modeling the adaptive immune system: predictions and simulations]
* Paper: [https://www.annualreviews.org/doi/pdf/10.1146/annurev-biodatasci-021920-100259 Immunoinformatics: Predicting Peptide–MHC Binding]
Optional
* Paper: [https://www.mcponline.org/content/18/12/2459.long NNAlign_MA; MHC Peptidome Deconvolution for Accurate MHC Binding Motif Characterization and Improved T-cell Epitope Predictions]
* Paper: [https://pubs.acs.org/doi/10.1021/acs.jproteome.9b00874 Improved Prediction of MHC II Antigen Presentation through Integration and Motif Deconvolution of Mass Spectrometry MHC Eluted Ligand Data]
|
Required
* Book: [https://teaching.healthtech.dtu.dk/material/22145/pdf/Lund_et_al_immunological_bioinformatics_2005_chapter_13.pdf Immuno. Bioinfo. Ch. 13]
* Book: [https://teaching.healthtech.dtu.dk/material/22145/pdf/Lund_et_al_immunological_bioinformatics_2005_chapter_14.pdf Immuno. Bioinfo. Ch. 14]
* Paper: [https://www.annualreviews.org/doi/10.1146/annurev-immunol-082119-124838 T Cell Epitope Predictions]
Optional
* Paper: [https://www.ncbi.nlm.nih.gov/pubmed/23097419 Simultaneous alignment and clustering of peptide data using a Gibbs sampling approach]
* Paper: [http://www.jimmunol.org/content/178/12/7890.long A Quantitative Analysis of the Variables Affecting the Repertoire of T Cell Specificities Recognized after Vaccinia Virus Infection]
* Paper: [https://www.ncbi.nlm.nih.gov/pubmed/24760079 Identification and HLA-tetramer-validation of human CD4+ and CD8+ T cell responses against HCMV proteins IE1 and IE2]
|
* [https://teaching.healthtech.dtu.dk/material/22145/pdf/Immunological_bioinformatics_Quiz_1_2019.pdf Mini Quiz]
* [[Media:Pymol-edu-license-2021.txt|Pymol license]]

Required
* None
Optional
* Paper: [https://academic.oup.com/nar/article/3787843 BepiPred 2.0]
* Paper: [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531324/ B-cell epitope prediction]
* Video: [http://www.youtube.com/watch?v=Z36dUduOk1Y Simplified B-cell walkthrough] (Nice and easy understandable explanation of B-cells)
* Resource: [https://pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/ PDB 101: Introduction to PDB Data]
|

* Rstudio: [https://rstudio.com/products/rstudio/download/ Get it] [https://datascienceplus.com/introduction-to-rstudio/ Quick guide] [https://teaching.healthtech.dtu.dk/22145/index.php/Getting_started_with_RStudio_Cloud,_R_and_rmarkdown Getting started]

Required
* Video: [https://www.youtube.com/watch?v=Na-Zc-xWCLE Immunology wars: A billion antibodies]
* Video: [https://www.youtube.com/watch?v=JJmqt40Z3mM Antibody (BCR) and TCR Diversity]
* Video: [https://www.youtube.com/watch?v=h9mqsllg1Cs Antibody Somatic (VDJ) Recombination I]
* Video: [https://www.youtube.com/watch?v=_D2x-dhh6Pg Antibody Somatic (VDJ) Recombination II]
* Book: [https://cn.inside.dtu.dk/cnnet/filesharing/download/8df4dfc2-e023-43b8-a2cd-1a00e1e902bc Kuby Ch. 7: The Organization and Expression of Lymphocyte Receptor Genes]
* Paper: [https://www.ncbi.nlm.nih.gov/pubmed/25300482 The immune epitope database (IEDB) 3.0.]
Optional
* None
|
Required
* Paper: [https://www.biorxiv.org/content/early/2018/10/02/433706 NetTCR: sequence-based prediction of TCR binding to peptide-MHC complexes using convolutional neural networks]
* Paper: [https://www.nature.com/articles/nbt.4303 T cell receptor fingerprinting enables in-depth characterization of the interactions governing recognition of peptide–MHC complexes]
* Paper: [https://www.nature.com/articles/s41598-019-50932-4 TCRpMHCmodels: Structural modelling of TCR-pMHC class I complexes]
* Paper: [https://www.sciencedirect.com/science/article/pii/S0161589017306211 Identification of the cognate peptide-MHC target of T cell receptors using molecular modeling and force field scoring]
* Tech report: [http://teaching.healthtech.dtu.dk/material/22145/ljess/10x_AN047_IP_A_New_Way_of_Exploring_Immunity_Digital.pdf A New Way of Exploring Immunity – Linking Highly Multiplexed Antigen Recognition to Immune Repertoire and Phenotype]
Optional
* None
|
Required
* None
Optional
* Paper: [https://www.ncbi.nlm.nih.gov/pubmed/27322891 Design and engineering of deimmunized biotherapeutics]
|
|}

==Project Period and Exam==

=== Project ===

'''Wednesday January 13th - Wednesday January 20nd - Project Work'''

Please note the following (***time has been updated***):
* The deadline for uploading the final project Poster presentation (i.e. ''not'' a report) to [https://www.inside.dtu.dk/ DTU inside] will be '''Wednesday January 20nd at 11.59AM'''
* It is a prerequisite for the exam to complete this assignment and as such, ''failure to meet the deadline will result in a failed exam''
* Furthermore and very important - Each group member is responsible for ''all'' aspects of the group work and subsequent presentation

'''Groups and Projects 2021'''

* Groups will be preset based on educational diversity

* [https://cn.inside.dtu.dk/cnnet/filesharing/download/950b168e-0786-4b7e-85bd-1389e9a61869 The groups list for 2021]

=== Exam Schedule ===

* General exam format will consist on 2 parts ([https://kurser.dtu.dk/course/22145 course learning objectives]):

Oral presentation of the poster project ~10 minutes for all group presentation + 5 minutes for questions (15 minutes total)
Date: January 21st 2021 (specific times per group to be announced)

Written exam ~20 questions 2hs, all conducted online on DTU Inside
Date: January 22st 2021

* Individual grades will be given after the finalization of the course

27685 Course programme 2017

2024-03-20T14:15:39Z

WikiSysop: Created page with "=Immunological Bioinformatics - #27685= [http://wiki.bio.dtu.dk/teachingmaterials/index.php/Course27685 '''Course homepage'''] '''Information for participants''' '''GENERAL DAILY SCHEDULE''' Lectures will be from 9 - 12 am, Lunch from 12 - 13, Exercises from 13 - 17 pm. '''PLACE: DTU Building 210 room 162 ''' Classes will be a mixture of lectures and group work. Most of the group work will consist of '''computer exercises''' (bring your own laptop). Please note..."

=Immunological Bioinformatics - #27685=

[http://wiki.bio.dtu.dk/teachingmaterials/index.php/Course27685 '''Course homepage''']

'''Information for participants'''

'''GENERAL DAILY SCHEDULE'''

Lectures will be from 9 - 12 am,
Lunch from 12 - 13,
Exercises from 13 - 17 pm.

'''PLACE: DTU Building 210 room 162 '''

Classes will be a mixture of lectures and group work. Most of the group work will consist of '''computer exercises''' (bring your own laptop).

Please note:
*The programme may change slightly along the way.
*The required readings for a class can be trusted one week in advance.
*The exact content of powerpoint slides and handouts may change up to the last minute!

----
'''Course Programme'''
''Please note that the programme is updated on a daily basis - click the 'refresh' button once in a while to make sure that you have the most updated information''
All files and materials can be found on CampusNet

'''LITERATURE:''' All literature will be available through CampusNet or through this wiki page

----
== Thursday, June 1 ==

''Introduction, immunology brush up, and databases''

# '''BACKGROUND TEXTS''': [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245432/ Introduction to Immunology ]
'''Optional reading: [https://mitpress.mit.edu/books/immunological-bioinformatics Immunological Bioinformatics]''', Chapter 4 p. 98-101

9.00 - 9.30: [[http://wiki.bio.dtu.dk/teaching/images/f/f3/01_course_presentation_2015.ppt.pdf Introduction to the course.]]<br>
Paolo Marcatili, CBS, DTU Systems Biology.

9:30-10:15: [[Media:20150604 CBS ImmunoBioinformatics Intro 1.pdf |Basic mechanisms of immune defense]], Søren Buus, KU
10.15 - 10.30: ''Coffee Break''

10.30 - 11.15: [[Media:20150604 CBS Immunoinformatics APC MHC 2.pdf | Antigen presentation to T-Cells]], Søren Buus, KU

11.15 - 12.00: The impact of Immunological Bioinformatics on immunological research, Søren Buus, KU

12.00 - 13.00: ''lunch break''

13.00 - 13.50: Group Formation and Preliminary Test <br>

14:00 - 16.00: [[Databases and web resources in Immunological Bioinformatics]]<br>
Paolo Marcatili <br>
Paolo Marcatili, CBS, DTU Systems Biology.

----

== Friday, June 2 ==

''Immunological target identification''

----

# '''BACKGROUND TEXTS''':

CGE tool box: [https://cn.inside.dtu.dk/cnnet/filesharing/download/31d9e306-1dcb-4365-82e9-a7de8a38c770 PDF]
Read the sections on PathogenFinder, VirulenceFinder and ResFinder

PathogenFinder paper: [https://cn.inside.dtu.dk/cnnet/filesharing/download/8a329d53-a71e-4bea-a6e9-128e2364cff7 PDF]

9:00 - 12:00: ''Bacterial pathogenicity and virulence''

Johanne Ahrenfeldt, PhD Student DTU Bioinformatics

9:00 - 9:45 Presentation on PathogenFinder

'''Slides:''' [[File:PathogenFinder.pdf]]

10:00 - 11:00 Exercises

[http://wiki.bio.dtu.dk/teaching/index.php/PathogenFinder PathogenFinder]

11:15-12:00 Presentation on VirulenceFinder

'''Slides:''' [[File:VirulenceFinder.pdf]]

12.00 - 13.00: ''lunch break''

13:00 - 15:00: ''Antibiotic resistance''

Johanne Ahrenfeldt, PhD Student DTU Bioinformatics

13:00 - 13:45 Presentation on ResFinder

'''Slides:''' [[File:ResFinder.pdf]]

14:00 - 15:00 Exercises in VirulenceFinder and ResFinder

[http://wiki.bio.dtu.dk/teaching/index.php/27683_Ex4 VirulenceFinder]

[http://wiki.bio.dtu.dk/teaching/index.php/27683_Ex5 ResFinder]

----
'''Functional annotation of protein sequences'''

Lecture: [[Media:Sequence anootation.pptx.pdf| Tools for sequence annotation]]<br>
Exercise: [[Annotation of Bacterial Sequences]]

----

== Tuesday, June 6==
----

''B- and T-cell receptors genetics and structure''

BACKGROUND TEXTS: antibody repertoire,<br>
[http://www.nature.com.proxy.findit.dtu.dk/nprot/journal/v9/n12/full/nprot.2014.189.html antibody modeling], <br>
[http://nar.oxfordjournals.org/content/early/2015/05/24/nar.gkv535.full TCR modeling]

9.00 - 10.00: [[Media:Maturation.pdf|TCR and BCR maturation.]]

10.30 - 12.00: [http://www.cbs.dtu.dk/courses/27685.imm/VDJ_Exercise/VDJ_2014.php Analysis of immunoglobulin gene rearrangements]<br>

Paolo Marcatili, CBS, DTU Systems Biology.

12.00 - 13.00: ''Lunch Break''

13.00 - 14.00: [[File:Antibody structure.pdf|TCR and BCR structure]] <br>
Paolo Marcatili

14.00 - 16.00: [[http://www.cbs.dtu.dk/courses/27485.imm/antibody_modeling.php Exercise on antibody structure prediction and analysis]]<br>
Paolo Marcatili, CBS, DTU Systems Biology.

----

== Wednesday, June 7==
----

''B cell epitope predictions''
# '''BACKGROUND TEXTS''': Chapter 3 + [https://academic.oup.com/nar/article/3787843 BepiPred 2.0] + [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531324/ B-cell epitope prediction]

# '''SUPPLEMENTARY''': [http://www.youtube.com/watch?v=Z36dUduOk1Y Simplified B-cell walkthrough] (Nice and easy understandable explanation of B-cells, also overview of other aspects of the immune system is available at this channel).

[https://cloud.swivl.com/v/8a300a8bb613ac2cc530bc011f8c8407 Video:Linear B cell epitope prediction] [[Media:Linear epitope prediction.pdf|slides]]<br>
[https://cloud.swivl.com/v/31b739f6386ff224b6a0d3a9df341215 Video:Conformational B cell epitope prediction] [[Media:Conformational epitope prediction.pdf|slides]]

10.00 - 12.00: Exercise: [http://www.cbs.dtu.dk/courses/27485.imm/epitope_2014.php B cell epitope predictions]. <br>
Exercise: [http://www.cbs.dtu.dk/courses/27485.imm/exercise_Bcell/index_2010.php optional].

12.00 - 13.00: ''Lunch Break''

13.00 - 13.15: Exercise round up

13:15- 13:30: Quiz

13.45 - 14.30: [http://www.cbs.dtu.dk/~pmar/humanization.pdf Antibody Humanization] <br>

14.30-16.00: [http://www.cbs.dtu.dk/courses/27685.imm/humanization_exercise.php Exercise on Antibody Humanization]

== Thursday June 8==
----

''T-cell Epitopes''
# '''BACKGROUND TEXTS''':



Optional readings: [http://www.cbs.dtu.dk/courses/27685.imm/reading/Ch4.pdf Immunological Bioinformatics], Chapter 4. [http://bioinformatics.oxfordjournals.org/cgi/reprint/23/24/3265 Modeling the adaptive immune system: predictions and simulations] [http://www.nature.com/nbt/journal/v24/n7/pdf/nbt1215.pdf A consensus epitope prediction approach identifies the breadth of murine TCD8+-cell responses to vaccinia virus],[http://www3.interscience.wiley.com/cgi-bin/fulltext/123476680/PDFSTART Major histocompatibility complex class I binding predictions as a tool in epitope discovery], [http://www3.interscience.wiley.com/cgi-bin/fulltext/123349058/PDFSTART MHC Class II epitope predictive algorithms].

9.00 - 9.30: Last Exercise round up

9.30 - 12.00: Prediction of MHC peptide binding using data mining techniques (PSSM's and ANN)

Rational epitope discovery using immunoinformatics

A little on MHC class II binding

''Coffee Break at some point around 10.30''

[http://www.cbs.dtu.dk/courses/27685.imm/presentations/MHCbinding_2017.pdf Slides [PDF]].
[http://www.cbs.dtu.dk/courses/27685.imm/presentations/Ex_Logo.pdf Logo handout].
[http://www.cbs.dtu.dk/courses/27685.imm/presentations/Ex_Logo_ans.pdf Answer Logo handout].
[http://www.cbs.dtu.dk/courses/27685.imm/presentations/NN_handout.pdf NN handout].<br>

Morten Nielsen, Department of Bio and Health Informatics .

12.00 - 13.00: ''Lunch Break''

13.00 - 16.00: [http://www.cbs.dtu.dk/courses/ILRI_workshop/presentations/Performance_measure.pdf Performance measures] <br>
Exercise - [http://www.cbs.dtu.dk/courses/27685.imm/exercise_MHC_bind/exercise_2017.php Prediction of MHC:peptide binding using PSSM and ANN].<br>
[http://www.cbs.dtu.dk/courses/27685.imm/exercise_MHC_bind/exercise_2012_ans.php Answers: Prediction of MHC:peptide binding using PSSM and ANN]. <br>
Morten Nielsen, Department of Bio and Health Informatics.

----

== Friday, June 9==
----

''Antigen processing and presentation, Supertypes, HLA clustering, and vaccine design''
# '''BACKGROUND TEXTS''': Capters 13-14.
Additional readings: [http://www.jimmunol.org/content/178/12/7890.long A Quantitative Analysis of the Variables Affecting the Repertoire of T Cell Specificities Recognized after Vaccinia Virus Infection] ; [http://www.jem.org/cgi/reprint/201/1/95 Identification of poxvirus CD8 T cell determinants to enable rational design and characterization of smallpox vaccines]

9.00 - 9.30: Exercise round up

9.30 - 10.00:[http://www.cbs.dtu.dk/courses/27685.imm/presentations/Supertypes_2017.pdf Supertypes and functional clustering of MHC molecules] <br>

Morten, CBS, Department of Bio and Health Informatics.

10.00 - 10.45: [http://www.cbs.dtu.dk/courses/27685.imm/presentations/Processing_Tcell_2017.pdf What defines a T cel epitope? Is there any thing beyond MHC binding?]

10.45 - 11.00: ''Coffee Break''

11.00 - 11.45: [http://www.cbs.dtu.dk/courses/27685.imm/presentations/Vaccine_design_2015.pdf Selecting the one in a million. Strategies for selecting peptide subsets, and vaccine design] <br>
Morten Nielsen, Department of Bio and Health Informatics.



12.00 - 13.00: ''Lunch Break''

13.00 - 16.00: Exercises: [http://www.cbs.dtu.dk/courses/27685.imm/exercise_HCVVaccine/exercise_HCVVaccine.php Development of vaccines against HCV.] <br>
[http://www.cbs.dtu.dk/courses/27685.imm/exercise_HCVVaccine/answers.pdf Answers]<br>
Morten Nielsen, Department of Bio and Health Informatics.

----

== Monday, June 12==
----

9.00 - 9.20: Question and round up from last week <br>
[http://www.cbs.dtu.dk/courses/27685.imm/presentations/Questions_for_Immunological_bioinformatics_MHC_TCR.pdf Quiz ] <br>

9.20 - 10.05: Use of Mass-spec data for epitope identification <br>
[http://www.cbs.dtu.dk/courses/27685.imm/presentations/GibbsCluster_2017.pdf Mass-spec elution data and Gibbs Clustering] <br>
Morten Nielsen, Department of Bio and Health Informatics.

10.05 - 10.20: ''Coffee Break''

10.20 - 12.00: Gibbs sampling approach for peptide clustering <br>
[http://www.cbs.dtu.dk/courses/27485.imm/exercise_Gibbs/exercise_gibbs.php The use of GibbsClustering for the analysis of ligand MS data]<br>

12.00 - 13.00: ''Lunch Break''

13.00 - 16.00: [[Media:Deimmunisation.pptx.pdf | Humanization and deimmunazation for cancer T cell therapy molecules]]

[[Exercise on CAR T-cell humanisation and de-immunisation]]

----

== Tuesday, June 13==

''Cancer immunology''

9.00 - 12.00 Seminars:<br>

9.00 - 9.50: [https://cn.inside.dtu.dk/cnnet/filesharing/download/590cbedc-f2ca-4ebd-8758-0d06f7eb1d49 Cancer Genomics]

Aron Charles Eklund, DTU Systems Biology<br>

10.00 - 10.50: High-throughput identification of T cell epitopes<br>
[http://wiki.bio.dtu.dk/teaching/index.php/File:Lecture_Monday_130616_SRH.pptx Lecture by Sine Reker Hadrup]<br>
Sine Reker Hadrup, DTU Vet<br>

11.00 - 11.50: [http://wiki.bio.dtu.dk/teaching/images/1/13/Donia_immunotherapy-compressed.pdf Cancer Immunotherapy]<br>
Marco Donia, KU and Herlev Hospital<br>

12.00 - 13.00: ''Lunch Break''

[http://wiki.bio.dtu.dk/teaching/images/5/5f/Project_work.pdf Introduction to project work]
[http://wiki.bio.dtu.dk/teaching/images/4/41/ImmuBio_Poster.pdf Poster Example]
Paolo Marcatili, DTU Systems Biology
----

== Wednesday, June 14 - June 20==
----
9.00 - 17.00: Project work

Power point presentations are fine as well, but keep it short and to the point

----

==Wednesday and Thursday, June 21-22==
----

9.00 - 17.00: exams

----
For more information, please contact [http://www.cbs.dtu.dk/staff/show-staff.php?id=1082 Paolo Marcatili]

Go to
# [http://www.cbs.dtu.dk/courses/27685.imm/index.php Main Course Page]
# [http://www.cbs.dtu.dk/courses/27685.imm/faq.php Frequently Asked Questions]

36685 Immunological Bioinformatics Course Program January 2018

2024-03-20T14:15:17Z

WikiSysop: Created page with " =Information for Course Attendees= The official course site can be [http://teaching.healthtech.dtu.dk/36685/index.php/36685_-_Immunological_Bioinformatics found here] '''General Daily Schedule''' * 09.00 - 12.00 Lectures * 12.00 - 13.00 Lunch * 13.00 - 17.00 Exercises Classes will be a mixture of lectures and group work. Most of the group work will consist of computer exercises (students are required to bring their own laptop). All literature will be available throu..."

