View source for 22145 Immunological Bioinformatics Course Programme January 2020

==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