https://teaching.healthtech.dtu.dk/22145/index.php?action=history&feed=atom&title=36685_Immunological_Bioinformatics_Course_Program_January_2018
36685 Immunological Bioinformatics Course Program January 2018 - Revision history
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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..."
2024-03-20T14:15:17Z
<p>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..."</p>
<p><b>New page</b></p><div><br />
=Information for Course Attendees=<br />
<br />
The official course site can be [http://teaching.healthtech.dtu.dk/36685/index.php/36685_-_Immunological_Bioinformatics found here]<br />
<br />
'''General Daily Schedule'''<br />
<br />
* 09.00 - 12.00 Lectures<br />
* 12.00 - 13.00 Lunch<br />
* 13.00 - 17.00 Exercises<br />
<br />
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.<br />
<br />
'''Location'''<br />
<br />
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].<br />
<br />
'''Other'''<br />
<br />
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!<br />
<br />
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.<br />
<br />
=Course Program=<br />
<br />
<br />
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== Tuesday, January 2nd - Introduction, Immunology Brush-up and Databases ==<br />
----<br />
<br />
'''Reading list'''<br />
<br />
* [http://www.bioinformatics.dtu.dk/english/Research_new/Health-informatics/Immunoinformatics-and-machine-learning Introduction to the Immunoinformatics and Machine Learning Group]<br />
* [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245432/ Introduction to Immunology]<br />
<br />
'''Schedule'''<br />
<br />
09.00 - 09.30 [[Media:Week_01_day_01_Introduction.pdf|Introduction to the course]], Leon Eyrich Jessen<br />
<br />
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<br />
<br />
10.15 - 10.30 ''Coffee Break''<br />
<br />
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<br />
<br />
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<br />
<br />
12.00 - 13.00 ''Lunch break''<br />
<br />
13.00 - 13.50 Group Formation and short quiz on immunology<br />
<br />
14:00 - 16.00 Exercise: [[Databases and web resources in Immunological Bioinformatics]]<br />
<br />
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<br />
== Wednesday, January 3rd - Bacterial Pathogenicity, Virulence and Phylogeny ==<br />
----<br />
<br />
'''Reading list'''<br />
<br />
* [https://cn.inside.dtu.dk/cnnet/filesharing/download/2766d4f0-5421-4221-9d2c-d456ca611de1 CGE tool box], read the sections on pathogenFinder, resFinder and virulenceFinder<br />
<br />
'''Schedule'''<br />
<br />
09:00 - 09:15 Recap: Yesterdays exercises, Leon Eyrich Jessen<br />
<br />
09:15 - 09:45 Lecture: [[Media:week_01_day_02_session_01_Ahrenfeldt_01.pdf|PathogenFinder]], Johanne Ahrenfeldt<br />
<br />
09:45 - 10:00 ''Coffee Break''<br />
<br />
10:00 - 11:00 Exercise: [http://wiki.bio.dtu.dk/teaching/index.php/PathogenFinder PathogenFinder], Johanne Ahrenfeldt<br />
<br />
11:15 - 12:00 Lecture: [[Media:week_01_day_02_session_01_Ahrenfeldt_02.pdf|VirulenceFinder]], Johanne Ahrenfeldt<br />
<br />
12:00 - 13:00 ''Lunch break''<br />
<br />
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<br />
<br />
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<br />
<br />
15:00 - 16:00 Lecture: Bacterial Phylogeny (slides [[Media:WGS_phylogeny_Johanne_01.pdf|1]], [[Media:WGS_phylogeny_Johanne_02.pdf|2]]), Johanne Ahrenfeldt<br />
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----<br />
<br />