=Information for Course Attendees=

The official course site can be [http://teaching.healthtech.dtu.dk/36685/index.php/36685_-_Immunological_Bioinformatics found here]

'''General Daily Schedule'''

* 09.00 - 12.00 Lectures
* 12.00 - 13.00 Lunch
* 13.00 - 17.00 Exercises

Classes will be a mixture of lectures and group work. Most of the group work will consist of computer exercises (students are required to bring their own laptop). All literature will be available through DTU inside or this site.

'''Location'''

DTU Lyngby Campus, Building 208, room 062 (Down the stairs in the basement). Should you be new to DTU, a map can be [http://www.dtu.dk/english/about/campuses/dtu-lyngby-campus found here].

'''Other'''

Please note, the course schedule may change slightly along the way. The required readings for a class can be trusted one week in advance. The exact content of powerpoint slides and handouts may change up to the last minute!

Classes will be a mixture of lectures and group work. Most of the group work will consist of computer exercises. Students are required to bring their own laptop.

=Course Program=




----
== Tuesday, January 2nd - Introduction, Immunology Brush-up and Databases ==
----

'''Reading list'''

* [http://www.bioinformatics.dtu.dk/english/Research_new/Health-informatics/Immunoinformatics-and-machine-learning Introduction to the Immunoinformatics and Machine Learning Group]
* [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245432/ Introduction to Immunology]

'''Schedule'''

09.00 - 09.30 [[Media:Week_01_day_01_Introduction.pdf|Introduction to the course]], Leon Eyrich Jessen

09:30 - 10:15 Lecture: [[Media:Week_01_day_01_session_02_Buus_01.pdf|Basic Mechanisms of Immune Defense]], [http://isim.ku.dk/staff/vip/?pure=en%2Fpersons%2Fsoeren-buus(994343ae-c005-48f6-afca-d9e657570abc)%2Fkeywords.html Professor Søren Buus], University of Copenhagen

10.15 - 10.30 ''Coffee Break''

10.30 - 11.15 Lecture: [[Media:Week_01_day_01_session_02_Buus_02.pdf|Antigen Capture and Presentation to T-lymphocytes]], [http://isim.ku.dk/staff/vip/?pure=en%2Fpersons%2Fsoeren-buus(994343ae-c005-48f6-afca-d9e657570abc)%2Fkeywords.html Professor Søren Buus], University of Copenhagen

11.15 - 12.00 Lecture: The Impact of Immunological Bioinformatics on Immunological Research (Slides [[Media:Week_01_day_01_session_02_Buus_03a.pdf|1]], [[Media:Week_01_day_01_session_02_Buus_03b.pdf|2]]), [http://isim.ku.dk/staff/vip/?pure=en%2Fpersons%2Fsoeren-buus(994343ae-c005-48f6-afca-d9e657570abc)%2Fkeywords.html Professor Søren Buus], University of Copenhagen

12.00 - 13.00 ''Lunch break''

13.00 - 13.50 Group Formation and short quiz on immunology

14:00 - 16.00 Exercise: [[Databases and web resources in Immunological Bioinformatics]]




----

== Wednesday, January 3rd - Bacterial Pathogenicity, Virulence and Phylogeny ==
----

'''Reading list'''

* [https://cn.inside.dtu.dk/cnnet/filesharing/download/2766d4f0-5421-4221-9d2c-d456ca611de1 CGE tool box], read the sections on pathogenFinder, resFinder and virulenceFinder

'''Schedule'''

09:00 - 09:15 Recap: Yesterdays exercises, Leon Eyrich Jessen

09:15 - 09:45 Lecture: [[Media:week_01_day_02_session_01_Ahrenfeldt_01.pdf|PathogenFinder]], Johanne Ahrenfeldt

09:45 - 10:00 ''Coffee Break''

10:00 - 11:00 Exercise: [http://wiki.bio.dtu.dk/teaching/index.php/PathogenFinder PathogenFinder], Johanne Ahrenfeldt

11:15 - 12:00 Lecture: [[Media:week_01_day_02_session_01_Ahrenfeldt_02.pdf|VirulenceFinder]], Johanne Ahrenfeldt

12:00 - 13:00 ''Lunch break''

13:00 - 14:00 Lecture: Antibiotic Resistance and ResFinder(slides [[Media:week_01_day_02_session_02_Ahrenfeldt_03a.pdf|1]], [[Media:week_01_day_02_session_02_Ahrenfeldt_03b.pdf|2]]), Johanne Ahrenfeldt

14:00 - 15:00 Exercise: [http://wiki.bio.dtu.dk/teaching/index.php/27683_Ex4 VirulenceFinder] and [http://wiki.bio.dtu.dk/teaching/index.php/27683_Ex5 ResFinder], Johanne Ahrenfeldt

15:00 - 16:00 Lecture: Bacterial Phylogeny (slides [[Media:WGS_phylogeny_Johanne_01.pdf|1]], [[Media:WGS_phylogeny_Johanne_02.pdf|2]]), Johanne Ahrenfeldt




----

== Thursday, January 4th - B- and T-cell Receptors Genetics and Structure ==
----

'''Reading list'''

* [http://www.nature.com.proxy.findit.dtu.dk/nprot/journal/v9/n12/full/nprot.2014.189.html Antibody Modeling]
* [http://nar.oxfordjournals.org/content/early/2015/05/24/nar.gkv535.full TCR Modeling]

'''Schedule'''

09:00 - 09:15 Recap: Yesterdays exercises, Leon Eyrich Jessen

09:15 - 10:00 Lecture: [[Media:Maturation.pdf|TCR and BCR maturation]], Leon Eyrich Jessen

10:00 - 10:15 ''Coffee Break''

10:15 - 12:00 Exercise: [http://www.cbs.dtu.dk/courses/27685.imm/VDJ_Exercise/VDJ_2014.php Analysis of immunoglobulin gene rearrangements], Leon Eyrich Jessen

12:00 - 13:00 ''Lunch Break''

13:00 - 14:00 Lecture: [[Media:Antibody structure.pdf|TCR and BCR structure]], Kamilla Kjærgaard Jensen

14:00 - 16:00 Exercise: [http://www.cbs.dtu.dk/courses/27485.imm/antibody_modeling.php Antibody Structure Prediction and Analysis], Kamilla Kjærgaard Jensen




----

== Friday, January 5th - B Cell Epitope Predictions ==
----

'''Reading list'''

* Paper: [https://academic.oup.com/nar/article/3787843 BepiPred 2.0]
* Paper: [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531324/ B-cell epitope prediction]
* Video: [http://www.youtube.com/watch?v=Z36dUduOk1Y Simplified B-cell walkthrough] (Nice and easy understandable explanation of B-cells)
* Resource: [https://pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/ PDB 101: Introduction to PDB Data]
* Optional: [https://academic.oup.com/nar/article/41/W1/W286/1111259 SigniSite paper] and [https://academic.oup.com/nar/article/41/W1/W286/1111259#supplementary-data supplementary data]

'''Schedule'''

09:00 - 09:15 Recap: Yesterdays exercises, Kamilla Kjærgaard Jensen

09:15 - 10:00 Lecture: [[Media:Homology-modeling-intro.pdf|Homology Modeling to Predict Antigen Structure]], Kamilla Kjærgaard Jensen

10:00 - 10:15 ''Coffee Break''

10:15 - 12:00 Exercise: [[Media:Homology-modeling-exercise.pdf|Homology Modeling to Predict Antigen Structure]], Kamilla Kjærgaard Jensen

12:00 - 13:00 ''Lunch Break''

13:00 - 13:30 Lecture: [[Media:Linear epitope prediction.pdf|Linear B cell epitope prediction]], Martin Closter Jespersen

13:30 - 14:00 Lecture: [[Media:Conformational epitope prediction.pdf|Conformational B cell epitope prediction]], Martin Closter Jespersen

14:00 - 15:00 Exercise: [http://www.cbs.dtu.dk/courses/27485.imm/epitope_2014.php B cell epitope predictions], Martin Closter Jespersen

15:00 - 15:30 Lecture: SigniSite for Protein Level Geno-/Phenotype Correlation (slides [[Media:Week_01_day_04_session_02_Jessen_01.pdf|1]], [[Media:Week_01_day_04_session_02_Jessen_02.pdf|2]]), Leon Eyrich Jessen

15:30 - 16:00 Exercise: [[signisite_exercise|Using SigniSite to identify resistance mutations]], Leon Eyrich Jessen




----

== Monday January 8th - T-cell Epitopes ==
----

'''Reading list'''

* [[Media:Lund_et_al_immunological_bioinformatics_2005_chapter_3.pdf| Immunological Bioinformatics Chapter 3]]
* [[Media:Lund_et_al_immunological_bioinformatics_2005_chapter_4.pdf| Immunological Bioinformatics Chapter 4]]
* Paper: [http://bioinformatics.oxfordjournals.org/cgi/reprint/23/24/3265 Modeling the adaptive immune system: predictions and simulations]

* Paper: [http://www3.interscience.wiley.com/cgi-bin/fulltext/123476680/PDFSTART Major histocompatibility complex class I binding predictions as a tool in epitope discovery]
* Paper: [http://www3.interscience.wiley.com/cgi-bin/fulltext/123349058/PDFSTART MHC Class II epitope predictive algorithms].

'''Schedule'''

09:00 - 09:30 Recap: Yesterdays exercises, Leon Eyrich Jessen

09:30 - 10:15 Prediction of MHC peptide binding using data mining techniques (PSSM's and ANN), Morten Nielsen

10:15 - 10:30 ''Coffee Break''

10:30 - 11:15 Rational epitope discovery using immunoinformatics, Morten Nielsen

11:15 - 12:00 A little on MHC class II binding, Morten Nielsen

Session materials: [http://www.cbs.dtu.dk/courses/27685.imm/presentations/MHCbinding_2018.pdf Slides [PDF]], [http://www.cbs.dtu.dk/courses/27685.imm/presentations/Ex_Logo.pdf Logo handout],

[http://www.cbs.dtu.dk/courses/27685.imm/presentations/NN_handout.pdf NN handout].

12:00 - 13:00: ''Lunch Break''

13:00 - 16:00: [http://www.cbs.dtu.dk/courses/ILRI_workshop/presentations/Performance_measure.pdf Performance measures]
Exercise - [http://www.cbs.dtu.dk/courses/27685.imm/exercise_MHC_bind/exercise_2018.php Prediction of MHC:peptide binding using PSSM and ANN]

Morten Nielsen, Department of Bio and Health Informatics.




----

== Tuesday, January 9th - Antigen Processing and Presentation, Supertypes, HLA Clustering, and Vaccine Design ==
----

'''Reading list'''

* [[Media:Lund_et_al_immunological_bioinformatics_2005_chapter_13.pdf|Chapter 13]]
* [[Media:Lund_et_al_immunological_bioinformatics_2005_chapter_14.pdf|Chapter 14]]
* [https://www.ncbi.nlm.nih.gov/pubmed/23097419 Simultaneous alignment and clustering of peptide data using a Gibbs sampling approach]
* Optional: [http://www.jimmunol.org/content/178/12/7890.long A Quantitative Analysis of the Variables Affecting the Repertoire of T Cell Specificities Recognized after Vaccinia Virus Infection]

* Optional: [https://www.ncbi.nlm.nih.gov/pubmed/24760079 Identification and HLA-tetramer-validation of human CD4+ and CD8+ T cell responses against HCMV proteins IE1 and IE2]

'''Schedule'''

09:00 - 09:30 Exercise round up, Morten Nielsen

09:30 - 10:00 [http://www.cbs.dtu.dk/courses/27685.imm/presentations/GibbsCluster_2016.pdf Identifying multiple sequence motifs in large scale peptide data sets]

10:00 - 10:30 [http://www.cbs.dtu.dk/courses/27685.imm/presentations/Supertypes_2017.pdf Supertypes and functional clustering of MHC molecules], Morten Nielsen

10:30 - 10:45 ''Coffee Break''

10:45 - 11:30 [http://www.cbs.dtu.dk/courses/27685.imm/presentations/Processing_Tcell_2017.pdf What defines a T cel epitope? Is there any thing beyond MHC binding?], Morten Nielsen

11:30 - 12:00 [http://www.cbs.dtu.dk/courses/27685.imm/presentations/Vaccine_design_2015.pdf Selecting the one in a million. Strategies for selecting peptide subsets, and vaccine design], Morten Nielsen

12:00 - 13:00 ''Lunch Break''

13:00 - 16:00 Exercises: [http://www.cbs.dtu.dk/courses/27685.imm/exercise_HCVVaccine/exercise_HCVVaccine_2018.php Development of vaccines against HCV],

Morten Nielsen




----

== Wednesday, January 10th - Chimeric Antigen Receptor (CAR) Immunotherapy ==
----

'''Reading list'''

* Paper: [https://link.springer.com/article/10.1007%2Fs13238-017-0411-9 Increasing the safety and efficacy of chimeric antigen receptor T cell therapy]
* Article: [https://www.the-scientist.com/?articles.view/articleNo/42462/title/The-CAR-T-Cell-Race The CAR T-Cell Race]

'''Scedule'''

09:00 - 09:15 Recap: Yesterdays exercises, Morten Nielsen

09:15 - 10:00 Lecture: [http://www.cbs.dtu.dk/~pmar/humanization.pdf Antibody Humanization], Paolo Marcatili

10:00 - 10:30 ''Coffee Break''

10:30 - 12:00 Exercise: [http://www.cbs.dtu.dk/courses/27685.imm/humanization_exercise.php Antibody Humanization], Paolo Marcatili

12:00 - 13:00 ''Lunch Break''

13:00 - 14:00 Lecture: [[Media:Deimmunisation.pptx.pdf | Humanization and deimmunazation for cancer T cell therapy molecules]], Paolo Marcatili

14:00 - 16:00 Exercise: [[Exercise on CAR T-cell humanisation and de-immunisation|CAR T-cell humanisation and de-immunisation]], Paolo Marcatili




----

== Thursday, January 11th - Seminar on Cancer Immunotherapy by Invited Speakers ==
----

'''Scedule'''

09:00 - 09:45 Clinical Associate Professor, MD, PhD, [http://forskning.ku.dk/find-en-forsker/?pure=da%2Fpersons%2Fmarco-donia(592383df-9101-495c-8282-62ddcf6b1d9f).html Marco Donia], UCPH/Herlev-Gentofte Hospital: [https://cn.inside.dtu.dk/cnnet/filesharing/download/b2e6cf69-5986-447a-aaeb-69ed0f219b35 Cancer Immunotherapy]

10:00 - 10:45 Professor [http://www.dtu.dk/service/telefonbog/person?id=99903&tab=2&qt=dtupublicationquery Sine Reker Hadrup], DTU Vet: [https://cn.inside.dtu.dk/cnnet/filesharing/download/43beae48-78bc-4677-aa09-026e20ef04ad Interrogating the antigen specific T cell recognition of cancer]

11:00 - 11:45 Associate Professor [http://www.dtu.dk/service/telefonbog/person?id=26586&tab=2&qt=dtupublicationquery Lars Rønn Olsen], DTU Bioinformatics: [[Media:LRO_imm_binf.pdf|Prediction of Immunotherapy Treatment Outcome]]

12:00 - 13:00 ''Lunch Break''

13:00 - 14:00 [[Media:intro_to_projects_2018.pdf|Introduction to project work and exam]], Leon Eyrich Jessen




----

== Friday, January 12th - Thursday January 18th - Project Work ==
----
09.00 - 17.00: Group project work

'''Groups and projects 2018'''

* G01 - Line, Solveig and Monica: ''"Peptide Vaccine Design against Epstein-Barr Virus for Prevention of Nasopharyngeal Cancer"''
* G02 - Mikael, Jacob and Kathrine: ''"Winter is coming - a bioinformatic approach to prepare for the next influenza virus"''
* G03 - Sandra, Esteban, Narasimha and Taner: ''"Zika virus vaccine for Brazilian Population"''
* G04 - Signe, Julie, Ina and Aimilia: ''"Identifying target epitopes for designing a vaccine against Acinetobacter baumannii"''
* G05 - Christian, Mikkel and Frank: ''"HIV vaccine development for sub-saharian Africans"''
* G06 - Keith, Nadia and Jeppe: ''"EViVa – Vaccine for EBV"''
* G07 - Sofie, Natasja and Ulla: ''"Zika-virus Vaccine Development"''




----

== Friday, January 19th - Exams ==
----
08:00 - 16:00 Exam day, Morten Nielsen and Leon Eyrich Jessen

'''Exam schedule'''

''Group 01''

* 07:55 - 08:00 G01 - Setup
* 08:00 - 08:15 G01 - Presentation
* 08:15 - 08:25 Line
* 08:25 - 08:35 Solveig
* 08:35 - 08:45 Monica
* 08:45 - 08:50 Grading

''Group 05''

* 08:55 - 09:00 G05 - Setup
* 09:00 - 09:15 G05 - Presentation
* 09:15 - 09:25 Christian
* 09:25 - 09:35 Mikkel
* 09:35 - 09:45 Frank
* 09:45 - 09:50 Grading

''Group 04''

* 09:55 - 10:00 G04 - Setup
* 10:00 - 10:15 G04 - Presentation
* 10:15 - 10:25 Signe
* 10:25 - 10:35 Julie
* 10:35 - 10:45 Ina
* 10:45 - 10:55 Aimilia
* 10:55 - 11:00 Grading

''Group 03''

* 11:05 - 11:10 G03 - Setup
* 11:10 - 11:25 G03 - Presentation
* 11:25 - 11:35 Sandra
* 11:35 - 11:45 Esteban
* 11:45 - 11:55 Narasimha
* 11:55 - 12:05 Taner
* 12:05 - 12:10 Grading

'''12:10 - 12:55 Lunch'''

''Group 02''

* 12:55 - 13:00 G02 - Setup
* 13:00 - 13:15 G02 - Presentation
* 13:15 - 13:25 Mikael
* 13:25 - 13:35 Jacob
* 13:35 - 13:45 Kathrine
* 13:45 - 13:50 Grading

''Group 06''

* 13:55 - 14:00 G06 - Setup
* 14:00 - 14:15 G06 - Presentation
* 14:15 - 14:25 Keith
* 14:25 - 14:35 Nadia
* 14:35 - 14:45 Jeppe
* 14:45 - 14:50 Grading

''Group 07''

* 14:55 - 15:00 G07 - Setup
* 15:00 - 15:15 G07 - Presentation
* 15:15 - 15:25 Sofie
* 15:25 - 15:35 Natasja
* 15:35 - 15:45 Ulla
* 15:45 - 15:50 Grading

36685 Immunological Bioinformatics Course Program January 2019

2024-03-20T14:14:52Z

WikiSysop: Created page with "=Information for Course Attendees= Main page for course site can be found [http://teaching.healthtech.dtu.dk/36685/index.php/36685_-_Immunological_Bioinformatics here]. Please note, that the program can be subject to changes or updates. Make sure to reload the page, to get the newest version of the program. '''Course responsible and main lecturers''' * [https://www.dtu.dk/english/service/phonebook/person?id=22554&tab=2&qt=dtupublicationquery Postdoc Leon Eyrich Jessen]..."

