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Immunological Bioinformatics - #27685

Information for participants

THIS PROGRAMME IS STILL PRELIMINARY AND MIGHT CHANGE BEFORE THE ACTUAL DATE!


GENERAL DAILY SCHEDULE
Lectures will be from 9 - 12 am,
Lunch from 12 - 13, and,
Exercises from 13 - 17 pm.

PLACE: DTU Building 204 room 243 (2nd floor)
LITTERATURE: All litterature will be available through CampusNet



PROGRAMS AND TOOLS
  • Flash 6 or better
    For following the lectures you need a browser with Flash 6 or better. Flash is freeware and can be downloaded by clicking on the link above
  • UNIX - Beginner's Guide to UNIX is available on-line.

  • For doing some of the exercises on our server you must be able to connect to the server using Secure Shell (SSH) and tunnel X through the connection.
    See informations on prerequisites on:
    Tools for SSH and X11


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

LITTERATURE: All litterature will be available through CampusNet


O Monday, June 10
Introduction, immunology brush up, and Unix
9.00 - 9.30
Introduction to the course.
Ole Lund, CBS, DTU Systems Biology.
9:30-10:15
Basic mechanisms of immune defense
Susanne Brix Pedersen, CBS, DTU Systems Biology.
10.15 - 10.45
Coffee Break
10.45 - 12.00
Basic mechanisms of immune defense continued
12.00 - 13.00
lunch break
13.00 - 13.30
Computer setup
13.30 - 14.30
Introduction to Immunological Bioinformatics.
Ole Lund, CBS, DTU Systems Biology.
14.30 - 16.00
Exercises: Unix and awk, a crash course
Ole Lund, CBS, DTU Systems Biology.

O Tuesday, June 11
Vaccines, antibodies, and epitopes
9.00 - 9.30
Yesterday's exercise round up
9.30 - 10.15
Adjuvants
Prof. Peter Heegaard, DTU-Vet
10.45 - 11.15
Antibodies and TCRs, development and selection.
Ole Lund, CBS, DTU Systems Biology.
11.15 - 12.00
lunch break
12.00 - 16.00
Molecular evolution
Molecular Evolution.     Handout exercise
Anders Gorm Pedersen, CBS, DTU Systems Biology.

O Wednesday, June 12
Vaccines, antibodies, and epitopes
9.00 - 12.00
Analysis of immunoglobolin gene rearrangements.
Ole Lund, CBS, DTU Systems Biology.
12.00 - 13.00
Lunch
13.00 - 14.00
Development of a subunit vaccine against TB
Prof. T. Mark Doherty, Coordinator, Research and Strategy, Infectious Disease Immunology, Statens Serum Institute
12.00 - 16.00
Exercises:
 
Databases and web resources in Immunological bioinformatics.
Ole Lund, CBS, DTU Systems Biology.
 

O Thursday June 13
B cell epitope predictions
9.00 - 9.30
Exercise round up
Ole Lund, Center for Biological Sequence Analysis, DTU Systems Biology.
9.30 - 10.00
Prediction of B cell epitopes
Jens Kringelum, Center for Biological Sequence Analysis, DTU Systems Biology.
10.00 - 12.00
Exercise: B cell epitope predictions.
Jens Kringelum, Center for Biological Sequence Analysis, DTU Systems Biology.
12.00 - 13.00
Lunch Break
13.00 - 13.15
Exercise round up
13.15 - 14.00
Peptide microarray-driven analysis of immune targets
Christian Skjødt Hansen, CBS, Systems Biology
14.00 - 14.30
Diagnostic biomarker discovery for parasitic diseases using high-density peptide microarrays
Santiago J Carmona, Institute for Biotechnology Research, University of San Martin, Buenos Aires, Argentina
14.45-16.00
SigniSite: Identification of residue-level genotype-phenotype correlations in protein multiple sequence alignments
Leon Jessen, Center for Biological Sequence Analysis, DTU Systems Biology.
Additional links
The SigniSite-2.0 Server
Abstract
Know Your Amino Acids

O Friday, June 14
Next generation sequencing, FACS data analysis
9.00 - 9.30
DNA sequencing
Mette Voldby Larsen, CBS, Department of Systems Biology, DTU
9.30 - 10.00
Exercise: Assembling NGS data
Mette Voldby Larsen, Center for Biological Sequence Analysis, DTU Systems Biology.
10.00 - 10.30
From DNA to protein
Mette Voldby Larsen, CBS, Department of Systems Biology, DTU
10.30 - 11.00
Exercise: Predicting genes using Prodigal
Mette Voldby Larsen, Center for Biological Sequence Analysis, DTU Systems Biology.
11.00 - 11.30
PathogenFinder
Salvatore Cosentino, CBS, Department of Systems Biology, DTU
11.30 - 12.00
Exercise: PathogenFinder
Mette Voldby Larsen, Center for Biological Sequence Analysis, DTU Systems Biology.
12.00 - 13.00
Lunch Break
13.00 - 14.00
Automated analysis of FACS data
Juliet Wairimu Fredriksen, PhD student, CBS, Department of Systems Biology, DTU
14.00 - 16.00
Exercise: Automated FACS data analysis

O Monday, June 17
T-cell Epitopes
9.00 - 9.30
Exercise from Friday round up
9.30 - 12.00
Prediction of MHC peptide binding using data mining techniques (PSSM's and ANN)
MHC polymorphism, sequences, and population data.
Rational epitope discovery using immunoinformatics
A little on MHC class II binding
Coffee Break at some point around 10.30
PDF.
NN handout.
Morten Nielsen, CBS, DTU Systems Biology.
11.15 - 12.00
Pan-specific MHC binding predictions (NetMHCcons and NetMHCIIpan-3.0)
Edita Karosiene
12.00 - 13.00
Lunch Break
13.00 - 16.00
Exercise:
Prediction of MHC:peptide binding using PSSM and ANN.
Morten Nielsen, CBS, DTU Systems Biology.

O Tuesday, June 18
Supertypes, HLA clustering, and vaccine design

9.00 - 9.30
Exercise round up
9.30 - 10.00
Performance measures
Supertypes and functional clustering of MHC molecules
Morten, CBS, DTU Systems Biology.
10.00 - 10.30
What defines a T cel epitope? Is there any thing beyond MHC binding?
10.30 - 10.45
Coffee Break
10.45 - 11.25
Selecting the one in a million. Strategies for selecting peptide subsets, and vaccine design
Morten Nielsen, CBS, DTU Systems Biology.
11.25 - 12.00
Identifying multiple sequence motifs in large scale peptide data sets
12.00 - 13.00
Lunch Break
13.00 - 16.00
Exercises: Development of vaccines against HCV.
Morten Nielsen, CBS, DTU Systems Biology.

O Wednesday, June 19 - June 25
9.00 - 17.00
Project work
Introduction to project work
Poster Guide

O Wednesday, June 26
9.00 - 17.00
Poster presentations


O Thursday, June 27
9.00 - 17.00
Exam.

O Friday, June 28
9.00 - 17.00
Exam.


For more information, please contact Ole Lund






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