View source for 36685 Immunological Bioinformatics Course Program January 2019

=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=

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== 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)

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== 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