=Information for Course Attendees=

Main page for course site can be found [http://teaching.healthtech.dtu.dk/36685/index.php/36685_-_Immunological_Bioinformatics here]. Please note, that the program can be subject to changes or updates. Make sure to reload the page, to get the newest version of the program.

'''Course responsible and main lecturers'''
* [https://www.dtu.dk/english/service/phonebook/person?id=22554&tab=2&qt=dtupublicationquery Postdoc Leon Eyrich Jessen], DTU Health Technology [LEJ]
* [https://www.dtu.dk/english/service/phonebook/person?id=34983&tab=2&qt=dtupublicationquery Associate Professor Paolo Marcatili], DTU Health Technology [PM]
* [https://www.dtu.dk/english/service/phonebook/person?id=5973&tab=2&qt=dtupublicationquery Professor Morten Nielsen], DTU Health Technology [MN]

'''Other lecturers'''
* [https://www.dtu.dk/english/service/phonebook/person?id=104623&cpid=240031&tab=3&qt=dtuprojectquery PhD student Birkir Reynisson], DTU Health Technology [BR]
* [https://isim.ku.dk/staff/vip/?pure=en%2Fpersons%2Fsoeren-buus(994343ae-c005-48f6-afca-d9e657570abc)%2Fpublications.html Professor Søren Buus], Department of Immunology and Microbiology, University of Copenhagen [SB]
* [https://research.regionh.dk/en/persons/troels-holz-borch(93e45377-0157-43eb-a421-6ac4d5b9b0f0).html Postdoc, MD, PhD, Troels Holz Borch], Center for Cancer Immune Therapy (CCIT), University of Copenhagen/Herlev-Gentofte Hospital
* [https://www.dtu.dk/english/service/phonebook/person?id=99903&tab=2&qt=dtupublicationquery Professor Sine Reker Hadrup], DTU Health Technology
* [https://www.dtu.dk/english/service/phonebook/person?id=26586&tab=2&qt=dtupublicationquery Associate Professor Lars Rønn Olsen], DTU Health Technology

'''General Daily Schedule'''

* 09.00 - 12.00 Lectures
* 12.00 - 13.00 Lunch
* 13.00 - 17.00 Exercises

Classes will be a mixture of lectures and group work. Most of the group work will consist of computer exercises (students are required to bring their own laptop). All literature will be available through DTU inside or this site.

'''Location'''

Teaching and exam will be at DTU Lyngby Campus in Building 208, room 062 (Down the stairs in the basement). Should you be new to DTU, a map of DTU Lyngby Campus can be found [http://www.dtu.dk/english/about/campuses/dtu-lyngby-campus here].

=Course Schedule Overview=

{| class="wikitable" style="font-size:80%;"
|+ Teaching Day 1-8
!
! Monday Jan. 7th
! Tuesday Jan. 8th
! Wednesday Jan. 9th
! Thursday Jan. 10th
! Friday Jan. 11th
! Monday Jan. 14th
! Tuesday Jan. 15th
! Wednesday Jan. 16th
|-
!
! Introduction, Basic Immunology and IEDB
! Genetics and Repertoires of B- and T-Cell Receptors
! Structure of B- and T- Cell Receptors and B-Cell Epitopes
! T-Cell Epitopes
! Antigen Processing and Presentation, HLA Clustering, and Vaccine Design
! Humanization, B- and T-Cell Interaction Models and Repertoires
! De-Immunization, Chimeric Antigen Receptor (CAR) Immunotherapy
! Seminar on Cancer Immunotherapy by Invited Speakers
|-
! 09.00 - 09.30
| Course Introduction [LEJ]
| Exercise recap [BR]
| Exercise recap [LEJ]
| Exercise recap [PM]
| Exercise recap [MN]
| Exercise recap [MN]
| [[Media:2019_day_06_R_exercise.txt | Exercise recap]] [LEJ]
|
|-
! 09.30 - 10.15
| Lecture: Basic Mechanisms of Immune Defence [SB]
| Introduction [LEJ]
| Lecture: [[Media:Antibody structure.pdf|TCR and BCR structure]] [PM]
| Lecture: Prediction of MHC peptide binding using PSSMs and ANNs [MN]. Session materials: [http://www.cbs.dtu.dk/courses/27685.imm/presentations/MHCbinding_2019.pdf Slides [PDF]], [http://www.cbs.dtu.dk/courses/27685.imm/presentations/Ex_Logo.pdf Logo handout], [http://www.cbs.dtu.dk/courses/27685.imm/presentations/Ex_Logo_ans.pdf Answer Logo handout]. [http://www.cbs.dtu.dk/courses/27685.imm/presentations/NN_handout.pdf NN handout].
| Lecture: [http://www.cbs.dtu.dk/courses/27685.imm/presentations/GibbsCluster_2019.pdf Identifying multiple sequence motifs in large scale peptide data sets] [MN]
| Lecture: [[http://www.cbs.dtu.dk/~pmar/humanization.pdf Antibody Humanization]] [PM]
| Lecture: Protein drug de-immunization [BR]
| [https://www.herlevhospital.dk/ccit-denmark/staff/Sider/Scientific-staff.aspx Clinical Research: Troels Holz Borch (MD, PhD, National Center for Cancer Immune Therapy, Herlev Hospital)]
|-
! 10.15 - 10.30
| Coffee Break
| Coffee Break
| Coffee Break
| Coffee Break
| Coffee Break
| Coffee Break
| Coffee Break
| Coffee Break
|-
! 10.30 - 11.15
| Lecture: Antigen Capture and Presentation to T-lymphocytes [SB]
| Group work [LEJ]
| Exercise: [[Antibody Structure Prediction and Analysis]] [PM]
| Lecture: Rational epitope discovery using immunoinformatics [MN]
| Lecture: [http://www.cbs.dtu.dk/courses/27685.imm/presentations/Supertypes_2017.pdf Supertypes and functional clustering of MHC molecules] [MN]
| Exercise: [[Antibody Humanization]] [PM]
| [[Exercise: Protein drug de-immunization]] [BR]
| [https://www.dtu.dk/english/service/phonebook/person?id=99903&cpid=257261&tab=2&qt=dtupublicationquery Wet lab molecular Research: Sine Reker Hadrup (Professor, PhD, DTU Health Technology)]
|-
! 11.15 - 12.00
| Lecture: The Impact of Immunological Bioinformatics on Immunological Research [SB]
| Group work [LEJ]
| Lecture: [[Media:Linear epitope prediction.pdf|Linear ]] and [[Media:Conformational epitope prediction.pdf|Conformational ]] B-cell epitope prediction [PM]
| Lecture: MHC class II binding and [http://www.cbs.dtu.dk/courses/ILRI_workshop/presentations/Performance_measure.pdf Performance measures] [MN]
| Lecture: [http://www.cbs.dtu.dk/courses/27685.imm/presentations/Processing_Tcell_2018.pdf What defines a T cel epitope? Is there any thing beyond MHC binding?], and [http://www.cbs.dtu.dk/courses/27685.imm/presentations/Vaccine_design_2019.pdf Selecting the one in a million. Strategies for selecting peptide subsets, and vaccine design] [MN]
| Lecture: Modelling TCR interactions (netTCR) [LEJ]
| Lecture: [[http://teaching.healthtech.dtu.dk/36685/images/8/87/Deimmunisation.pptx.pdf Humanization and deimmunization for cancer T cell therapy molecules]] [PM]
| [https://www.dtu.dk/english/service/phonebook/person?id=26586&tab=2&qt=dtupublicationquery Dry lab bioinformatics Research: Lars Rønn Olsen (Associate Professor, PhD, DTU Health Technology)]
|-
! 12.00 - 13.00
| Lunch Break
| Lunch Break
| Lunch Break
| Lunch Break
| Lunch Break
| Lunch Break
| Lunch Break
| Lunch Break
|-
! 13.00 - 17.00
| [[Exercise: Immune Epitope Database]] [BR]
| Group work and presentations [LEJ]
| Exercise: [http://www.cbs.dtu.dk/courses/27485.imm/epitope_2014.php B cell epitope predictions] [PM]
| Exercise:[http://www.cbs.dtu.dk/courses/27685.imm/exercise_MHC_bind/exercise_2019.php Prediction of MHC:peptide binding using PSSM and ANN]
[http://www.cbs.dtu.dk/courses/27685.imm/exercise_MHC_bind/exercise_2017_ans.php Answers: Prediction of MHC:peptide binding using PSSM and ANN]
| Exercise: [http://www.cbs.dtu.dk/courses/27685.imm/exercise_HCVVaccine/exercise_HCVVaccine_2019.php Development of vaccines against HCV] [MN] [http://www.cbs.dtu.dk/courses/27485.imm/exercise_HCVVaccine/answers.pdf Answers]
| [[Exercise: Working with peptide data]] [LEJ]
| Exercise: [[http://teaching.healthtech.dtu.dk/36685/index.php/Exercise_on_CAR_T-cell_humanisation_and_de-immunisation CAR T-cell humanisation and de-immunisation]] [PM]
| [[Media:20190116_projects_intro.pdf|Introduction to project work and exam]] [LEJ]
|-
! Background materials
|
* [https://www.bioinformatics.dtu.dk/research2018/research-groups/immunoinformatics-and-machine-learning1 Immunoinformatics and Machine Learning Introduction]
* [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245432/ An introduction to immunology and immunopathology]
* [https://www.ncbi.nlm.nih.gov/pubmed/25300482 The immune epitope database (IEDB) 3.0.]
| None
|
* Miniquiz: [[Media:Immunological bioinformatics Quiz 1 2019.pdf]]
* Pymol license file: [[Media:Pymol-edu-license.txt]]

Optional Support materials:
* Paper: [https://academic.oup.com/nar/article/3787843 BepiPred 2.0]
* Paper: [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531324/ B-cell epitope prediction]
* Video: [http://www.youtube.com/watch?v=Z36dUduOk1Y Simplified B-cell walkthrough] (Nice and easy understandable explanation of B-cells)
* Resource: [https://pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/ PDB 101: Introduction to PDB Data]
|
* [[Media:Lund_et_al_immunological_bioinformatics_2005_chapter_3.pdf| Immunological Bioinformatics Chapter 3]]
* [[Media:Lund_et_al_immunological_bioinformatics_2005_chapter_4.pdf| Immunological Bioinformatics Chapter 4]]
* Paper: [http://bioinformatics.oxfordjournals.org/cgi/reprint/23/24/3265 Modeling the adaptive immune system: predictions and simulations]
* Paper: [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2913210 Major histocompatibility complex class I binding predictions as a tool in epitope discovery]
* Paper: [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2913211 MHC Class II epitope predictive algorithms]
|
* [[Media:Lund_et_al_immunological_bioinformatics_2005_chapter_13.pdf|Chapter 13]]
* [[Media:Lund_et_al_immunological_bioinformatics_2005_chapter_14.pdf|Chapter 14]]
* [https://www.ncbi.nlm.nih.gov/pubmed/23097419 Simultaneous alignment and clustering of peptide data using a Gibbs sampling approach]
* Optional: [http://www.jimmunol.org/content/178/12/7890.long A Quantitative Analysis of the Variables Affecting the Repertoire of T Cell Specificities Recognized after Vaccinia Virus Infection]
* Optional: [https://www.ncbi.nlm.nih.gov/pubmed/24760079 Identification and HLA-tetramer-validation of human CD4+ and CD8+ T cell responses against HCMV proteins IE1 and IE2]
|
* Optional: [https://www.biorxiv.org/content/early/2018/10/02/433706 NetTCR: sequence-based prediction of TCR binding to peptide-MHC complexes using convolutional neural networks]
|
* Optional: [https://ac.els-cdn.com/S0959440X16300604/1-s2.0-S0959440X16300604-main.pdf?_tid=ddd4f38a-e8b4-46c9-95bd-7ff5c5813933&acdnat=1547455118_65062a3cf2e7531ba3b52cd7cbf8ed32 Design and engineering of deimmunized biotherapeutics]
|
|}

=Project Period and Exam=





== Thursday, January 17th - Wednesday January 23rd - Project Work ==

''Please note: The deadline for uploading the final project presentation will be Wednesday January 23rd at 23.59. It is a prerequisite for the exam to complete this assignment. Furthermore, please note, that you are responsible for all aspects of the group work and subsequent presentation''

09.00 - 17.00: Group project work

'''Groups and Projects 2019'''

The following groups counting 36 students in total, have been formed:

* G01 - (4p): Andreas (s134890), Asbjørn (s143849), Galal (s154802), Chaza (s144491)
* G02 - (4p): Madeeha (s154213), Amera (s130076), Alla (s061664), Asma (s161091)
* G03 - (4p): Cirkeline (s133643), Dorthe (s175824), Milena (milvu), Kristine (s111518)
* G04 - (4p): Marie (s143921), Catrine (s136574), Mikkel (s183049), Mikkel (s190095)
* G05 - (4p): Anna M (s136582), Pernille (s144499), Helena (s144530), Sebastian (s163691)
* G06 - (3p): Steinunn (s182233), Hrafnhildur (s182471), Vladislav (s182333)
* G07 - (3p): Ricki (s134898), Maria (s134878), Anna-Lisa (s190228)
* G08 - (5p): Lasse (s134887), Lasse (s173158), Anna (s124062), Jacob (s163726), Jakob (s163698)
* G09 - (5p): Daniel (s181782), Juan (s182441), Shreya (s181330), Kent (s133497), Adrianna (s181311)





== Exam Schedule, Thursday-Friday, January 24-25th ==

''The exam will be in the same room as the teaching, i.e. building 208, room 062''

'''09:00 - 16:00 Thursday January 24th, Exam day 1, Morten Nielsen and Leon Eyrich Jessen'''

''Group 1''

* 09:00 - 09:15 Presentation incl. questions
* 09:15 - 09:25 G01_1 Chaza (s144491)
* 09:25 - 09:35 G01_2 Asbjørn (s143849)
* 09:35 - 09:45 G01_3 Galal (s154802)
* 09:45 - 09:55 G01_4 Andreas (s134890)
* 09:55 - 10:00 Grading

''Group 9''

* 10:00 - 10:15 Presentation incl. questions
* 10:15 - 10:25 G09_1 Adrianna (s181311)
* 10:25 - 10:35 G09_2 Kent (s133497)
* 10:35 - 10:45 G09_3 Juan (s182441)
* 10:45 - 10:55 G09_4 Daniel (s181782)
* 10:55 - 11:05 G09_5 Shreya (s181330)
* 11:05 - 11:10 Grading

''Group 4''

* 11:10 - 11:25 Presentation incl. questions
* 11:25 - 11:35 G04_1 Marie (s143921)
* 11:35 - 11:45 G04_2 Mikkel (s183049)
* 11:45 - 11:55 G04_3 Mikkel (s190095)
* 11:55 - 12:05 G04_4 Catrine (s136574)
* 12:05 - 12:10 Grading

''Lunch break''

''Group 2''

* 13:00 - 13:15 Presentation incl. questions
* 13:15 - 13:25 G02_1 Madeeha (s154213)
* 13:25 - 13:35 G02_2 Asma (s161091)
* 13:35 - 13:45 G02_3 Amera (s130076)
* 13:45 - 13:55 G02_4 Alla (s061664)
* 13:55 - 14:00 Grading

''Group 7''

* 14:00 - 14:15 Presentation incl. questions
* 14:15 - 14:25 G07_1 Ricki (s134898)
* 14:25 - 14:35 G07_2 Anna-Lisa (s190228)
* 14:35 - 14:45 G07_3 Maria (s134878)
* 14:45 - 14:50 Grading

''Break''

''Group 3''

* 15:00 - 15:15 Presentation incl. questions
* 15:15 - 15:25 G03_1 Kristine (s111518)
* 15:25 - 15:35 G03_2 Cirkeline (s133643)
* 15:35 - 15:45 G03_3 Dorthe (s175824)
* 15:45 - 15:55 G03_4 Milena (milvu)
* 15:55 - 16:00 Grading

'''09:00 - 12:00 Friday January 25th, Exam day 2, Morten Nielsen and Leon Eyrich Jessen'''

''Group 5''

* 09:00 - 09:15 Presentation incl. questions
* 09:15 - 09:25 G05_1 Anna M (s136582)
* 09:25 - 09:35 G05_2 Sebastian (s163691)
* 09:35 - 09:45 G05_3 Helena (s144530)
* 09:45 - 09:55 G05_4 Pernille (s144499)
* 09:55 - 10:00 Grading

''Group 8''

* 10:00 - 10:15 Presentation incl. questions
* 10:15 - 10:25 G08_1 Jakob (s163726)
* 10:25 - 10:35 G08_2 Lasse (s134887)
* 10:35 - 10:45 G08_3 Lasse (s173158)
* 10:45 - 10:55 G08_4 Jakob (s163698)
* 10:55 - 11:05 G08_5 Anna (s124062)
* 11:05 - 11:10 Grading

''Group 6''

* 11:10 - 11:25 Presentation incl. questions
* 11:25 - 11:35 G06_1 Steinunn (s182233)
* 11:35 - 11:45 G06_2 Vladislav (s182333)
* 11:45 - 11:55 G06_3 Hrafnhildur (s182471)
* 11:55 - 12:00 Grading

22145 Immunological Bioinformatics Course Programme January 2020

2024-03-20T14:14:22Z

WikiSysop: Created page with "==Information for Course Participants== '''Course Format''' * Classes will be a mixture of lectures and group work * Most of the group work will consist of computer exercises, students are required to bring their own laptop * All learning resources will be available through DTU inside or this site * Expected time usage: [https://www.dtu.dk/english/Education/Course-base 1 ECTS point equals approx. 28 hours], this translates to an expected time usage of ~10 hours/day for..."

==Information for Course Participants==

'''Course Format'''
* Classes will be a mixture of lectures and group work
* Most of the group work will consist of computer exercises, students are required to bring their own laptop
* All learning resources will be available through DTU inside or this site
* Expected time usage: [https://www.dtu.dk/english/Education/Course-base 1 ECTS point equals approx. 28 hours], this translates to an expected time usage of ~10 hours/day for a 5 ECTS 3-week course

'''Course Ressources'''
* [http://teaching.healthtech.dtu.dk/22145/index.php/22145_-_Immunological_Bioinformatics Official course website]
* [https://kurser.dtu.dk/course/22145 Official course description]
* IMPORTANT: Please note, that the below course programme can be subject to changes or updates. Make sure to reload the page, to get the newest version of the programme.