== Thursday, January 4th - B- and T-cell Receptors Genetics and Structure ==<br />
----<br />
<br />
'''Reading list'''<br />
<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]<br />
<br />
'''Schedule'''<br />
<br />
09:00 - 09:15 Recap: Yesterdays exercises, Leon Eyrich Jessen<br />
<br />
09:15 - 10:00 Lecture: [[Media:Maturation.pdf|TCR and BCR maturation]], Leon Eyrich Jessen<br />
<br />
10:00 - 10:15 ''Coffee Break''<br />
<br />
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<br />
<br />
12:00 - 13:00 ''Lunch Break''<br />
<br />
13:00 - 14:00 Lecture: [[Media:Antibody structure.pdf|TCR and BCR structure]], Kamilla Kjærgaard Jensen<br />
<br />
14:00 - 16:00 Exercise: [http://www.cbs.dtu.dk/courses/27485.imm/antibody_modeling.php Antibody Structure Prediction and Analysis], Kamilla Kjærgaard Jensen<br />
<br />
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<br />
== Friday, January 5th - B Cell Epitope Predictions ==<br />
----<br />
<br />
'''Reading list'''<br />
<br />
* Paper: [https://academic.oup.com/nar/article/3787843 BepiPred 2.0]<br />
* Paper: [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531324/ B-cell epitope prediction]<br />
* Video: [http://www.youtube.com/watch?v=Z36dUduOk1Y Simplified B-cell walkthrough] (Nice and easy understandable explanation of B-cells)<br />
* Resource: [https://pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/ PDB 101: Introduction to PDB Data]<br />
* 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]<br />
<br />
'''Schedule'''<br />
<br />
09:00 - 09:15 Recap: Yesterdays exercises, Kamilla Kjærgaard Jensen<br />
<br />
09:15 - 10:00 Lecture: [[Media:Homology-modeling-intro.pdf|Homology Modeling to Predict Antigen Structure]], Kamilla Kjærgaard Jensen<br />
<br />
10:00 - 10:15 ''Coffee Break''<br />
<br />
10:15 - 12:00 Exercise: [[Media:Homology-modeling-exercise.pdf|Homology Modeling to Predict Antigen Structure]], Kamilla Kjærgaard Jensen<br />
<br />
12:00 - 13:00 ''Lunch Break''<br />
<br />
13:00 - 13:30 Lecture: [[Media:Linear epitope prediction.pdf|Linear B cell epitope prediction]], Martin Closter Jespersen<br />
<br />
13:30 - 14:00 Lecture: [[Media:Conformational epitope prediction.pdf|Conformational B cell epitope prediction]], Martin Closter Jespersen<br />
<br />
14:00 - 15:00 Exercise: [http://www.cbs.dtu.dk/courses/27485.imm/epitope_2014.php B cell epitope predictions], Martin Closter Jespersen<br />
<br />
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<br />
<br />
15:30 - 16:00 Exercise: [[signisite_exercise|Using SigniSite to identify resistance mutations]], Leon Eyrich Jessen<br />
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<br />
== Monday January 8th - T-cell Epitopes == <br />
----<br />
<br />
'''Reading list'''<br />
<br />
* [[Media:Lund_et_al_immunological_bioinformatics_2005_chapter_3.pdf| Immunological Bioinformatics Chapter 3]]<br />
* [[Media:Lund_et_al_immunological_bioinformatics_2005_chapter_4.pdf| Immunological Bioinformatics Chapter 4]]<br />
* Paper: [http://bioinformatics.oxfordjournals.org/cgi/reprint/23/24/3265 Modeling the adaptive immune system: predictions and simulations]<br />
<!--* [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] --><br />
* Paper: [http://www3.interscience.wiley.com/cgi-bin/fulltext/123476680/PDFSTART Major histocompatibility complex class I binding predictions as a tool in epitope discovery]<br />
* Paper: [http://www3.interscience.wiley.com/cgi-bin/fulltext/123349058/PDFSTART MHC Class II epitope predictive algorithms]. <br />
<br />
'''Schedule'''<br />
