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..."

2024-03-20T14:15:39Z

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..."

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=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!

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'''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

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== 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.]] 
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 

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

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== Friday, June 2 ==

''Immunological target identification''

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# '''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]

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'''Functional annotation of protein sequences'''

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

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== Tuesday, June 6==
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''B- and T-cell receptors genetics and structure''

BACKGROUND TEXTS: antibody repertoire, 
[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]

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] 

Paolo Marcatili, CBS, DTU Systems Biology.

12.00 - 13.00: ''Lunch Break''

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

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

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== Wednesday, June 7==
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''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]] 
[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]. 
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] 

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

== Thursday June 8==
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''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]. 

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] 
Exercise - [http://www.cbs.dtu.dk/courses/27685.imm/exercise_MHC_bind/exercise_2017.php Prediction of MHC:peptide binding using PSSM and ANN]. 
[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]. 
Morten Nielsen, Department of Bio and Health Informatics.

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== Friday, June 9==
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''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] 

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] 
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.] 
[http://www.cbs.dtu.dk/courses/27685.imm/exercise_HCVVaccine/answers.pdf Answers] 
Morten Nielsen, Department of Bio and Health Informatics.

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== Monday, June 12==
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9.00 - 9.20: Question and round up from last week 
[http://www.cbs.dtu.dk/courses/27685.imm/presentations/Questions_for_Immunological_bioinformatics_MHC_TCR.pdf Quiz ] 

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

10.05 - 10.20: ''Coffee Break''

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

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]]

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== Tuesday, June 13==

''Cancer immunology''

9.00 - 12.00 Seminars: 

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 

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

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

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

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

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==Wednesday and Thursday, June 21-22==
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9.00 - 17.00: exams

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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]

27685 Course programme 2017 - Revision history