'''Course Teachers'''
* [LEJ] [https://www.dtu.dk/english/service/phonebook/person?id=22554&cpid=257113&tab=2&qt=dtupublicationquery Leon Eyrich Jessen]
* [PM] [https://www.dtu.dk/english/service/phonebook/person?id=34983&cpid=257128&tab=2&qt=dtupublicationquery Paolo Marcatili]
* [MN] [https://www.dtu.dk/english/service/phonebook/person?id=5973&cpid=214020&tab=1&qt=dtupublicationquery Morten Nielsen]
* [BR] [https://www.dtu.dk/english/service/phonebook/person?id=104623&cpid=257289&tab=3&qt=dtuprojectquery Birkir Reynisson]
* [HP] [https://www.dtu.dk/service/telefonbog/person?id=88645&cpid=262443&tab=3&qt=dtuprojectquery Helle Rus Povlsen]

'''General Daily Schedule'''

* 09.00 - 12.00 Lectures
* 12.00 - 13.00 Lunch
* 13.00 - 17.00 Exercises

'''Location'''

* Building and room: Building 208, room 062 (Down the stairs, through the glass doors on your left)
* Should you be new to DTU, a map of DTU Lyngby Campus is available [[Media:Dtu_lyngby_campus.png|here]]

'''Profiles of Invited Speakers for Seminar on Cancer Immunotherapy'''
* Clinical perspective: [https://research.ku.dk/search/?pure=en%2Fpersons%2F458748 MD, PhD, Clinical Associate Professor Marco Donia, Center for Cancer Immune Therapy (CCIT) and Unit for Experimental Cancer Treatment (EFEK), Herlev-Gentofte Hospital and University of Copenhagen]
* Molecular Biology perspective: [https://www.dtu.dk/english/service/phonebook/person?id=99903&tab=2&qt=dtupublicationquery MSc, PhD, Professor Sine Reker Hadrup, Section for Experimental and Translational Immunology, Department of Health Technology, Technical University of Denmark]
* Bioinformatics perspective: [https://www.dtu.dk/english/service/phonebook/person?id=26586&tab=2&qt=dtupublicationquery MSc, PhD, Associate Professor Lars Rønn Olsen, Section for Bioinformatics, Department of Health Technology, Technical University of Denmark]
* Biomedical Industry perspective: [http://evaxion-biotech.com/portfolio/christian-garde-2/ MSc, PhD, Bioinformatics Specialist Christian Garde, Evaxion Biotech A/S]

==2020 Course Schedule Overview==

{| class="wikitable" style="font-size:75%;"
|+ Teaching Day 1-8
!
! Monday Jan. 6th
! Tuesday Jan. 7th
! Wednesday Jan. 8th
! Thursday Jan. 9th
! Friday Jan. 10th
! Monday Jan. 13th
! Tuesday Jan. 14th
! Wednesday Jan. 15th
|-
! Topic
! Introduction and Basic Immunology
! B-/T-Cell Receptor Genetics, Repertoires and the IEDB
! Protein Structure of B-/T-Cell Receptors and B-Cell Epitopes
! T-Cell Epitopes
! Antigen Processing and Presentation, HLA Clustering, and Vaccine Design
! Antibody Humanization and T-Cell Interaction Models
! De-Immunization and Chimeric Antigen Receptor (CAR) Immunotherapy
! Mini-symposium on Cancer Immunotherapy by Invited Speakers
|-
! 09.00 - 09.30
| [http://teaching.healthtech.dtu.dk/material/22145/ljess/22145_course_introduction_2020.pdf Course Introduction] [LEJ]
| Exercise: [[T-Cell Receptor Repertoires]] [LEJ]
| Exercise recap [BR]
| Exercise recap [PM]
| Exercise recap [MN]
| Exercise recap [MN]
| [http://teaching.healthtech.dtu.dk/material/22145/ljess/TCRpMHC_analysis.html Exercise recap] [LEJ]
| Talk 1+2 NB! [https://www.dtu.dk/om-dtu/kontakt-og-besoeg/find-vej/dtu-moedecenter Meeting room 1, in B101, 1st floor]
|-
! 09.30 - 10.15
| [[Micro_Project_on_Basic_Immunology|Micro project group work]] [LEJ]
| Exercise: [[T-Cell Receptor Repertoires]] [LEJ]
| Lecture: [[Media:Antibody structure.pdf|TCR and BCR structure]] [PM]
| Lecture: Prediction of MHC peptide binding using PSSMs and ANNs [MN]. Session materials: [http://www.cbs.dtu.dk/courses/27685.imm/presentations/MHCbinding_2020.pdf Slides [PDF]], [http://www.cbs.dtu.dk/courses/27685.imm/presentations/Ex_Logo.pdf Logo handout], [http://www.cbs.dtu.dk/courses/27685.imm/presentations/Ex_Logo_ans.pdf Answer Logo handout]. [http://www.cbs.dtu.dk/courses/27685.imm/presentations/NN_handout.pdf NN handout].
| Lecture: GibbsClustering. Identifying multiple sequence motifs in large scale peptide data sets] [http://www.cbs.dtu.dk/courses/27685.imm/presentations/GibbsCluster_2019.pdf Slides [MN]
| Lecture: [http://www.cbs.dtu.dk/~pmar/humanization.pdf Antibody Humanization] [PM]
| Lecture: [http://teaching.healthtech.dtu.dk/material/22145/birey/DeimmunePresenation.pdf Protein Drug Deimmunization] [BR]
| Talk 1+2 NB! [https://www.dtu.dk/om-dtu/kontakt-og-besoeg/find-vej/dtu-moedecenter Meeting room 1, in B101, 1st floor]
|-
! 10.15 - 10.30
! Break
! Break
! Break
! Break
! Break
! Break
! Break
! Break
|-
! 10.30 - 11.15
| [[Micro_Project_on_Basic_Immunology|Micro project group work]] [LEJ]
| Exercise: [[T-Cell Receptor Repertoires]] [LEJ]
| Exercise: [[Antibody Structure Prediction and Analysis]] [PM]
| Lecture: Rational epitope discovery using immunoinformatics [MN]
| Lecture: [http://www.cbs.dtu.dk/courses/27685.imm/presentations/Supertypes_2017.pdf Supertypes and functional clustering of MHC molecules] [MN]
| Exercise: [[Antibody Humanization]] [PM]
| [[Exercise:_Protein_drug_de-immunization]], [http://teaching.healthtech.dtu.dk/material/22145/birey/DeimmunizationExerciseEPO.ipynb Ipython notebook with solution to exercise, not mandatory] [BR]
| Talk 3+4 NB! [https://www.dtu.dk/om-dtu/kontakt-og-besoeg/find-vej/dtu-moedecenter Meeting room 1, in B101, 1st floor]
|-
! 11.15 - 12.00
| [[Micro_Project_on_Basic_Immunology|Micro project group work]] [LEJ]
| Exercise recap and B-/T-Cell Receptor Genetics and Repertoires wrap up [LEJ] [http://teaching.healthtech.dtu.dk/material/22145/ljess/repertoire_analysis.html Suggested answers]
| Lecture: [[Media:Linear epitope prediction.pdf|Linear ]] and [[Media:Conformational epitope prediction.pdf|Conformational ]] B-cell epitope prediction [PM]
| Lecture: MHC class II binding and [http://www.cbs.dtu.dk/courses/ILRI_workshop/presentations/Performance_measure.pdf Performance measures] [MN]
| Lecture: [http://www.cbs.dtu.dk/courses/27685.imm/presentations/Processing_Tcell_2018.pdf What defines a T cel epitope? Is there any thing beyond MHC binding?], and [http://www.cbs.dtu.dk/courses/27685.imm/presentations/Vaccine_design_2019.pdf Selecting the one in a million. Strategies for selecting peptide subsets, and vaccine design] [MN]
| Lecture: Single cell technologies for T-cell epitopes [http://teaching.healthtech.dtu.dk/material/22145/herpov/intro_SC.pdf presentation1] [http://teaching.healthtech.dtu.dk/material/22145/herpov/single_cell.pdf presentation2] [HP]
| Lecture: [http://teaching.healthtech.dtu.dk/36685/images/8/87/Deimmunisation.pptx.pdf Humanization and deimmunization for cancer T cell therapy molecules] [PM]
| Talk 3+4 NB! [https://www.dtu.dk/om-dtu/kontakt-og-besoeg/find-vej/dtu-moedecenter Meeting room 1, in B101, 1st floor]
|-
! 12.00 - 13.00
! Lunch Break
! Lunch Break
! Lunch Break
! Lunch Break
! Lunch Break
! Lunch Break
! Lunch Break
! Lunch Break
|-
! 13.00 - 17.00
| [[Micro_Project_on_Basic_Immunology|Micro project group work]] [LEJ]
| Exercise: [http://teaching.healthtech.dtu.dk/22145/index.php/Exercise:_Immune_Epitope_Database The Immune Epitope Database] [BR]
| Exercise: [http://www.cbs.dtu.dk/courses/27485.imm/epitope_2014.php B cell epitope predictions] [PM]
| Exercise:[http://www.cbs.dtu.dk/courses/27685.imm/exercise_MHC_bind/exercise_2019.php Prediction of MHC:peptide binding using PSSM and ANN]
[http://www.cbs.dtu.dk/courses/27685.imm/exercise_MHC_bind/exercise_2019_ans.php Answers: Prediction of MHC:peptide binding using PSSM and ANN]
| Exercise: [http://www.cbs.dtu.dk/courses/27685.imm/exercise_HCVVaccine/exercise_HCVVaccine_2020.php Development of vaccines against HCV] [MN] [http://www.cbs.dtu.dk/courses/27485.imm/exercise_HCVVaccine/answers_2020.pdf Answers]
| Exercise: [[Single cell technologies for T-cell epitopes]] [LEJ], Lecture: [http://teaching.healthtech.dtu.dk/material/22145/ljess/20200113_netTCR_talk.pdf Modelling TCRpMHC interactions] [LEJ]
| Exercise: [http://teaching.healthtech.dtu.dk/36685/index.php/Exercise_on_CAR_T-cell_humanisation_and_de-immunisation CAR T-cell humanisation and de-immunisation] [PM]
| [http://teaching.healthtech.dtu.dk/material/22145/ljess/20200114_Introduction_to_Project_Period_and_Exam.pdf Introduction to project work and exam] [LEJ]
|- style="vertical-align: top;" |
! Learning Resources
|
Required
* Video: [https://www.youtube.com/watch?v=K09xzIQ8zsg Tumour immunology and immunotherapy]
* Video: [https://www.youtube.com/watch?v=vponeaNiewE Decoding cancer immunology: Hunting hidden tumours]
Optional
* None
|
Required
* Paper: [https://www.ncbi.nlm.nih.gov/pubmed/25300482 The immune epitope database (IEDB) 3.0.]
* Video: [https://www.youtube.com/watch?v=Na-Zc-xWCLE Immunology wars: A billion antibodies]
* Video: [https://www.youtube.com/watch?v=JJmqt40Z3mM Antibody (BCR) and TCR Diversity]
* Video: [https://www.youtube.com/watch?v=h9mqsllg1Cs Antibody Somatic (VDJ) Recombination I]
* Video: [https://www.youtube.com/watch?v=_D2x-dhh6Pg Antibody Somatic (VDJ) Recombination II]
* Book: [https://cn.inside.dtu.dk/cnnet/filesharing/download/8df4dfc2-e023-43b8-a2cd-1a00e1e902bc Kuby Ch. 7: The Organization and Expression of Lymphocyte Receptor Genes]
Optional
* None
|
* [[Media:Immunological bioinformatics Quiz 1 2019.pdf|Mini Quiz]]
* [[Media:Pymol-edu-license-2020.txt|Pymol license]]

Required
* None
Optional
* Paper: [https://academic.oup.com/nar/article/3787843 BepiPred 2.0]
* Paper: [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531324/ B-cell epitope prediction]
* Video: [http://www.youtube.com/watch?v=Z36dUduOk1Y Simplified B-cell walkthrough] (Nice and easy understandable explanation of B-cells)
* Resource: [https://pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/ PDB 101: Introduction to PDB Data]
|
Required
* Book: [[Media:Lund_et_al_immunological_bioinformatics_2005_chapter_3.pdf| Immuno. Bioinfo. Ch. 3]]
* Book: [[Media:Lund_et_al_immunological_bioinformatics_2005_chapter_4.pdf| Immuno. Bioinfo. Ch. 4]]
* Paper: [http://bioinformatics.oxfordjournals.org/cgi/reprint/23/24/3265 Modeling the adaptive immune system: predictions and simulations]
* Paper: [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2913210 Major histocompatibility complex class I binding predictions as a tool in epitope discovery]
* Paper: [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2913211 MHC Class II epitope predictive algorithms]
|
Required
* Book: [[Media:Lund_et_al_immunological_bioinformatics_2005_chapter_13.pdf| Immuno. Bioinfo. Ch. 13]]
* Book: [[Media:Lund_et_al_immunological_bioinformatics_2005_chapter_14.pdf| Immuno. Bioinfo. Ch. 14]]
* Paper: [https://www.ncbi.nlm.nih.gov/pubmed/23097419 Simultaneous alignment and clustering of peptide data using a Gibbs sampling approach]
Optional
* Paper: [http://www.jimmunol.org/content/178/12/7890.long A Quantitative Analysis of the Variables Affecting the Repertoire of T Cell Specificities Recognized after Vaccinia Virus Infection]
* Paper: [https://www.ncbi.nlm.nih.gov/pubmed/24760079 Identification and HLA-tetramer-validation of human CD4+ and CD8+ T cell responses against HCMV proteins IE1 and IE2]
|
Required
* Paper: [https://www.biorxiv.org/content/early/2018/10/02/433706 NetTCR: sequence-based prediction of TCR binding to peptide-MHC complexes using convolutional neural networks]
* Paper: [https://www.nature.com/articles/nbt.4303 T cell receptor fingerprinting enables in-depth characterization of the interactions governing recognition of peptide–MHC complexes]
* Paper: [https://www.nature.com/articles/s41598-019-50932-4 TCRpMHCmodels: Structural modelling of TCR-pMHC class I complexes]
* Paper: [https://www.sciencedirect.com/science/article/pii/S0161589017306211 Identification of the cognate peptide-MHC target of T cell receptors using molecular modeling and force field scoring]
* Tech report: [http://teaching.healthtech.dtu.dk/material/22145/ljess/10x_AN047_IP_A_New_Way_of_Exploring_Immunity_Digital.pdf A New Way of Exploring Immunity – Linking Highly Multiplexed Antigen Recognition to Immune Repertoire and Phenotype]
Optional
* None
|
Required
* None
Optional
* Paper: [https://www.ncbi.nlm.nih.gov/pubmed/27322891 Design and engineering of deimmunized biotherapeutics]
|
|}

==Project Period and Exam==

=== Project ===

'''Wednesday January 15th - Wednesday January 22nd - Project Work'''

Please note the following:
* The deadline for uploading the final project presentation (i.e. ''not'' a report) to [https://www.inside.dtu.dk/ DTU inside] will be '''Wednesday January 22nd at 23.59'''
* It is a prerequisite for the exam to complete this assignment and as such, ''failure to meet the deadline will result in a failed exam''
* Furthermore and very important - Each group member is responsible for ''all'' aspects of the group work and subsequent presentation

'''Groups and Projects 2020'''

Each group will consist of 4-5 students

[https://cn.inside.dtu.dk/cnnet/filesharing/download/0d9e8289-c2b3-4169-8174-09c6b08e2adb Click here to see 2020 group list]

=== Exam Schedule ===

* General exam format will be ~10-12 minutes of project presentation followed by 2-3 minutes questions, so 15 min in total and then a ~10 minute individual exam in the project and general [https://kurser.dtu.dk/course/22145 course learning objectives]
* Individual grades will be given after all group members have completed the oral exam
* In the same room as the teaching, i.e. building 208, room 062
* Conducted by Morten Nielsen and Leon Eyrich Jessen

Random draw:

set.seed(498401)
sample(1:10)
[1] 5 8 9 6 2 4 1 3 10 7

==== Thursday January 23rd ====

* 09:00 - 10:00 Group 5
* 10:00 - 11:00 Group 8
* 11:00 - 12:00 Group 9
* Lunch
* 13:00 - 14:00 Group 6
* 14:00 - 15:00 Group 2
* 15:00 - 16:00 Group 4

==== Friday January 24th ====

* 09:00 - 10:00 Group 1
* 10:00 - 11:00 Group 3
* 11:00 - 12:00 Group 10
* Lunch
* 13:00 - 14:00 Group 7

22145 Immunological Bioinformatics Course Programme January 2021

2024-03-20T14:12:22Z

WikiSysop:

= COURSE PLAN FOR 2021 =

==EXAM==

The pdf with the exam will be uploaded here on Friday January 22nd, 13 - 15hs



'''Guidelines'''

* The exam will be made available at the wiki at 13.00hs. Upload a '''pdf''' with your answers '''no later than 15.00hs on DTU inside''' written exam assignment.
* You must connect at Zoom 5 minutes before the exam, and have the '''camera turned ON during the whole exam'''. Failing to meet this requirement will invalidate the exam.
* This is an '''individual exam'''. Remember sharing or copying answers is not allowed and will be severely punished according to DTU rules and code-of-honor.

==Information for Course Participants==

'''Course Format'''
* NEWS! Due to new restrictions on Covid19 this course will be completely conducted online and all classes will be recorded and uploaded
* Due to group work on some classes, it will be mandatory that you are connected and work online on the allocated time for those
* This will be needed for the entire first day, the question and answer sessions, and the final exam
* Classes will be a mixture of lectures, group work and individual exercises
* Most of the group work will consist of computer exercises, where students are required to use their laptops
* General Question and Answer will be live and uploaded after the session
* Specif Question and Answers for exercise-lectures will be held on Piazza, where you need to create an user
* All learning resources will be available through DTU inside or this site
* Expected time usage: [https://www.dtu.dk/english/Education/Course-base 1 ECTS point equals approx. 28 hours], this translates to an expected time usage of ~10 hours/day for a 5 ECTS 3-week course

'''Course Resources'''
* [http://teaching.healthtech.dtu.dk/22145/index.php/22145_-_Immunological_Bioinformatics Official course website]
* [https://kurser.dtu.dk/course/22145 Official course description]
* [https://dtudk.zoom.us/meeting/register/u5Ypc-iupjIuGtzs8eF0RlM5xijlcFdwQaQq ZOOM link for live classes(registration with DTU mail needed)]
* [https://piazza.com/dtu.dk/fall2020/22145 Piazza link for Q&A on exercises]
* IMPORTANT: Please note, that the below course programme can be subject to changes or updates. Make sure to reload the page, to get the newest version of the programme.

'''Course Teachers'''
* [CB] [https://www.dtu.dk/english/service/phonebook/Person?id=142840&cpid=263035&tab=2&qt=dtupublicationquery Carolina Barra]
* [PM] [https://www.dtu.dk/english/service/phonebook/person?id=34983&cpid=257128&tab=2&qt=dtupublicationquery Paolo Marcatili]
* [MN] [https://www.dtu.dk/english/service/phonebook/person?id=5973&cpid=214020&tab=1&qt=dtupublicationquery Morten Nielsen]
* [BR] [https://www.dtu.dk/english/service/phonebook/person?id=104623&cpid=257289&tab=3&qt=dtuprojectquery Birkir Reynisson]
* [HP] [https://www.dtu.dk/service/telefonbog/person?id=88645&cpid=262443&tab=3&qt=dtuprojectquery Helle Rus Povlsen]
* [MV] [https://www.dtu.dk/english/service/phonebook/Person?id=129355&cpid=257376&tab=2&qt=dtuprojectquery Milena Vujovic]
* [AM] [https://www.dtu.dk/english/service/phonebook/Person?id=124312&cpid=274573&tab=3&qt=dtuprojectquery Alessandro Montemurro]

'''General Daily Schedule'''

* 09.00 - 12.00 Lectures
* 12.00 - 13.00 Lunch
* 13.00 - 13.30 Live sessions Q&A
* 13.30 - 17.00 Exercises

'''Location'''

* NOTE: This edition of the course will be completely online

'''Profiles of Invited Speakers for Mini Symposium'''
* Clinical perspective: [https://research.ku.dk/search/?pure=en%2Fpersons%2F458748 MD, PhD, Clinical Associate Professor Marco Donia, Center for Cancer Immune Therapy (CCIT) and Unit for Experimental Cancer Treatment (EFEK), Herlev-Gentofte Hospital and University of Copenhagen]
* Molecular Biology perspective: [https://www.dtu.dk/service/telefonbog/person?id=102741&cpid=&tab=2&qt=dtupublicationquery PhD, Adjunkt Professor Sunil Kumar Saini, Section for Experimental and Translational Immunology, Department of Health Technology, Technical University of Denmark]
* Biomedical Industry perspective: upon confirmation.
* Bioinformatics Industry perspective: [https://www.vaccibody.com/management/ PhD, Head of Bioinformatics Monika Sekelja, Vaccibody A/S]