<br />
09:00 - 09:30 Recap: Yesterdays exercises, Leon Eyrich Jessen<br />
<br />
09:30 - 10:15 Prediction of MHC peptide binding using data mining techniques (PSSM's and ANN), Morten Nielsen<br />
<br />
10:15 - 10:30 ''Coffee Break''<br />
<br />
10:30 - 11:15 Rational epitope discovery using immunoinformatics, Morten Nielsen<br />
<br />
11:15 - 12:00 A little on MHC class II binding, Morten Nielsen<br />
<br />
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], <br />
<!--[http://www.cbs.dtu.dk/courses/27685.imm/presentations/Ex_Logo_ans.pdf Answer Logo handout].--><br />
[http://www.cbs.dtu.dk/courses/27685.imm/presentations/NN_handout.pdf NN handout].<br />
<br />
12:00 - 13:00: ''Lunch Break''<br />
<br />
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_2018.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.<br />
<br />
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== Tuesday, January 9th - Antigen Processing and Presentation, Supertypes, HLA Clustering, and Vaccine Design ==<br />
----<br />
<br />
'''Reading list'''<br />
<br />
* [[Media:Lund_et_al_immunological_bioinformatics_2005_chapter_13.pdf|Chapter 13]]<br />
* [[Media:Lund_et_al_immunological_bioinformatics_2005_chapter_14.pdf|Chapter 14]]<br />
* [https://www.ncbi.nlm.nih.gov/pubmed/23097419 Simultaneous alignment and clustering of peptide data using a Gibbs sampling approach]<br />
* 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]<br />
<!-- * Optional: [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] --><br />
* 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]<br />
<br />
'''Schedule'''<br />
<br />
09:00 - 09:30 Exercise round up, Morten Nielsen<br />
<br />
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] <br />
<br />
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<br />
<br />
10:30 - 10:45 ''Coffee Break''<br />
<br />
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 <br />
<br />
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<br />
<br />
12:00 - 13:00 ''Lunch Break''<br />
<br />
13:00 - 16:00 Exercises: [http://www.cbs.dtu.dk/courses/27685.imm/exercise_HCVVaccine/exercise_HCVVaccine_2018.php Development of vaccines against HCV], <br />
<!--[http://www.cbs.dtu.dk/courses/27685.imm/exercise_HCVVaccine/answers.pdf Answers] --><br />
Morten Nielsen<br />
<br />
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== Wednesday, January 10th - Chimeric Antigen Receptor (CAR) Immunotherapy ==<br />
----<br />
<br />
'''Reading list'''<br />
<br />
* Paper: [https://link.springer.com/article/10.1007%2Fs13238-017-0411-9 Increasing the safety and efficacy of chimeric antigen receptor T cell therapy]<br />
* Article: [https://www.the-scientist.com/?articles.view/articleNo/42462/title/The-CAR-T-Cell-Race The CAR T-Cell Race]<br />
<br />
'''Scedule'''<br />
<br />
09:00 - 09:15 Recap: Yesterdays exercises, Morten Nielsen<br />
<br />
09:15 - 10:00 Lecture: [http://www.cbs.dtu.dk/~pmar/humanization.pdf Antibody Humanization], Paolo Marcatili<br />
<br />
10:00 - 10:30 ''Coffee Break''<br />
<br />
10:30 - 12:00 Exercise: [http://www.cbs.dtu.dk/courses/27685.imm/humanization_exercise.php Antibody Humanization], Paolo Marcatili<br />
<br />
12:00 - 13:00 ''Lunch Break''<br />
<br />
13:00 - 14:00 Lecture: [[Media:Deimmunisation.pptx.pdf | Humanization and deimmunazation for cancer T cell therapy molecules]], Paolo Marcatili<br />
<br />
14:00 - 16:00 Exercise: [[Exercise on CAR T-cell humanisation and de-immunisation|CAR T-cell humanisation and de-immunisation]], Paolo Marcatili<br />
