22145 Immunological Bioinformatics Course Programme January 2021 - Revision history

WikiSysop: /* 2021 Course Schedule Overview */

2024-03-20T14:49:26Z

2021 Course Schedule Overview

WikiSysop: /* 2021 Course Schedule Overview */

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2021 Course Schedule Overview

← Older revision		Revision as of 16:39, 20 March 2024
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	\| 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]].		\| 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: [[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 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: [[Antibody Humanization]] [PM]
	\| Exercise: <!--[[Exercise:_Protein_drug_de-immunization\|Protein drug de-immunization]]-->[[Protein Drug Deimmunization]] [BR]		\| Exercise: <!--[[Exercise:_Protein_drug_de-immunization\|Protein drug de-immunization]]-->[[Protein Drug Deimmunization]] [BR]
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	* [https://teaching.healthtech.dtu.dk/material/22145/pdf/Immunological_bioinformatics_Quiz_1_2019.pdf Mini Quiz]		* [https://teaching.healthtech.dtu.dk/material/22145/pdf/Immunological_bioinformatics_Quiz_1_2019.pdf Mini Quiz]
	* [~~[Media~~:Pymol-edu-license-2021.txt\|Pymol license]]		* [https://teaching.healthtech.dtu.dk/material/22145/pdf/Pymol-edu-license-2021.txt Pymol license]

	Required		Required

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2021 Course Schedule Overview

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2021 Course Schedule Overview

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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..."

2024-03-20T10:28:03Z

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..."

New page

= 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

← Older revision		Revision as of 16:49, 20 March 2024
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	\| 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: 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: 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]		\| 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]		\| 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]
	\|-		\|-
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	\| 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: 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://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]		\| 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!		\| Talk 4: TBC Live!
	\|-		\|-
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	\| 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/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: [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: [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: [[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]		\| 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]		\| '''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;" \|		\|- style="vertical-align: top;" \|
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	* Paper: [https://www.nature.com/articles/s41598-019-50932-4 TCRpMHCmodels: Structural modelling of TCR-pMHC class I 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]		* 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]		* 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		Optional
	* None		* None

← Older revision		Revision as of 16:36, 20 March 2024
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	\| 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: 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: 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]		\| 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]		[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: [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]
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	\| 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: 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: 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: [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: 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: 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]
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	\| 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: [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: 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: [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: 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://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]
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	\|		\|
	Required		Required
	* Book: [~~[Media~~: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_3.pdf Immuno. Bioinfo. Ch. 3]
	* Book: [~~[Media~~:Lund_et_al_immunological_bioinformatics_2005_chapter_4.pdf\| Immuno. Bioinfo. Ch. 4]]		* 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: [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]		* Paper: [https://www.annualreviews.org/doi/pdf/10.1146/annurev-biodatasci-021920-100259 Immunoinformatics: Predicting Peptide–MHC Binding]
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	\|		\|
	Required		Required
	* Book: [~~[Media~~: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_13.pdf Immuno. Bioinfo. Ch. 13]
	* Book: [~~[Media~~:Lund_et_al_immunological_bioinformatics_2005_chapter_14.pdf\| Immuno. Bioinfo. Ch. 14]]		* 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]		* Paper: [https://www.annualreviews.org/doi/10.1146/annurev-immunol-082119-124838 T Cell Epitope Predictions]
	Optional		Optional
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	* 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]		* 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]]		* [https://teaching.healthtech.dtu.dk/material/22145/pdf/Immunological_bioinformatics_Quiz_1_2019.pdf Mini Quiz]
	* [[Media:Pymol-edu-license-2021.txt\|Pymol license]]		* [[Media:Pymol-edu-license-2021.txt\|Pymol license]]