==2021 Course Schedule Overview==

{| class="wikitable" style="font-size:75%;"
|+ Teaching Day 1-8
!
! Monday Jan. 4th
! Tuesday Jan. 5th
! Wednesday Jan. 6th
! Thursday Jan. 7th
! Friday Jan. 8th
! Monday Jan. 11th
! Tuesday Jan. 12th
! Wednesday Jan. 13th
|-
! Topic
! Introduction and Basic Immunology
! T-Cell Epitopes
! Antigen Processing and Presentation, HLA Clustering, and Vaccine Design
! Protein Structure of B-/T-Cell Receptors and B-Cell Epitopes
! Immunopeptidomics, T-Cell Repertoires and the IEDB
! Antibody Humanization and T-Cell Interaction Models
! De-Immunization and Chimeric Antigen Receptor (CAR) Immunotherapy
! Mini-symposium on Immunoinformatics by Invited Speakers
|-
! 09.00 - 09.30
| [http://www.cbs.dtu.dk/courses/27685.imm/presentations/Carol/Course_Introduction_2021.pdf Course Introduction] '''Live on Zoom''' Recording: [http://www.cbs.dtu.dk/courses/27685.imm/recordings/22145_2021/Introduction_IB.mp4 MP4] [CB]
| Lecture: Prediction of MHC peptide binding Part 1 [MN]. Session materials: [http://www.cbs.dtu.dk/courses/27685.imm/presentations/MHCbinding_2020_part1.pdf Slides [PDF]]. Recording: [http://www.cbs.dtu.dk/courses/27685.imm/recordings/MHC_part1.mp4 [MP4]], Logo handout: [http://www.cbs.dtu.dk/courses/27685.imm/presentations/Ex_Logo.pdf [PDF]], [http://www.cbs.dtu.dk/courses/27685.imm/presentations/Ex_Logo_ans.pdf Answer Logo handout] Logo handout Recording [http://www.cbs.dtu.dk/courses/27685.imm/recordings/Ex_Logo.mp4 [MP4]].
| Lecture: MHC motif deconvolution - Identifying sequence motifs in large scale ligand data sets [MN]. Session materials: [http://www.cbs.dtu.dk/courses/27685.imm/presentations/MHCMotifDecon_2021.pdf Slides [PDF]]. Recording: [http://www.cbs.dtu.dk/courses/27685.imm/recordings/MHCMotifDecon_2021.mp4 [MP4]].
| Lecture: [[Media:Antibody structure.pdf|TCR and BCR structure]]. Recording: [https://youtu.be/HP-zcAugLkk Antibody Modelling] [PM]
[https://youtu.be/8dzwdlKTUXI Solution]
| Lecture: [http://www.cbs.dtu.dk/courses/27685.imm/presentations/Carol/Immunopeptidomics_2021.pdf Immunopeptidomics] '''Live on Zoom''' Recording: [http://www.cbs.dtu.dk/courses/27685.imm/recordings/22145_2021/Immunopeptidomics_CB.mp4 MP4] [CB]
| Lecture: [https://teaching.healthtech.dtu.dk/22145/images/e/ec/Humanization_2021_notabhu_reduced.pdf Antibody Humanization] [https://youtu.be/WXMrdDSHA6M Video] [PM]
| Lecture: Protein Drug Deimmunization '''Live on Zoom''' [http://www.cbs.dtu.dk/courses/27685.imm/deimmune_Presentation/2021_01_12_Deimmunization_22145.pdf pdf] [http://www.cbs.dtu.dk/courses/27685.imm/deimmune_Presentation/2021_01_12_DeimmunePresentation.mp4 mp4] [BR]
| Talk 1: '''Cancer immunotherapy in the clinic.''' Marco Donia '''Live!''' [http://www.cbs.dtu.dk/courses/27685.imm/recordings/22145_2021/Talk1_MarcoDonia.mp4 video]
|-
! 09.30 - 10.15
| [[Micro_Project_on_Basic_Immunology|Micro project group work]] '''Live on Zoom''' [CB]
| Lecture: Prediction of MHC peptide binding part 2 [MN]. Session materials: [http://www.cbs.dtu.dk/courses/27685.imm/presentations/MHCbinding_2020_part2.pdf Slides [PDF]]. Recording: [http://www.cbs.dtu.dk/courses/27685.imm/recordings/MHC_part2.mp4 [MP4]]. NN handout [http://www.cbs.dtu.dk/courses/27685.imm/presentations/NN_handout.pdf [PDF]]. NN handout Recording [http://www.cbs.dtu.dk/courses/27685.imm/recordings/Ex_NN.mp4 [MP4]].
| Lecture: What defines a T cell epitope? Is there any thing beyond MHC binding? [MN] Session materials: [http://www.cbs.dtu.dk/courses/27685.imm/presentations/Processing_Tcell_2018.pdf Slides [PDF]]. Recording: [http://www.cbs.dtu.dk/courses/27685.imm/recordings/Processing_Tcell_2018.mp4 [MP4]].
| Exercise: [[Antibody Structure Prediction and Analysis]] Recording: [https://youtu.be/5t7aUkXVuwk Exercise] [PM]
| Exercise files: [[File: Peptides-HD-DR2b.txt|Peptides]] [[File: Alleles-HD-DR2b.txt |Alleles_list]] Answers: [http://www.cbs.dtu.dk/courses/27685.imm/presentations/Carol/Exercise_guidelines_answers.pdf Answers]'''Live on Zoom''' [CB]
| Exercise: [[Antibody Humanization]] [PM]
| Exercise: [[Protein Drug Deimmunization]] [BR]
| Talk 2: '''SARS-CoV-2 full genome profiling for T cell immunity and immunodominance in COVID-19 infection.''' Sunil Kumar Saini '''Live!''' [http://www.cbs.dtu.dk/courses/27685.imm/recordings/22145_2021/Talk2_SunilSaini.mp4 video]
|-
! 10.15 - 10.30
! Break
! Break
! Break
! Break
! Break
! Break
! Break
! Break
|-
! 10.30 - 11.15
| [[Micro_Project_on_Basic_Immunology|Micro project group work]] '''Live on Zoom''' [CB]
| Lecture: Prediction of MHC peptide binding part 3 [MN]. Session materials: [http://www.cbs.dtu.dk/courses/27685.imm/presentations/MHCbinding_2020_part3.pdf Slides [PDF]]. Recording: [http://www.cbs.dtu.dk/courses/27685.imm/recordings/MHC_part3.mp4 [MP4]].
| Lecture: Selecting the one in a million. Strategies for selecting peptide subsets, and vaccine design [MN]. Session materials: [http://www.cbs.dtu.dk/courses/27685.imm/presentations/Vaccine_design_2019.pdf Slides [PDF]]. Recording: [http://www.cbs.dtu.dk/courses/27685.imm/recordings/Vaccine_design_2019.mp4 [MP4]].
| Lecture: [[Media:Linear epitope prediction.pdf|Linear ]] B-cell epitope prediction. Recording: [https://youtu.be/Ukk5XJfuh6k] [PM]
| Lecture: T-Cell Receptor Repertoires '''Live on Zoom''' [http://www.cbs.dtu.dk/courses/27685.imm/presentations/Carol/20210108MV_Tcell_receptor_repertoires_updated.pdf Slides] Recording: [[http://www.cbs.dtu.dk/courses/27685.imm/recordings/22145_2021/20210108MV_Tcell_receptor_repertoires.mp4 [MP4]] [MV]
| Lecture: Single cell technologies for T-cell epitopes [http://www.cbs.dtu.dk/courses/27685.imm/presentations/Carol/single_cell_general.pdf Single Cell] and [http://www.cbs.dtu.dk/courses/27685.imm/presentations/Carol/nettcr_project.pdf NetTCR Project] [http://www.cbs.dtu.dk/courses/27685.imm/recordings/22145_2021/Single_cell.mp4 video]'''Live on Zoom''' [HP]
| Lecture: [http://teaching.healthtech.dtu.dk/36685/images/8/87/Deimmunisation.pptx.pdf Humanization and deimmunization for cancer T cell therapy molecules] [http://www.cbs.dtu.dk/courses/27685.imm/recordings/22145_2021/Deimmunisation_CART-cells.mp4 video] [PM]
| Talk 3: '''The utilization of bioinformatics to guide drug design.''' Monika Sekelja '''Live!''' [http://www.cbs.dtu.dk/courses/27685.imm/recordings/22145_2021/Talk3_MonikaSekelja.mp4 video]
|-
! 11.15 - 12.00
| [[Micro_Project_on_Basic_Immunology|Micro project group work]] '''Live on Zoom''' [CB]
| Lecture: [http://www.cbs.dtu.dk/courses/ILRI_workshop/presentations/Performance_measure.pdf Performance measures] [MN]. Recording: [http://www.cbs.dtu.dk/courses/22125/recordings/Performance_measure.mp4 [MP4]].
| Lecture: Selecting the one in a million. Strategies for selecting peptide subsets, and vaccine design [MN] cont.
| Lecture: [[Media:Conformational epitope prediction.pdf|Conformational ]] B-cell epitope prediction. Recording: [https://youtu.be/xg8Wf4rNsqw][PM]
| Lecture: The Immune Epitope Database & Tools '''Live on Zoom''' [http://www.cbs.dtu.dk/courses/27685.imm/presentations/Carol/2021_01_08_IEDB.pdf PDF] [http://www.cbs.dtu.dk/courses/27685.imm/recordings/2021_01_08_IEDB_Presentation.mp4 mp4] [BR]
| Lecture: [http://www.cbs.dtu.dk/courses/27685.imm/presentations/Carol/netTCR_interactions_2021.pdf Modelling TCRpMHC interactions] [http://www.cbs.dtu.dk/courses/27685.imm/recordings/22145_2021/NetTCR_video.mp4 video]'''Live on Zoom''' [AM]
| Lecture: [http://teaching.healthtech.dtu.dk/36685/images/8/87/Deimmunisation.pptx.pdf Humanization and deimmunization for cancer T cell therapy molecules] [PM]
| Talk 4: TBC Live!
|-
! 12.00 - 13.00
! Lunch Break
! Lunch Break
! Lunch Break
! Lunch Break
! Lunch Break
! Lunch Break
! Lunch Break
! Lunch Break
|-
! 13.00 - 13.30
| '''Live:''' Q&A Session [CB]
| '''Live:''' Quiz: [https://kursusquiz.dtu.dk/quiz/solochallenge/398/holding/571?lang=en MHC binding]. Q&A Session [MN]. Recordings: [http://www.cbs.dtu.dk/courses/27685.imm//recordings/QA_2021-01-05_1.mp4 R1 [MP4]]. [http://www.cbs.dtu.dk/courses/27685.imm//recordings/QA_2021-01-05_2.mp4 R2 [MP4]]. [http://www.cbs.dtu.dk/courses/27685.imm//recordings/QA_2021-01-05_3.mp4 R3 [MP4]].
| '''Live:''' Exercise recap [MN]. Quiz: [https://kursusquiz.dtu.dk/quiz/solochallenge/400/holding/578?lang=en MHC processing, epitope discovery and vaccine design]. Q&A Session [MN]. Recordings: [http://www.cbs.dtu.dk/courses/27685.imm//recordings/QA_2021-01-06.mp4 R1 [MP4]].
| '''Live:''' Exercise recap [MN] Recordings: [http://www.cbs.dtu.dk/courses/27685.imm//recordings/QA_2021-01-07.mp4 R1 [MP4]].
| '''Live:''' Exercise recap Recordings: [http://www.cbs.dtu.dk/courses/27685.imm//recordings/22145_2021/PM_live_recap_exercises_Ab_TCRs.mp4 [MP4]] [PM]
| '''Live:''' Exercise recap [http://www.cbs.dtu.dk/courses/27685.imm/recordings/22145_2021/Live_exercise_recap_immunopeptidomics_IEDB_CB_BR.mp4 video] [CB] and [BR]
| '''Live:''' Exercise recap [http://www.cbs.dtu.dk/courses/27685.imm/recordings/22145_2021/HP_exercise_recap_single_cell_netTCR.mp4 video] [HP]
| '''Live:''' Exercise recap [PM]
|-
! 13.30 - 17.00
| [[Micro_Project_on_Basic_Immunology|Micro project group work]] '''Live on Zoom''' [http://www.cbs.dtu.dk/courses/27685.imm/recordings/22145_2021/Group_Presentations_day1part1.mp4 Presentations_part1] [http://www.cbs.dtu.dk/courses/27685.imm/recordings/22145_2021/Group_Presentations_day1part2.mp4 Presentations_part2] [CB]
| Exercise:[http://www.cbs.dtu.dk/courses/27685.imm/exercise_MHC_bind/exercise_2019.php Prediction of MHC:peptide binding using PSSM and ANN]
[http://www.cbs.dtu.dk/courses/27685.imm/exercise_MHC_bind/exercise_2019_ans.php Answers: Prediction of MHC:peptide binding using PSSM and ANN]
| Exercise: [http://www.cbs.dtu.dk/courses/27685.imm/exercise_HCVVaccine/exercise_HCVVaccine_2021.php Development of vaccines against HCV] [MN] [http://www.cbs.dtu.dk/courses/27685.imm/exercise_HCVVaccine/exercise_HCVVaccine_2021_ans.php Answers]
| Exercise: [http://www.cbs.dtu.dk/courses/27485.imm/epitope_2014.php B cell epitope predictions] [PM]
| Exercise: [https://teaching.healthtech.dtu.dk/22145/index.php/T-Cell_Receptor_Repertoires#Retrieve_and_Upload_Repertoire_data T-Cell Receptor Repertoires] [MV] [http://teaching.healthtech.dtu.dk/material/22145/ljess/repertoire_analysis.html Suggested answers] Exercise: [[IEDB]] [BR]
| Exercise: [[Single cell technologies for T-cell epitopes]] [HP]
| Exercise: [http://teaching.healthtech.dtu.dk/36685/index.php/Exercise_on_CAR_T-cell_humanisation_and_de-immunisation CAR T-cell humanisation and de-immunisation] [PM]
| '''Live on Zoom''' [http://www.cbs.dtu.dk/courses/27685.imm/presentations/Carol/project_and_exam.pdf Introduction to project and exam] [CB]
|- style="vertical-align: top;" |
! Learning Resources
|
Required
* Paper: [https://onlinelibrary.wiley.com/doi/abs/10.1002/bies.201900200 Peptide Presentation to T Cells: Solving the Immunogenic Puzzle]
* Video: [https://www.youtube.com/watch?v=K09xzIQ8zsg Tumour immunology and immunotherapy]
* Video: [https://www.youtube.com/watch?v=vponeaNiewE Decoding cancer immunology: Hunting hidden tumours]
Optional
* Video: [https://www.youtube.com/watch?v=fSEFXl2XQpc Back to Basics]
|
Required
* Book: [[Media:Lund_et_al_immunological_bioinformatics_2005_chapter_3.pdf| Immuno. Bioinfo. Ch. 3]]
* Book: [[Media:Lund_et_al_immunological_bioinformatics_2005_chapter_4.pdf| Immuno. Bioinfo. Ch. 4]]
* Paper: [http://bioinformatics.oxfordjournals.org/cgi/reprint/23/24/3265 Modeling the adaptive immune system: predictions and simulations]
* Paper: [https://www.annualreviews.org/doi/pdf/10.1146/annurev-biodatasci-021920-100259 Immunoinformatics: Predicting Peptide–MHC Binding]
Optional
* Paper: [https://www.mcponline.org/content/18/12/2459.long NNAlign_MA; MHC Peptidome Deconvolution for Accurate MHC Binding Motif Characterization and Improved T-cell Epitope Predictions]
* Paper: [https://pubs.acs.org/doi/10.1021/acs.jproteome.9b00874 Improved Prediction of MHC II Antigen Presentation through Integration and Motif Deconvolution of Mass Spectrometry MHC Eluted Ligand Data]
|
Required
* Book: [[Media:Lund_et_al_immunological_bioinformatics_2005_chapter_13.pdf| Immuno. Bioinfo. Ch. 13]]
* Book: [[Media:Lund_et_al_immunological_bioinformatics_2005_chapter_14.pdf| Immuno. Bioinfo. Ch. 14]]
* Paper: [https://www.annualreviews.org/doi/10.1146/annurev-immunol-082119-124838 T Cell Epitope Predictions]
Optional
* Paper: [https://www.ncbi.nlm.nih.gov/pubmed/23097419 Simultaneous alignment and clustering of peptide data using a Gibbs sampling approach]
* Paper: [http://www.jimmunol.org/content/178/12/7890.long A Quantitative Analysis of the Variables Affecting the Repertoire of T Cell Specificities Recognized after Vaccinia Virus Infection]
* Paper: [https://www.ncbi.nlm.nih.gov/pubmed/24760079 Identification and HLA-tetramer-validation of human CD4+ and CD8+ T cell responses against HCMV proteins IE1 and IE2]
|
* [[Media:Immunological bioinformatics Quiz 1 2019.pdf|Mini Quiz]]
* [[Media:Pymol-edu-license-2021.txt|Pymol license]]

Required
* None
Optional
* Paper: [https://academic.oup.com/nar/article/3787843 BepiPred 2.0]
* Paper: [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531324/ B-cell epitope prediction]
* Video: [http://www.youtube.com/watch?v=Z36dUduOk1Y Simplified B-cell walkthrough] (Nice and easy understandable explanation of B-cells)
* Resource: [https://pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/ PDB 101: Introduction to PDB Data]
|

* Rstudio: [https://rstudio.com/products/rstudio/download/ Get it] [https://datascienceplus.com/introduction-to-rstudio/ Quick guide] [https://teaching.healthtech.dtu.dk/22145/index.php/Getting_started_with_RStudio_Cloud,_R_and_rmarkdown Getting started]

Required
* Video: [https://www.youtube.com/watch?v=Na-Zc-xWCLE Immunology wars: A billion antibodies]
* Video: [https://www.youtube.com/watch?v=JJmqt40Z3mM Antibody (BCR) and TCR Diversity]
* Video: [https://www.youtube.com/watch?v=h9mqsllg1Cs Antibody Somatic (VDJ) Recombination I]
* Video: [https://www.youtube.com/watch?v=_D2x-dhh6Pg Antibody Somatic (VDJ) Recombination II]
* Book: [https://cn.inside.dtu.dk/cnnet/filesharing/download/8df4dfc2-e023-43b8-a2cd-1a00e1e902bc Kuby Ch. 7: The Organization and Expression of Lymphocyte Receptor Genes]
* Paper: [https://www.ncbi.nlm.nih.gov/pubmed/25300482 The immune epitope database (IEDB) 3.0.]
Optional
* None
|
Required
* Paper: [https://www.biorxiv.org/content/early/2018/10/02/433706 NetTCR: sequence-based prediction of TCR binding to peptide-MHC complexes using convolutional neural networks]
* Paper: [https://www.nature.com/articles/nbt.4303 T cell receptor fingerprinting enables in-depth characterization of the interactions governing recognition of peptide–MHC complexes]
* Paper: [https://www.nature.com/articles/s41598-019-50932-4 TCRpMHCmodels: Structural modelling of TCR-pMHC class I complexes]
* Paper: [https://www.sciencedirect.com/science/article/pii/S0161589017306211 Identification of the cognate peptide-MHC target of T cell receptors using molecular modeling and force field scoring]
* Tech report: [http://teaching.healthtech.dtu.dk/material/22145/ljess/10x_AN047_IP_A_New_Way_of_Exploring_Immunity_Digital.pdf A New Way of Exploring Immunity – Linking Highly Multiplexed Antigen Recognition to Immune Repertoire and Phenotype]
Optional
* None
|
Required
* None
Optional
* Paper: [https://www.ncbi.nlm.nih.gov/pubmed/27322891 Design and engineering of deimmunized biotherapeutics]
|
|}

==Project Period and Exam==

=== Project ===

'''Wednesday January 13th - Wednesday January 20nd - Project Work'''

Please note the following (***time has been updated***):
* The deadline for uploading the final project Poster presentation (i.e. ''not'' a report) to [https://www.inside.dtu.dk/ DTU inside] will be '''Wednesday January 20nd at 11.59AM'''
* It is a prerequisite for the exam to complete this assignment and as such, ''failure to meet the deadline will result in a failed exam''
* Furthermore and very important - Each group member is responsible for ''all'' aspects of the group work and subsequent presentation

'''Groups and Projects 2021'''

* Groups will be preset based on educational diversity

* [https://cn.inside.dtu.dk/cnnet/filesharing/download/950b168e-0786-4b7e-85bd-1389e9a61869 The groups list for 2021]

=== Exam Schedule ===

* General exam format will consist on 2 parts ([https://kurser.dtu.dk/course/22145 course learning objectives]):

Oral presentation of the poster project ~10 minutes for all group presentation + 5 minutes for questions (15 minutes total)
Date: January 21st 2021 (specific times per group to be announced)

Written exam ~20 questions 2hs, all conducted online on DTU Inside
Date: January 22st 2021

* Individual grades will be given after the finalization of the course

22145 Immunological Bioinformatics Course Programme January 2021

2024-03-20T14:01:15Z

WikiSysop: /* 2021 Course Schedule Overview */

= COURSE PLAN FOR 2021 =

==EXAM==

The pdf with the exam will be uploaded here on Friday January 22nd, 13 - 15hs



'''Guidelines'''

* The exam will be made available at the wiki at 13.00hs. Upload a '''pdf''' with your answers '''no later than 15.00hs on DTU inside''' written exam assignment.
* You must connect at Zoom 5 minutes before the exam, and have the '''camera turned ON during the whole exam'''. Failing to meet this requirement will invalidate the exam.
* This is an '''individual exam'''. Remember sharing or copying answers is not allowed and will be severely punished according to DTU rules and code-of-honor.