<br />
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----<br />
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== Thursday, January 11th - Seminar on Cancer Immunotherapy by Invited Speakers ==<br />
----<br />
<br />
'''Scedule'''<br />
<br />
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]<br />
<br />
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]<br />
<br />
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]]<br />
<br />
12:00 - 13:00 ''Lunch Break''<br />
<br />
13:00 - 14:00 [[Media:intro_to_projects_2018.pdf|Introduction to project work and exam]], Leon Eyrich Jessen<br />
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== Friday, January 12th - Thursday January 18th - Project Work ==<br />
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09.00 - 17.00: Group project work<br />
<br />
'''Groups and projects 2018'''<br />
<br />
* G01 - Line, Solveig and Monica: ''"Peptide Vaccine Design against Epstein-Barr Virus for Prevention of Nasopharyngeal Cancer"''<br />
* G02 - Mikael, Jacob and Kathrine: ''"Winter is coming - a bioinformatic approach to prepare for the next influenza virus"''<br />
* G03 - Sandra, Esteban, Narasimha and Taner: ''"Zika virus vaccine for Brazilian Population"''<br />
* G04 - Signe, Julie, Ina and Aimilia: ''"Identifying target epitopes for designing a vaccine against Acinetobacter baumannii"''<br />
* G05 - Christian, Mikkel and Frank: ''"HIV vaccine development for sub-saharian Africans"''<br />
* G06 - Keith, Nadia and Jeppe: ''"EViVa – Vaccine for EBV"''<br />
* G07 - Sofie, Natasja and Ulla: ''"Zika-virus Vaccine Development"''<br />
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== Friday, January 19th - Exams ==<br />
----<br />
08:00 - 16:00 Exam day, Morten Nielsen and Leon Eyrich Jessen<br />
<br />
'''Exam schedule'''<br />
<br />
''Group 01''<br />
<br />
* 07:55 - 08:00 G01 - Setup<br />
* 08:00 - 08:15 G01 - Presentation<br />
* 08:15 - 08:25 Line<br />
* 08:25 - 08:35 Solveig<br />
* 08:35 - 08:45 Monica<br />
* 08:45 - 08:50 Grading<br />
<br />
''Group 05''<br />
<br />
* 08:55 - 09:00 G05 - Setup<br />
* 09:00 - 09:15 G05 - Presentation<br />
* 09:15 - 09:25 Christian<br />
* 09:25 - 09:35 Mikkel<br />
* 09:35 - 09:45 Frank<br />
* 09:45 - 09:50 Grading<br />
<br />
''Group 04''<br />
<br />
* 09:55 - 10:00 G04 - Setup<br />
* 10:00 - 10:15 G04 - Presentation<br />
* 10:15 - 10:25 Signe<br />
* 10:25 - 10:35 Julie<br />
* 10:35 - 10:45 Ina<br />
* 10:45 - 10:55 Aimilia<br />
* 10:55 - 11:00 Grading<br />
<br />
''Group 03''<br />
<br />
* 11:05 - 11:10 G03 - Setup<br />
* 11:10 - 11:25 G03 - Presentation<br />
* 11:25 - 11:35 Sandra<br />
* 11:35 - 11:45 Esteban<br />
* 11:45 - 11:55 Narasimha<br />
* 11:55 - 12:05 Taner<br />
* 12:05 - 12:10 Grading<br />
<br />
'''12:10 - 12:55 Lunch'''<br />
<br />
''Group 02''<br />
<br />
* 12:55 - 13:00 G02 - Setup<br />
* 13:00 - 13:15 G02 - Presentation<br />
* 13:15 - 13:25 Mikael<br />
* 13:25 - 13:35 Jacob<br />
* 13:35 - 13:45 Kathrine<br />
* 13:45 - 13:50 Grading<br />
<br />
''Group 06''<br />
<br />
* 13:55 - 14:00 G06 - Setup<br />
* 14:00 - 14:15 G06 - Presentation<br />
* 14:15 - 14:25 Keith<br />
* 14:25 - 14:35 Nadia<br />
* 14:35 - 14:45 Jeppe<br />
* 14:45 - 14:50 Grading<br />
<br />
''Group 07''<br />
<br />
* 14:55 - 15:00 G07 - Setup<br />
* 15:00 - 15:15 G07 - Presentation<br />
* 15:15 - 15:25 Sofie<br />
* 15:25 - 15:35 Natasja<br />
* 15:35 - 15:45 Ulla<br />
* 15:45 - 15:50 Grading</div>
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