==Information for Course Participants==

'''Course Format'''
* NEWS! Due to new restrictions on Covid19 this course will be completely conducted online and all classes will be recorded and uploaded
* Due to group work on some classes, it will be mandatory that you are connected and work online on the allocated time for those
* This will be needed for the entire first day, the question and answer sessions, and the final exam
* Classes will be a mixture of lectures, group work and individual exercises
* Most of the group work will consist of computer exercises, where students are required to use their laptops
* General Question and Answer will be live and uploaded after the session
* Specif Question and Answers for exercise-lectures will be held on Piazza, where you need to create an user
* All learning resources will be available through DTU inside or this site
* Expected time usage: [https://www.dtu.dk/english/Education/Course-base 1 ECTS point equals approx. 28 hours], this translates to an expected time usage of ~10 hours/day for a 5 ECTS 3-week course

'''Course Resources'''
* [http://teaching.healthtech.dtu.dk/22145/index.php/22145_-_Immunological_Bioinformatics Official course website]
* [https://kurser.dtu.dk/course/22145 Official course description]
* [https://dtudk.zoom.us/meeting/register/u5Ypc-iupjIuGtzs8eF0RlM5xijlcFdwQaQq ZOOM link for live classes(registration with DTU mail needed)]
* [https://piazza.com/dtu.dk/fall2020/22145 Piazza link for Q&A on exercises]
* IMPORTANT: Please note, that the below course programme can be subject to changes or updates. Make sure to reload the page, to get the newest version of the programme.

'''Course Teachers'''
* [CB] [https://www.dtu.dk/english/service/phonebook/Person?id=142840&cpid=263035&tab=2&qt=dtupublicationquery Carolina Barra]
* [PM] [https://www.dtu.dk/english/service/phonebook/person?id=34983&cpid=257128&tab=2&qt=dtupublicationquery Paolo Marcatili]
* [MN] [https://www.dtu.dk/english/service/phonebook/person?id=5973&cpid=214020&tab=1&qt=dtupublicationquery Morten Nielsen]
* [BR] [https://www.dtu.dk/english/service/phonebook/person?id=104623&cpid=257289&tab=3&qt=dtuprojectquery Birkir Reynisson]
* [HP] [https://www.dtu.dk/service/telefonbog/person?id=88645&cpid=262443&tab=3&qt=dtuprojectquery Helle Rus Povlsen]
* [MV] [https://www.dtu.dk/english/service/phonebook/Person?id=129355&cpid=257376&tab=2&qt=dtuprojectquery Milena Vujovic]
* [AM] [https://www.dtu.dk/english/service/phonebook/Person?id=124312&cpid=274573&tab=3&qt=dtuprojectquery Alessandro Montemurro]

'''General Daily Schedule'''

* 09.00 - 12.00 Lectures
* 12.00 - 13.00 Lunch
* 13.00 - 13.30 Live sessions Q&A
* 13.30 - 17.00 Exercises

'''Location'''

* NOTE: This edition of the course will be completely online

'''Profiles of Invited Speakers for Mini Symposium'''
* Clinical perspective: [https://research.ku.dk/search/?pure=en%2Fpersons%2F458748 MD, PhD, Clinical Associate Professor Marco Donia, Center for Cancer Immune Therapy (CCIT) and Unit for Experimental Cancer Treatment (EFEK), Herlev-Gentofte Hospital and University of Copenhagen]
* Molecular Biology perspective: [https://www.dtu.dk/service/telefonbog/person?id=102741&cpid=&tab=2&qt=dtupublicationquery PhD, Adjunkt Professor Sunil Kumar Saini, Section for Experimental and Translational Immunology, Department of Health Technology, Technical University of Denmark]
* Biomedical Industry perspective: upon confirmation.
* Bioinformatics Industry perspective: [https://www.vaccibody.com/management/ PhD, Head of Bioinformatics Monika Sekelja, Vaccibody A/S]

==2021 Course Schedule Overview==

{| class="wikitable" style="font-size:75%;"
|+ Teaching Day 1-8
!
! Monday Jan. 4th
! Tuesday Jan. 5th
! Wednesday Jan. 6th
! Thursday Jan. 7th
! Friday Jan. 8th
! Monday Jan. 11th
! Tuesday Jan. 12th
! Wednesday Jan. 13th
|-
! Topic
! Introduction and Basic Immunology
! T-Cell Epitopes
! Antigen Processing and Presentation, HLA Clustering, and Vaccine Design
! Protein Structure of B-/T-Cell Receptors and B-Cell Epitopes
! Immunopeptidomics, T-Cell Repertoires and the IEDB
! Antibody Humanization and T-Cell Interaction Models
! De-Immunization and Chimeric Antigen Receptor (CAR) Immunotherapy
! Mini-symposium on Immunoinformatics by Invited Speakers
|-
! 09.00 - 09.30
| [https://teaching.healthtech.dtu.dk/morten_teaching/27485.imm/presentations/Carol/Course_Introduction_2021.pdf Course Introduction] '''Live on Zoom''' Recording: [https://teaching.healthtech.dtu.dk/morten_teaching/27685.imm/recordings/22145_2021/Introduction_IB.mp4 MP4] [CB]
| Lecture: Prediction of MHC peptide binding Part 1 [MN]. Session materials: [https://teaching.healthtech.dtu.dk/morten_teaching/27685.imm/presentations/MHCbinding_2020_part1.pdf Slides [PDF]]. Recording: [https://teaching.healthtech.dtu.dk/morten_teaching/27685.imm/recordings/MHC_part1.mp4 [MP4]], Logo handout: [https://teaching.healthtech.dtu.dk/morten_teaching/27685.imm/presentations/Ex_Logo.pdf [PDF]], [https://teaching.healthtech.dtu.dk/morten_teaching/27685.imm/presentations/Ex_Logo_ans.pdf Answer Logo handout] Logo handout Recording [https://teaching.healthtech.dtu.dk/morten_teaching/27685.imm/recordings/Ex_Logo.mp4 [MP4]].
| Lecture: MHC motif deconvolution - Identifying sequence motifs in large scale ligand data sets [MN]. Session materials: [https://teaching.healthtech.dtu.dk/morten_teaching/27685.imm/presentations/MHCMotifDecon_2021.pdf Slides [PDF]]. Recording: [https://teaching.healthtech.dtu.dk/morten_teaching/27685.imm/recordings/MHCMotifDecon_2021.mp4 [MP4]].
| Lecture: [[Media:Antibody structure.pdf|TCR and BCR structure]]. Recording: [https://youtu.be/HP-zcAugLkk Antibody Modelling] [PM]
[https://youtu.be/8dzwdlKTUXI Solution]
| Lecture: [https://teaching.healthtech.dtu.dk/morten_teaching/27685.imm/presentations/Carol/Immunopeptidomics_2021.pdf Immunopeptidomics] '''Live on Zoom''' Recording: [https://teaching.healthtech.dtu.dk/morten_teaching/27685.imm/recordings/22145_2021/Immunopeptidomics_CB.mp4 MP4] [CB]
| Lecture: [https://teaching.healthtech.dtu.dk/22145/images/e/ec/Humanization_2021_notabhu_reduced.pdf Antibody Humanization] [https://youtu.be/WXMrdDSHA6M Video] [PM]
| Lecture: Protein Drug Deimmunization '''Live on Zoom''' [https://teaching.healthtech.dtu.dk/morten_teaching/27685.imm/deimmune_Presentation/2021_01_12_Deimmunization_22145.pdf pdf] [https://teaching.healthtech.dtu.dk/morten_teaching/27685.imm/deimmune_Presentation/2021_01_12_DeimmunePresentation.mp4 mp4] [BR]
| Talk 1: '''Cancer immunotherapy in the clinic.''' Marco Donia '''Live!''' [https://teaching.healthtech.dtu.dk/morten_teaching/27685.imm/recordings/22145_2021/Talk1_MarcoDonia.mp4 video]
|-
! 09.30 - 10.15
| [[Micro_Project_on_Basic_Immunology|Micro project group work]] '''Live on Zoom''' [CB]
| Lecture: Prediction of MHC peptide binding part 2 [MN]. Session materials: [https://teaching.healthtech.dtu.dk/morten_teaching/27685.imm/presentations/MHCbinding_2020_part2.pdf Slides [PDF]]. Recording: [https://teaching.healthtech.dtu.dk/morten_teaching/27685.imm/recordings/MHC_part2.mp4 [MP4]]. NN handout [https://teaching.healthtech.dtu.dk/morten_teaching/27685.imm/presentations/NN_handout.pdf [PDF]]. NN handout Recording [https://teaching.healthtech.dtu.dk/morten_teaching/27685.imm/recordings/Ex_NN.mp4 [MP4]].
| Lecture: What defines a T cell epitope? Is there any thing beyond MHC binding? [MN] Session materials: [https://teaching.healthtech.dtu.dk/morten_teaching/27685.imm/presentations/Processing_Tcell_2018.pdf Slides [PDF]]. Recording: [https://teaching.healthtech.dtu.dk/morten_teaching/27685.imm/recordings/Processing_Tcell_2018.mp4 [MP4]].
| Exercise: [[Antibody Structure Prediction and Analysis]] Recording: [https://youtu.be/5t7aUkXVuwk Exercise] [PM]
| Exercise files: [[File: Peptides-HD-DR2b.txt|Peptides]] [[File: Alleles-HD-DR2b.txt |Alleles_list]] Answers: [https://teaching.healthtech.dtu.dk/morten_teaching/27685.imm/presentations/Carol/Exercise_guidelines_answers.pdf Answers]'''Live on Zoom''' [CB]
| Exercise: [[Antibody Humanization]] [PM]
| Exercise: [[Protein Drug Deimmunization]] [BR]
| Talk 2: '''SARS-CoV-2 full genome profiling for T cell immunity and immunodominance in COVID-19 infection.''' Sunil Kumar Saini '''Live!''' [https://teaching.healthtech.dtu.dk/morten_teaching/27685.imm/recordings/22145_2021/Talk2_SunilSaini.mp4 video]
|-
! 10.15 - 10.30
! Break
! Break
! Break
! Break
! Break
! Break
! Break
! Break
|-
! 10.30 - 11.15
| [[Micro_Project_on_Basic_Immunology|Micro project group work]] '''Live on Zoom''' [CB]
| Lecture: Prediction of MHC peptide binding part 3 [MN]. Session materials: [https://teaching.healthtech.dtu.dk/morten_teaching/27685.imm/presentations/MHCbinding_2020_part3.pdf Slides [PDF]]. Recording: [https://teaching.healthtech.dtu.dk/morten_teaching/27685.imm/recordings/MHC_part3.mp4 [MP4]].
| Lecture: Selecting the one in a million. Strategies for selecting peptide subsets, and vaccine design [MN]. Session materials: [https://teaching.healthtech.dtu.dk/morten_teaching/27685.imm/presentations/Vaccine_design_2019.pdf Slides [PDF]]. Recording: [https://teaching.healthtech.dtu.dk/morten_teaching/27685.imm/recordings/Vaccine_design_2019.mp4 [MP4]].
| Lecture: [[Media:Linear epitope prediction.pdf|Linear ]] B-cell epitope prediction. Recording: [https://youtu.be/Ukk5XJfuh6k] [PM]
| Lecture: T-Cell Receptor Repertoires '''Live on Zoom''' [https://teaching.healthtech.dtu.dk/morten_teaching/27685.imm/presentations/Carol/20210108MV_Tcell_receptor_repertoires_updated.pdf Slides] Recording: [[https://teaching.healthtech.dtu.dk/morten_teaching/27685.imm/recordings/22145_2021/20210108MV_Tcell_receptor_repertoires.mp4 [MP4]] [MV]
| Lecture: Single cell technologies for T-cell epitopes [https://teaching.healthtech.dtu.dk/morten_teaching/27685.imm/presentations/Carol/single_cell_general.pdf Single Cell] and [https://teaching.healthtech.dtu.dk/morten_teaching/27685.imm/presentations/Carol/nettcr_project.pdf NetTCR Project] [https://teaching.healthtech.dtu.dk/morten_teaching/27685.imm/recordings/22145_2021/Single_cell.mp4 video]'''Live on Zoom''' [HP]
| Lecture: [http://teaching.healthtech.dtu.dk/36685/images/8/87/Deimmunisation.pptx.pdf Humanization and deimmunization for cancer T cell therapy molecules] [https://teaching.healthtech.dtu.dk/morten_teaching/27685.imm/recordings/22145_2021/Deimmunisation_CART-cells.mp4 video] [PM]
| Talk 3: '''The utilization of bioinformatics to guide drug design.''' Monika Sekelja '''Live!''' [https://teaching.healthtech.dtu.dk/morten_teaching/27685.imm/recordings/22145_2021/Talk3_MonikaSekelja.mp4 video]
|-
! 11.15 - 12.00
| [[Micro_Project_on_Basic_Immunology|Micro project group work]] '''Live on Zoom''' [CB]
| Lecture: [https://teaching.healthtech.dtu.dk/morten_teaching/ILRI_workshop/presentations/Performance_measure.pdf Performance measures] [MN]. Recording: [https://teaching.healthtech.dtu.dk/morten_teaching/22125/recordings/Performance_measure.mp4 [MP4]].
| Lecture: Selecting the one in a million. Strategies for selecting peptide subsets, and vaccine design [MN] cont.
| Lecture: [[Media:Conformational epitope prediction.pdf|Conformational ]] B-cell epitope prediction. Recording: [https://youtu.be/xg8Wf4rNsqw][PM]
| Lecture: The Immune Epitope Database & Tools '''Live on Zoom''' [https://teaching.healthtech.dtu.dk/morten_teaching/27685.imm/presentations/Carol/2021_01_08_IEDB.pdf PDF] [https://teaching.healthtech.dtu.dk/morten_teaching/27685.imm/recordings/2021_01_08_IEDB_Presentation.mp4 mp4] [BR]
| Lecture: [https://teaching.healthtech.dtu.dk/morten_teaching/27685.imm/presentations/Carol/netTCR_interactions_2021.pdf Modelling TCRpMHC interactions] [https://teaching.healthtech.dtu.dk/morten_teaching/27685.imm/recordings/22145_2021/NetTCR_video.mp4 video]'''Live on Zoom''' [AM]
| Lecture: [http://teaching.healthtech.dtu.dk/36685/images/8/87/Deimmunisation.pptx.pdf Humanization and deimmunization for cancer T cell therapy molecules] [PM]
| Talk 4: TBC Live!
|-
! 12.00 - 13.00
! Lunch Break
! Lunch Break
! Lunch Break
! Lunch Break
! Lunch Break
! Lunch Break
! Lunch Break
! Lunch Break
|-
! 13.00 - 13.30
| '''Live:''' Q&A Session [CB]
| '''Live:''' Quiz: [https://kursusquiz.dtu.dk/quiz/solochallenge/398/holding/571?lang=en MHC binding]. Q&A Session [MN]. Recordings: [https://teaching.healthtech.dtu.dk/morten_teaching/27685.imm//recordings/QA_2021-01-05_1.mp4 R1 [MP4]]. [https://teaching.healthtech.dtu.dk/morten_teaching/27685.imm//recordings/QA_2021-01-05_2.mp4 R2 [MP4]]. [https://teaching.healthtech.dtu.dk/morten_teaching/27685.imm//recordings/QA_2021-01-05_3.mp4 R3 [MP4]].
| '''Live:''' Exercise recap [MN]. Quiz: [https://kursusquiz.dtu.dk/quiz/solochallenge/400/holding/578?lang=en MHC processing, epitope discovery and vaccine design]. Q&A Session [MN]. Recordings: [https://teaching.healthtech.dtu.dk/morten_teaching/27685.imm//recordings/QA_2021-01-06.mp4 R1 [MP4]].
| '''Live:''' Exercise recap [MN] Recordings: [https://teaching.healthtech.dtu.dk/morten_teaching/27685.imm//recordings/QA_2021-01-07.mp4 R1 [MP4]].
| '''Live:''' Exercise recap Recordings: [https://teaching.healthtech.dtu.dk/morten_teaching/27685.imm//recordings/22145_2021/PM_live_recap_exercises_Ab_TCRs.mp4 [MP4]] [PM]
| '''Live:''' Exercise recap [https://teaching.healthtech.dtu.dk/morten_teaching/27685.imm/recordings/22145_2021/Live_exercise_recap_immunopeptidomics_IEDB_CB_BR.mp4 video] [CB] and [BR]
| '''Live:''' Exercise recap [https://teaching.healthtech.dtu.dk/morten_teaching/27685.imm/recordings/22145_2021/HP_exercise_recap_single_cell_netTCR.mp4 video] [HP]
| '''Live:''' Exercise recap [PM]
|-
! 13.30 - 17.00
| [[Micro_Project_on_Basic_Immunology|Micro project group work]] '''Live on Zoom''' [https://teaching.healthtech.dtu.dk/morten_teaching/27685.imm/recordings/22145_2021/Group_Presentations_day1part1.mp4 Presentations_part1] [https://teaching.healthtech.dtu.dk/morten_teaching/27685.imm/recordings/22145_2021/Group_Presentations_day1part2.mp4 Presentations_part2] [CB]
| Exercise:[https://teaching.healthtech.dtu.dk/morten_teaching/27685.imm/exercise_MHC_bind/exercise_2019.php Prediction of MHC:peptide binding using PSSM and ANN]
[https://teaching.healthtech.dtu.dk/morten_teaching/27685.imm/exercise_MHC_bind/exercise_2019_ans.php Answers: Prediction of MHC:peptide binding using PSSM and ANN]
| Exercise: [https://teaching.healthtech.dtu.dk/morten_teaching/27685.imm/exercise_HCVVaccine/exercise_HCVVaccine_2021.php Development of vaccines against HCV] [MN] [https://teaching.healthtech.dtu.dk/morten_teaching/27685.imm/exercise_HCVVaccine/exercise_HCVVaccine_2021_ans.php Answers]
| Exercise: [https://teaching.healthtech.dtu.dk/morten_teaching/27485.imm/epitope_2014.php B cell epitope predictions] [PM]
| Exercise: [https://teaching.healthtech.dtu.dk/22145/index.php/T-Cell_Receptor_Repertoires#Retrieve_and_Upload_Repertoire_data T-Cell Receptor Repertoires] [MV] [http://teaching.healthtech.dtu.dk/material/22145/ljess/repertoire_analysis.html Suggested answers] Exercise: [[IEDB]] [BR]
| Exercise: [[Single cell technologies for T-cell epitopes]] [HP]
| Exercise: [http://teaching.healthtech.dtu.dk/36685/index.php/Exercise_on_CAR_T-cell_humanisation_and_de-immunisation CAR T-cell humanisation and de-immunisation] [PM]
| '''Live on Zoom''' [https://teaching.healthtech.dtu.dk/morten_teaching/27685.imm/presentations/Carol/project_and_exam.pdf Introduction to project and exam] [CB]
|- style="vertical-align: top;" |
! Learning Resources
|
Required
* Paper: [https://onlinelibrary.wiley.com/doi/abs/10.1002/bies.201900200 Peptide Presentation to T Cells: Solving the Immunogenic Puzzle]
* Video: [https://www.youtube.com/watch?v=K09xzIQ8zsg Tumour immunology and immunotherapy]
* Video: [https://www.youtube.com/watch?v=vponeaNiewE Decoding cancer immunology: Hunting hidden tumours]
Optional
* Video: [https://www.youtube.com/watch?v=fSEFXl2XQpc Back to Basics]
|
Required
* Book: [[Media:Lund_et_al_immunological_bioinformatics_2005_chapter_3.pdf| Immuno. Bioinfo. Ch. 3]]
* Book: [[Media:Lund_et_al_immunological_bioinformatics_2005_chapter_4.pdf| Immuno. Bioinfo. Ch. 4]]
* Paper: [http://bioinformatics.oxfordjournals.org/cgi/reprint/23/24/3265 Modeling the adaptive immune system: predictions and simulations]
* Paper: [https://www.annualreviews.org/doi/pdf/10.1146/annurev-biodatasci-021920-100259 Immunoinformatics: Predicting Peptide–MHC Binding]
Optional
* Paper: [https://www.mcponline.org/content/18/12/2459.long NNAlign_MA; MHC Peptidome Deconvolution for Accurate MHC Binding Motif Characterization and Improved T-cell Epitope Predictions]
* Paper: [https://pubs.acs.org/doi/10.1021/acs.jproteome.9b00874 Improved Prediction of MHC II Antigen Presentation through Integration and Motif Deconvolution of Mass Spectrometry MHC Eluted Ligand Data]
|
Required
* Book: [[Media:Lund_et_al_immunological_bioinformatics_2005_chapter_13.pdf| Immuno. Bioinfo. Ch. 13]]
* Book: [[Media:Lund_et_al_immunological_bioinformatics_2005_chapter_14.pdf| Immuno. Bioinfo. Ch. 14]]
* Paper: [https://www.annualreviews.org/doi/10.1146/annurev-immunol-082119-124838 T Cell Epitope Predictions]
Optional
* Paper: [https://www.ncbi.nlm.nih.gov/pubmed/23097419 Simultaneous alignment and clustering of peptide data using a Gibbs sampling approach]
* Paper: [http://www.jimmunol.org/content/178/12/7890.long A Quantitative Analysis of the Variables Affecting the Repertoire of T Cell Specificities Recognized after Vaccinia Virus Infection]
* Paper: [https://www.ncbi.nlm.nih.gov/pubmed/24760079 Identification and HLA-tetramer-validation of human CD4+ and CD8+ T cell responses against HCMV proteins IE1 and IE2]
|
* [[Media:Immunological bioinformatics Quiz 1 2019.pdf|Mini Quiz]]
* [[Media:Pymol-edu-license-2021.txt|Pymol license]]

Required
* None
Optional
* Paper: [https://academic.oup.com/nar/article/3787843 BepiPred 2.0]
* Paper: [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531324/ B-cell epitope prediction]
* Video: [http://www.youtube.com/watch?v=Z36dUduOk1Y Simplified B-cell walkthrough] (Nice and easy understandable explanation of B-cells)
* Resource: [https://pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/ PDB 101: Introduction to PDB Data]
|

* Rstudio: [https://rstudio.com/products/rstudio/download/ Get it] [https://datascienceplus.com/introduction-to-rstudio/ Quick guide] [https://teaching.healthtech.dtu.dk/22145/index.php/Getting_started_with_RStudio_Cloud,_R_and_rmarkdown Getting started]

Required
* Video: [https://www.youtube.com/watch?v=Na-Zc-xWCLE Immunology wars: A billion antibodies]
* Video: [https://www.youtube.com/watch?v=JJmqt40Z3mM Antibody (BCR) and TCR Diversity]
* Video: [https://www.youtube.com/watch?v=h9mqsllg1Cs Antibody Somatic (VDJ) Recombination I]
* Video: [https://www.youtube.com/watch?v=_D2x-dhh6Pg Antibody Somatic (VDJ) Recombination II]
* Book: [https://cn.inside.dtu.dk/cnnet/filesharing/download/8df4dfc2-e023-43b8-a2cd-1a00e1e902bc Kuby Ch. 7: The Organization and Expression of Lymphocyte Receptor Genes]
* Paper: [https://www.ncbi.nlm.nih.gov/pubmed/25300482 The immune epitope database (IEDB) 3.0.]
Optional
* None
|
Required
* Paper: [https://www.biorxiv.org/content/early/2018/10/02/433706 NetTCR: sequence-based prediction of TCR binding to peptide-MHC complexes using convolutional neural networks]
* Paper: [https://www.nature.com/articles/nbt.4303 T cell receptor fingerprinting enables in-depth characterization of the interactions governing recognition of peptide–MHC complexes]
* Paper: [https://www.nature.com/articles/s41598-019-50932-4 TCRpMHCmodels: Structural modelling of TCR-pMHC class I complexes]
* Paper: [https://www.sciencedirect.com/science/article/pii/S0161589017306211 Identification of the cognate peptide-MHC target of T cell receptors using molecular modeling and force field scoring]
* Tech report: [http://teaching.healthtech.dtu.dk/material/22145/ljess/10x_AN047_IP_A_New_Way_of_Exploring_Immunity_Digital.pdf A New Way of Exploring Immunity – Linking Highly Multiplexed Antigen Recognition to Immune Repertoire and Phenotype]
Optional
* None
|
Required
* None
Optional
* Paper: [https://www.ncbi.nlm.nih.gov/pubmed/27322891 Design and engineering of deimmunized biotherapeutics]
|
|}

==Project Period and Exam==

=== Project ===

'''Wednesday January 13th - Wednesday January 20nd - Project Work'''

Please note the following (***time has been updated***):
* The deadline for uploading the final project Poster presentation (i.e. ''not'' a report) to [https://www.inside.dtu.dk/ DTU inside] will be '''Wednesday January 20nd at 11.59AM'''
* It is a prerequisite for the exam to complete this assignment and as such, ''failure to meet the deadline will result in a failed exam''
* Furthermore and very important - Each group member is responsible for ''all'' aspects of the group work and subsequent presentation

'''Groups and Projects 2021'''

* Groups will be preset based on educational diversity

* [https://cn.inside.dtu.dk/cnnet/filesharing/download/950b168e-0786-4b7e-85bd-1389e9a61869 The groups list for 2021]

=== Exam Schedule ===

* General exam format will consist on 2 parts ([https://kurser.dtu.dk/course/22145 course learning objectives]):

Oral presentation of the poster project ~10 minutes for all group presentation + 5 minutes for questions (15 minutes total)
Date: January 21st 2021 (specific times per group to be announced)

Written exam ~20 questions 2hs, all conducted online on DTU Inside
Date: January 22st 2021

* Individual grades will be given after the finalization of the course

22145 Immunological Bioinformatics Course Programme January 2021

2024-03-20T10:28:03Z

WikiSysop: Created page with "= COURSE PLAN FOR 2021 = ==EXAM== The pdf with the exam will be uploaded here on Friday January 22nd, 13 - 15hs  '''Guidelines''' * The exam will be made available at the wiki at 13.00hs. Upload a '''pdf''' with your answers '''no later than 15.00hs on DTU inside''' written exam assignment. * You must connect at Zoom 5 minutes before the exam, and have the '''camera turned ON during the whole exam'''. Failing to meet this requireme..."

= COURSE PLAN FOR 2021 =

==EXAM==

The pdf with the exam will be uploaded here on Friday January 22nd, 13 - 15hs



'''Guidelines'''

* The exam will be made available at the wiki at 13.00hs. Upload a '''pdf''' with your answers '''no later than 15.00hs on DTU inside''' written exam assignment.
* You must connect at Zoom 5 minutes before the exam, and have the '''camera turned ON during the whole exam'''. Failing to meet this requirement will invalidate the exam.
* This is an '''individual exam'''. Remember sharing or copying answers is not allowed and will be severely punished according to DTU rules and code-of-honor.

==Information for Course Participants==

'''Course Format'''
* NEWS! Due to new restrictions on Covid19 this course will be completely conducted online and all classes will be recorded and uploaded
* Due to group work on some classes, it will be mandatory that you are connected and work online on the allocated time for those
* This will be needed for the entire first day, the question and answer sessions, and the final exam
* Classes will be a mixture of lectures, group work and individual exercises
* Most of the group work will consist of computer exercises, where students are required to use their laptops
* General Question and Answer will be live and uploaded after the session
* Specif Question and Answers for exercise-lectures will be held on Piazza, where you need to create an user
* All learning resources will be available through DTU inside or this site
* Expected time usage: [https://www.dtu.dk/english/Education/Course-base 1 ECTS point equals approx. 28 hours], this translates to an expected time usage of ~10 hours/day for a 5 ECTS 3-week course

'''Course Resources'''
* [http://teaching.healthtech.dtu.dk/22145/index.php/22145_-_Immunological_Bioinformatics Official course website]
* [https://kurser.dtu.dk/course/22145 Official course description]
* [https://dtudk.zoom.us/meeting/register/u5Ypc-iupjIuGtzs8eF0RlM5xijlcFdwQaQq ZOOM link for live classes(registration with DTU mail needed)]
* [https://piazza.com/dtu.dk/fall2020/22145 Piazza link for Q&A on exercises]
* IMPORTANT: Please note, that the below course programme can be subject to changes or updates. Make sure to reload the page, to get the newest version of the programme.

'''Course Teachers'''
* [CB] [https://www.dtu.dk/english/service/phonebook/Person?id=142840&cpid=263035&tab=2&qt=dtupublicationquery Carolina Barra]
* [PM] [https://www.dtu.dk/english/service/phonebook/person?id=34983&cpid=257128&tab=2&qt=dtupublicationquery Paolo Marcatili]
* [MN] [https://www.dtu.dk/english/service/phonebook/person?id=5973&cpid=214020&tab=1&qt=dtupublicationquery Morten Nielsen]
* [BR] [https://www.dtu.dk/english/service/phonebook/person?id=104623&cpid=257289&tab=3&qt=dtuprojectquery Birkir Reynisson]
* [HP] [https://www.dtu.dk/service/telefonbog/person?id=88645&cpid=262443&tab=3&qt=dtuprojectquery Helle Rus Povlsen]
* [MV] [https://www.dtu.dk/english/service/phonebook/Person?id=129355&cpid=257376&tab=2&qt=dtuprojectquery Milena Vujovic]
* [AM] [https://www.dtu.dk/english/service/phonebook/Person?id=124312&cpid=274573&tab=3&qt=dtuprojectquery Alessandro Montemurro]

'''General Daily Schedule'''

* 09.00 - 12.00 Lectures
* 12.00 - 13.00 Lunch
* 13.00 - 13.30 Live sessions Q&A
* 13.30 - 17.00 Exercises

'''Location'''

* NOTE: This edition of the course will be completely online

'''Profiles of Invited Speakers for Mini Symposium'''
* Clinical perspective: [https://research.ku.dk/search/?pure=en%2Fpersons%2F458748 MD, PhD, Clinical Associate Professor Marco Donia, Center for Cancer Immune Therapy (CCIT) and Unit for Experimental Cancer Treatment (EFEK), Herlev-Gentofte Hospital and University of Copenhagen]
* Molecular Biology perspective: [https://www.dtu.dk/service/telefonbog/person?id=102741&cpid=&tab=2&qt=dtupublicationquery PhD, Adjunkt Professor Sunil Kumar Saini, Section for Experimental and Translational Immunology, Department of Health Technology, Technical University of Denmark]
* Biomedical Industry perspective: upon confirmation.
* Bioinformatics Industry perspective: [https://www.vaccibody.com/management/ PhD, Head of Bioinformatics Monika Sekelja, Vaccibody A/S]

==2021 Course Schedule Overview==

{| class="wikitable" style="font-size:75%;"
|+ Teaching Day 1-8
!
! Monday Jan. 4th
! Tuesday Jan. 5th
! Wednesday Jan. 6th
! Thursday Jan. 7th
! Friday Jan. 8th
! Monday Jan. 11th
! Tuesday Jan. 12th
! Wednesday Jan. 13th
|-
! Topic
! Introduction and Basic Immunology
! T-Cell Epitopes
! Antigen Processing and Presentation, HLA Clustering, and Vaccine Design
! Protein Structure of B-/T-Cell Receptors and B-Cell Epitopes
! Immunopeptidomics, T-Cell Repertoires and the IEDB
! Antibody Humanization and T-Cell Interaction Models
! De-Immunization and Chimeric Antigen Receptor (CAR) Immunotherapy
! Mini-symposium on Immunoinformatics by Invited Speakers
|-
! 09.00 - 09.30
| [http://www.cbs.dtu.dk/courses/27685.imm/presentations/Carol/Course_Introduction_2021.pdf Course Introduction] '''Live on Zoom''' Recording: [http://www.cbs.dtu.dk/courses/27685.imm/recordings/22145_2021/Introduction_IB.mp4 MP4] [CB]
| Lecture: Prediction of MHC peptide binding Part 1 [MN]. Session materials: [http://www.cbs.dtu.dk/courses/27685.imm/presentations/MHCbinding_2020_part1.pdf Slides [PDF]]. Recording: [http://www.cbs.dtu.dk/courses/27685.imm/recordings/MHC_part1.mp4 [MP4]], Logo handout: [http://www.cbs.dtu.dk/courses/27685.imm/presentations/Ex_Logo.pdf [PDF]], [http://www.cbs.dtu.dk/courses/27685.imm/presentations/Ex_Logo_ans.pdf Answer Logo handout] Logo handout Recording [http://www.cbs.dtu.dk/courses/27685.imm/recordings/Ex_Logo.mp4 [MP4]].
| Lecture: MHC motif deconvolution - Identifying sequence motifs in large scale ligand data sets [MN]. Session materials: [http://www.cbs.dtu.dk/courses/27685.imm/presentations/MHCMotifDecon_2021.pdf Slides [PDF]]. Recording: [http://www.cbs.dtu.dk/courses/27685.imm/recordings/MHCMotifDecon_2021.mp4 [MP4]].
| Lecture: [[Media:Antibody structure.pdf|TCR and BCR structure]]. Recording: [https://youtu.be/HP-zcAugLkk Antibody Modelling] [PM]
[https://youtu.be/8dzwdlKTUXI Solution]
| Lecture: [http://www.cbs.dtu.dk/courses/27685.imm/presentations/Carol/Immunopeptidomics_2021.pdf Immunopeptidomics] '''Live on Zoom''' Recording: [http://www.cbs.dtu.dk/courses/27685.imm/recordings/22145_2021/Immunopeptidomics_CB.mp4 MP4] [CB]
| Lecture: [https://teaching.healthtech.dtu.dk/22145/images/e/ec/Humanization_2021_notabhu_reduced.pdf Antibody Humanization] [https://youtu.be/WXMrdDSHA6M Video] [PM]
| Lecture: Protein Drug Deimmunization '''Live on Zoom''' [http://www.cbs.dtu.dk/courses/27685.imm/deimmune_Presentation/2021_01_12_Deimmunization_22145.pdf pdf] [http://www.cbs.dtu.dk/courses/27685.imm/deimmune_Presentation/2021_01_12_DeimmunePresentation.mp4 mp4] [BR]
| Talk 1: '''Cancer immunotherapy in the clinic.''' Marco Donia '''Live!''' [http://www.cbs.dtu.dk/courses/27685.imm/recordings/22145_2021/Talk1_MarcoDonia.mp4 video]
|-
! 09.30 - 10.15
| [[Micro_Project_on_Basic_Immunology|Micro project group work]] '''Live on Zoom''' [CB]
| Lecture: Prediction of MHC peptide binding part 2 [MN]. Session materials: [http://www.cbs.dtu.dk/courses/27685.imm/presentations/MHCbinding_2020_part2.pdf Slides [PDF]]. Recording: [http://www.cbs.dtu.dk/courses/27685.imm/recordings/MHC_part2.mp4 [MP4]]. NN handout [http://www.cbs.dtu.dk/courses/27685.imm/presentations/NN_handout.pdf [PDF]]. NN handout Recording [http://www.cbs.dtu.dk/courses/27685.imm/recordings/Ex_NN.mp4 [MP4]].
| Lecture: What defines a T cell epitope? Is there any thing beyond MHC binding? [MN] Session materials: [http://www.cbs.dtu.dk/courses/27685.imm/presentations/Processing_Tcell_2018.pdf Slides [PDF]]. Recording: [http://www.cbs.dtu.dk/courses/27685.imm/recordings/Processing_Tcell_2018.mp4 [MP4]].
| Exercise: [[Antibody Structure Prediction and Analysis]] Recording: [https://youtu.be/5t7aUkXVuwk Exercise] [PM]
| Exercise files: [[File: Peptides-HD-DR2b.txt|Peptides]] [[File: Alleles-HD-DR2b.txt |Alleles_list]] Answers: [http://www.cbs.dtu.dk/courses/27685.imm/presentations/Carol/Exercise_guidelines_answers.pdf Answers]'''Live on Zoom''' [CB]
| Exercise: [[Antibody Humanization]] [PM]
| Exercise: [[Protein Drug Deimmunization]] [BR]
| Talk 2: '''SARS-CoV-2 full genome profiling for T cell immunity and immunodominance in COVID-19 infection.''' Sunil Kumar Saini '''Live!''' [http://www.cbs.dtu.dk/courses/27685.imm/recordings/22145_2021/Talk2_SunilSaini.mp4 video]
|-
! 10.15 - 10.30
! Break
! Break
! Break
! Break
! Break
! Break
! Break
! Break
|-
! 10.30 - 11.15
| [[Micro_Project_on_Basic_Immunology|Micro project group work]] '''Live on Zoom''' [CB]
| Lecture: Prediction of MHC peptide binding part 3 [MN]. Session materials: [http://www.cbs.dtu.dk/courses/27685.imm/presentations/MHCbinding_2020_part3.pdf Slides [PDF]]. Recording: [http://www.cbs.dtu.dk/courses/27685.imm/recordings/MHC_part3.mp4 [MP4]].
| Lecture: Selecting the one in a million. Strategies for selecting peptide subsets, and vaccine design [MN]. Session materials: [http://www.cbs.dtu.dk/courses/27685.imm/presentations/Vaccine_design_2019.pdf Slides [PDF]]. Recording: [http://www.cbs.dtu.dk/courses/27685.imm/recordings/Vaccine_design_2019.mp4 [MP4]].
| Lecture: [[Media:Linear epitope prediction.pdf|Linear ]] B-cell epitope prediction. Recording: [https://youtu.be/Ukk5XJfuh6k] [PM]
| Lecture: T-Cell Receptor Repertoires '''Live on Zoom''' [http://www.cbs.dtu.dk/courses/27685.imm/presentations/Carol/20210108MV_Tcell_receptor_repertoires_updated.pdf Slides] Recording: [[http://www.cbs.dtu.dk/courses/27685.imm/recordings/22145_2021/20210108MV_Tcell_receptor_repertoires.mp4 [MP4]] [MV]
| Lecture: Single cell technologies for T-cell epitopes [http://www.cbs.dtu.dk/courses/27685.imm/presentations/Carol/single_cell_general.pdf Single Cell] and [http://www.cbs.dtu.dk/courses/27685.imm/presentations/Carol/nettcr_project.pdf NetTCR Project] [http://www.cbs.dtu.dk/courses/27685.imm/recordings/22145_2021/Single_cell.mp4 video]'''Live on Zoom''' [HP]
| Lecture: [http://teaching.healthtech.dtu.dk/36685/images/8/87/Deimmunisation.pptx.pdf Humanization and deimmunization for cancer T cell therapy molecules] [http://www.cbs.dtu.dk/courses/27685.imm/recordings/22145_2021/Deimmunisation_CART-cells.mp4 video] [PM]
| Talk 3: '''The utilization of bioinformatics to guide drug design.''' Monika Sekelja '''Live!''' [http://www.cbs.dtu.dk/courses/27685.imm/recordings/22145_2021/Talk3_MonikaSekelja.mp4 video]
|-
! 11.15 - 12.00
| [[Micro_Project_on_Basic_Immunology|Micro project group work]] '''Live on Zoom''' [CB]
| Lecture: [http://www.cbs.dtu.dk/courses/ILRI_workshop/presentations/Performance_measure.pdf Performance measures] [MN]. Recording: [http://www.cbs.dtu.dk/courses/22125/recordings/Performance_measure.mp4 [MP4]].
| Lecture: Selecting the one in a million. Strategies for selecting peptide subsets, and vaccine design [MN] cont.
| Lecture: [[Media:Conformational epitope prediction.pdf|Conformational ]] B-cell epitope prediction. Recording: [https://youtu.be/xg8Wf4rNsqw][PM]
| Lecture: The Immune Epitope Database & Tools '''Live on Zoom''' [http://www.cbs.dtu.dk/courses/27685.imm/presentations/Carol/2021_01_08_IEDB.pdf PDF] [http://www.cbs.dtu.dk/courses/27685.imm/recordings/2021_01_08_IEDB_Presentation.mp4 mp4] [BR]
| Lecture: [http://www.cbs.dtu.dk/courses/27685.imm/presentations/Carol/netTCR_interactions_2021.pdf Modelling TCRpMHC interactions] [http://www.cbs.dtu.dk/courses/27685.imm/recordings/22145_2021/NetTCR_video.mp4 video]'''Live on Zoom''' [AM]
| Lecture: [http://teaching.healthtech.dtu.dk/36685/images/8/87/Deimmunisation.pptx.pdf Humanization and deimmunization for cancer T cell therapy molecules] [PM]
| Talk 4: TBC Live!
|-
! 12.00 - 13.00
! Lunch Break
! Lunch Break
! Lunch Break
! Lunch Break
! Lunch Break
! Lunch Break
! Lunch Break
! Lunch Break
|-
! 13.00 - 13.30
| '''Live:''' Q&A Session [CB]
| '''Live:''' Quiz: [https://kursusquiz.dtu.dk/quiz/solochallenge/398/holding/571?lang=en MHC binding]. Q&A Session [MN]. Recordings: [http://www.cbs.dtu.dk/courses/27685.imm//recordings/QA_2021-01-05_1.mp4 R1 [MP4]]. [http://www.cbs.dtu.dk/courses/27685.imm//recordings/QA_2021-01-05_2.mp4 R2 [MP4]]. [http://www.cbs.dtu.dk/courses/27685.imm//recordings/QA_2021-01-05_3.mp4 R3 [MP4]].
| '''Live:''' Exercise recap [MN]. Quiz: [https://kursusquiz.dtu.dk/quiz/solochallenge/400/holding/578?lang=en MHC processing, epitope discovery and vaccine design]. Q&A Session [MN]. Recordings: [http://www.cbs.dtu.dk/courses/27685.imm//recordings/QA_2021-01-06.mp4 R1 [MP4]].
| '''Live:''' Exercise recap [MN] Recordings: [http://www.cbs.dtu.dk/courses/27685.imm//recordings/QA_2021-01-07.mp4 R1 [MP4]].
| '''Live:''' Exercise recap Recordings: [http://www.cbs.dtu.dk/courses/27685.imm//recordings/22145_2021/PM_live_recap_exercises_Ab_TCRs.mp4 [MP4]] [PM]
| '''Live:''' Exercise recap [http://www.cbs.dtu.dk/courses/27685.imm/recordings/22145_2021/Live_exercise_recap_immunopeptidomics_IEDB_CB_BR.mp4 video] [CB] and [BR]
| '''Live:''' Exercise recap [http://www.cbs.dtu.dk/courses/27685.imm/recordings/22145_2021/HP_exercise_recap_single_cell_netTCR.mp4 video] [HP]
| '''Live:''' Exercise recap [PM]
|-
! 13.30 - 17.00
| [[Micro_Project_on_Basic_Immunology|Micro project group work]] '''Live on Zoom''' [http://www.cbs.dtu.dk/courses/27685.imm/recordings/22145_2021/Group_Presentations_day1part1.mp4 Presentations_part1] [http://www.cbs.dtu.dk/courses/27685.imm/recordings/22145_2021/Group_Presentations_day1part2.mp4 Presentations_part2] [CB]
| Exercise:[http://www.cbs.dtu.dk/courses/27685.imm/exercise_MHC_bind/exercise_2019.php Prediction of MHC:peptide binding using PSSM and ANN]
[http://www.cbs.dtu.dk/courses/27685.imm/exercise_MHC_bind/exercise_2019_ans.php Answers: Prediction of MHC:peptide binding using PSSM and ANN]
| Exercise: [http://www.cbs.dtu.dk/courses/27685.imm/exercise_HCVVaccine/exercise_HCVVaccine_2021.php Development of vaccines against HCV] [MN] [http://www.cbs.dtu.dk/courses/27685.imm/exercise_HCVVaccine/exercise_HCVVaccine_2021_ans.php Answers]
| Exercise: [http://www.cbs.dtu.dk/courses/27485.imm/epitope_2014.php B cell epitope predictions] [PM]
| Exercise: [https://teaching.healthtech.dtu.dk/22145/index.php/T-Cell_Receptor_Repertoires#Retrieve_and_Upload_Repertoire_data T-Cell Receptor Repertoires] [MV] [http://teaching.healthtech.dtu.dk/material/22145/ljess/repertoire_analysis.html Suggested answers] Exercise: [[IEDB]] [BR]
| Exercise: [[Single cell technologies for T-cell epitopes]] [HP]
| Exercise: [http://teaching.healthtech.dtu.dk/36685/index.php/Exercise_on_CAR_T-cell_humanisation_and_de-immunisation CAR T-cell humanisation and de-immunisation] [PM]
| '''Live on Zoom''' [http://www.cbs.dtu.dk/courses/27685.imm/presentations/Carol/project_and_exam.pdf Introduction to project and exam] [CB]
|- style="vertical-align: top;" |
! Learning Resources
|
Required
* Paper: [https://onlinelibrary.wiley.com/doi/abs/10.1002/bies.201900200 Peptide Presentation to T Cells: Solving the Immunogenic Puzzle]
* Video: [https://www.youtube.com/watch?v=K09xzIQ8zsg Tumour immunology and immunotherapy]
* Video: [https://www.youtube.com/watch?v=vponeaNiewE Decoding cancer immunology: Hunting hidden tumours]
Optional
* Video: [https://www.youtube.com/watch?v=fSEFXl2XQpc Back to Basics]
|
Required
* Book: [[Media:Lund_et_al_immunological_bioinformatics_2005_chapter_3.pdf| Immuno. Bioinfo. Ch. 3]]
* Book: [[Media:Lund_et_al_immunological_bioinformatics_2005_chapter_4.pdf| Immuno. Bioinfo. Ch. 4]]
* Paper: [http://bioinformatics.oxfordjournals.org/cgi/reprint/23/24/3265 Modeling the adaptive immune system: predictions and simulations]
* Paper: [https://www.annualreviews.org/doi/pdf/10.1146/annurev-biodatasci-021920-100259 Immunoinformatics: Predicting Peptide–MHC Binding]
Optional
* Paper: [https://www.mcponline.org/content/18/12/2459.long NNAlign_MA; MHC Peptidome Deconvolution for Accurate MHC Binding Motif Characterization and Improved T-cell Epitope Predictions]
* Paper: [https://pubs.acs.org/doi/10.1021/acs.jproteome.9b00874 Improved Prediction of MHC II Antigen Presentation through Integration and Motif Deconvolution of Mass Spectrometry MHC Eluted Ligand Data]
|
Required
* Book: [[Media:Lund_et_al_immunological_bioinformatics_2005_chapter_13.pdf| Immuno. Bioinfo. Ch. 13]]
* Book: [[Media:Lund_et_al_immunological_bioinformatics_2005_chapter_14.pdf| Immuno. Bioinfo. Ch. 14]]
* Paper: [https://www.annualreviews.org/doi/10.1146/annurev-immunol-082119-124838 T Cell Epitope Predictions]
Optional
* Paper: [https://www.ncbi.nlm.nih.gov/pubmed/23097419 Simultaneous alignment and clustering of peptide data using a Gibbs sampling approach]
* Paper: [http://www.jimmunol.org/content/178/12/7890.long A Quantitative Analysis of the Variables Affecting the Repertoire of T Cell Specificities Recognized after Vaccinia Virus Infection]
* Paper: [https://www.ncbi.nlm.nih.gov/pubmed/24760079 Identification and HLA-tetramer-validation of human CD4+ and CD8+ T cell responses against HCMV proteins IE1 and IE2]
|
* [[Media:Immunological bioinformatics Quiz 1 2019.pdf|Mini Quiz]]
* [[Media:Pymol-edu-license-2021.txt|Pymol license]]

Required
* None
Optional
* Paper: [https://academic.oup.com/nar/article/3787843 BepiPred 2.0]
* Paper: [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531324/ B-cell epitope prediction]
* Video: [http://www.youtube.com/watch?v=Z36dUduOk1Y Simplified B-cell walkthrough] (Nice and easy understandable explanation of B-cells)
* Resource: [https://pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/ PDB 101: Introduction to PDB Data]
|

* Rstudio: [https://rstudio.com/products/rstudio/download/ Get it] [https://datascienceplus.com/introduction-to-rstudio/ Quick guide] [https://teaching.healthtech.dtu.dk/22145/index.php/Getting_started_with_RStudio_Cloud,_R_and_rmarkdown Getting started]

Required
* Video: [https://www.youtube.com/watch?v=Na-Zc-xWCLE Immunology wars: A billion antibodies]
* Video: [https://www.youtube.com/watch?v=JJmqt40Z3mM Antibody (BCR) and TCR Diversity]
* Video: [https://www.youtube.com/watch?v=h9mqsllg1Cs Antibody Somatic (VDJ) Recombination I]
* Video: [https://www.youtube.com/watch?v=_D2x-dhh6Pg Antibody Somatic (VDJ) Recombination II]
* Book: [https://cn.inside.dtu.dk/cnnet/filesharing/download/8df4dfc2-e023-43b8-a2cd-1a00e1e902bc Kuby Ch. 7: The Organization and Expression of Lymphocyte Receptor Genes]
* Paper: [https://www.ncbi.nlm.nih.gov/pubmed/25300482 The immune epitope database (IEDB) 3.0.]
Optional
* None
|
Required
* Paper: [https://www.biorxiv.org/content/early/2018/10/02/433706 NetTCR: sequence-based prediction of TCR binding to peptide-MHC complexes using convolutional neural networks]
* Paper: [https://www.nature.com/articles/nbt.4303 T cell receptor fingerprinting enables in-depth characterization of the interactions governing recognition of peptide–MHC complexes]
* Paper: [https://www.nature.com/articles/s41598-019-50932-4 TCRpMHCmodels: Structural modelling of TCR-pMHC class I complexes]
* Paper: [https://www.sciencedirect.com/science/article/pii/S0161589017306211 Identification of the cognate peptide-MHC target of T cell receptors using molecular modeling and force field scoring]
* Tech report: [http://teaching.healthtech.dtu.dk/material/22145/ljess/10x_AN047_IP_A_New_Way_of_Exploring_Immunity_Digital.pdf A New Way of Exploring Immunity – Linking Highly Multiplexed Antigen Recognition to Immune Repertoire and Phenotype]
Optional
* None
|
Required
* None
Optional
* Paper: [https://www.ncbi.nlm.nih.gov/pubmed/27322891 Design and engineering of deimmunized biotherapeutics]
|
|}

==Project Period and Exam==

=== Project ===

'''Wednesday January 13th - Wednesday January 20nd - Project Work'''

Please note the following (***time has been updated***):
* The deadline for uploading the final project Poster presentation (i.e. ''not'' a report) to [https://www.inside.dtu.dk/ DTU inside] will be '''Wednesday January 20nd at 11.59AM'''
* It is a prerequisite for the exam to complete this assignment and as such, ''failure to meet the deadline will result in a failed exam''
* Furthermore and very important - Each group member is responsible for ''all'' aspects of the group work and subsequent presentation

'''Groups and Projects 2021'''

* Groups will be preset based on educational diversity

* [https://cn.inside.dtu.dk/cnnet/filesharing/download/950b168e-0786-4b7e-85bd-1389e9a61869 The groups list for 2021]

=== Exam Schedule ===

* General exam format will consist on 2 parts ([https://kurser.dtu.dk/course/22145 course learning objectives]):

Oral presentation of the poster project ~10 minutes for all group presentation + 5 minutes for questions (15 minutes total)
Date: January 21st 2021 (specific times per group to be announced)

Written exam ~20 questions 2hs, all conducted online on DTU Inside
Date: January 22st 2021

* Individual grades will be given after the finalization of the course

22145 - Immunological Bioinformatics

2024-03-20T10:24:06Z

WikiSysop:

[[File:immunoinformatics_venn_diagram_small.png|right]]

'''Course Programme'''



'''About'''

* '''Course responsible'''

[https://www.dtu.dk/person/carolina-barra-quaglia?id=142840&entity=profile Carolina Barra Quaglia] — Associate professor, course responsible.

[https://www.dtu.dk/person/morten-nielsen?id=5973&entity=profile Morten Nielsen] — Professor, course responsible.

* '''Schedule''': Every year in the fall 13-weeks period, see [https://www.dtu.dk/english/education/student-guide/studying-at-dtu/academic-calendar DTU Academic Calendar]
* '''Location''': See this year's course program above
* '''Exam''': Poster presentation + written exam
* '''Textbook''': No textbook. The learning resources will be stated in the course program
* '''Course Description''': For full course description, please see the [https://kurser.dtu.dk/course/22145 DTU Course Base]

'''General course objectives'''

* The course has an applied focus centered around the suite of prediction servers from the [https://www.healthtech.dtu.dk/Forskning/DIGITAL-HEALTH-AND-BIOLOGICAL-MODELLING/Section-Bioinformatics/Group-Immunoinformatics-and-Machine-Learning IML group]
* Theory and application of computational methods in context with the prediction of immune responses, moreover:
** The involvement of TCR and BCR and MHC class I/II in inducing an immune response
** The structural and genetic characteristics of the TCR and BCR and MHC class I/II and corresponding epitopes
** Computational methods for modeling TCR and BCR and MHC class I/II and respective epitope interactions
** Application and challenges of the above in disease context, i.e. vaccinology of infectious diseases and cancer
* General engineering competencies are included in the form of theory in context with concrete application and group-based project work, where the students are responsible for planning, designing, implementing, and communicating a project.

'''Essential Software and Resources'''

* Students should bring their own laptop with internet access to class
* Students should [http://pymol.org/2/#download install PyMol] on their laptops. The PyMOL Education License file will be supplied during class. An introduction to PyMOL can be found '''in a place that does not exist and should be updated'''.
* Also, students should [https://rstudio.com/products/rstudio/download install Rstudio] on their laptops. Rstudio is free and does not require any license. An introduction can be found [https://datascienceplus.com/introduction-to-rstudio/ here]
* The course focuses on computational methods for proteins and peptides in an immunological context, so it is recommended, that students have a grasp of the biochemical profile of each of the [http://www.mathiasbader.de/studium/biology/index.php?lng=en the 20 proteinogenic amino acids]
* A brief introduction to the ''Immunoinformatics and Machine Learning'' group can be found here [https://www.healthtech.dtu.dk/Forskning/DIGITAL-HEALTH-AND-BIOLOGICAL-MODELLING/Section-Bioinformatics/Group-Immunoinformatics-and-Machine-Learning here]

'''Questions?'''

Please read the [https://kurser.dtu.dk/course/22145 detailed course description], for any questions not covered by this, please contact [https://kurser.dtu.dk/course/22145 course responsible]

'''Previous versions of the course'''
* [[22145_Immunological_Bioinformatics_Course_Programme_January_2021|January 2021]]
* [[22145_Immunological_Bioinformatics_Course_Programme_January_2020|January 2020]]
* [[36685_Immunological_Bioinformatics_Course_Program_January_2019|January 2019]]
* [[36685_Immunological_Bioinformatics_Course_Program_January_2018|January 2018]]
* [[27685_Course_programme_2017|June 2017]]

File:Immunoinformatics venn diagram small.png

2024-03-20T10:22:59Z

WikiSysop:

22145 - Immunological Bioinformatics

2024-03-20T10:18:48Z

WikiSysop: Created page with "right '''Course Programme'''  '''About''' * '''Course responsible''' [https://www.dtu.dk/person/carolina-barra-quaglia?id=142840&entity=profile Carolina Barra Quaglia] — Associate professor, course responsible. [https://www.dtu.dk/person/morten-nielsen?id=5973&entity=profile Morten Nielsen] — Professor, course responsib..."

[[File:immunoinformatics_venn_diagram_small.png|right]]

'''Course Programme'''



'''About'''

* '''Course responsible'''

[https://www.dtu.dk/person/carolina-barra-quaglia?id=142840&entity=profile Carolina Barra Quaglia] — Associate professor, course responsible.

[https://www.dtu.dk/person/morten-nielsen?id=5973&entity=profile Morten Nielsen] — Professor, course responsible.

* '''Schedule''': Every year in the fall 13-weeks period, see [https://www.dtu.dk/english/education/student-guide/studying-at-dtu/academic-calendar DTU Academic Calendar]
* '''Location''': See this year's course program above
* '''Exam''': Poster presentation + written exam
* '''Textbook''': No textbook. The learning resources will be stated in the course program
* '''Course Description''': For full course description, please see the [https://kurser.dtu.dk/course/22145 DTU Course Base]

'''General course objectives'''

* The course has an applied focus centered around the suite of prediction servers from the [https://www.healthtech.dtu.dk/Forskning/DIGITAL-HEALTH-AND-BIOLOGICAL-MODELLING/Section-Bioinformatics/Group-Immunoinformatics-and-Machine-Learning IML group]
* Theory and application of computational methods in context with the prediction of immune responses, moreover:
** The involvement of TCR and BCR and MHC class I/II in inducing an immune response
** The structural and genetic characteristics of the TCR and BCR and MHC class I/II and corresponding epitopes
** Computational methods for modeling TCR and BCR and MHC class I/II and respective epitope interactions
** Application and challenges of the above in disease context, i.e. vaccinology of infectious diseases and cancer
* General engineering competencies are included in the form of theory in context with concrete application and group-based project work, where the students are responsible for planning, designing, implementing, and communicating a project.

'''Essential Software and Resources'''

* Students should bring their own laptop with internet access to class
* Students should [http://pymol.org/2/#download install PyMol] on their laptops. The PyMOL Education License file will be supplied during class. An introduction to PyMOL can be found [http://wiki.bio.dtu.dk/teaching/index.php/PyMOL here]
* Also, students should [https://rstudio.com/products/rstudio/download install Rstudio] on their laptops. Rstudio is free and does not require any license. An introduction can be found [https://datascienceplus.com/introduction-to-rstudio/ here]
* The course focuses on computational methods for proteins and peptides in an immunological context, so it is recommended, that students have a grasp of the biochemical profile of each of the [http://www.mathiasbader.de/studium/biology/index.php?lng=en the 20 proteinogenic amino acids]
* A brief introduction to the ''Immunoinformatics and Machine Learning'' group can be found here [https://www.healthtech.dtu.dk/Forskning/DIGITAL-HEALTH-AND-BIOLOGICAL-MODELLING/Section-Bioinformatics/Group-Immunoinformatics-and-Machine-Learning here]

'''Questions?'''

Please read the [https://kurser.dtu.dk/course/22145 detailed course description], for any questions not covered by this, please contact [https://kurser.dtu.dk/course/22145 course responsible]

'''Previous versions of the course'''
* [[22145_Immunological_Bioinformatics_Course_Programme_January_2021|January 2021]]
* [[22145_Immunological_Bioinformatics_Course_Programme_January_2020|January 2020]]
* [[36685_Immunological_Bioinformatics_Course_Program_January_2019|January 2019]]
* [[36685_Immunological_Bioinformatics_Course_Program_January_2018|January 2018]]
* [[27685_Course_programme_2017|June 2017]]

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