Immunogenomics course

Fall 2020 - Bioinformatics Institute - Saint Petersburg, Russia

Lectures:

  • Dates: Oct 7th, 2020 – Dec 12th, 2020

  • Thu, 8:00 am PST / 7:00 pm Saint Petersburg

Course stuff:

  • Yana Safonova, remote instructor

  • Anastasia Vinogradova, assistant

Syllabus

Immunology is a field of biology studying defensive mechanisms of living organisms. Emergence of sequencing data has revolutionized the field of modern biology and especially immunology. One of the results of this revolution is an ability to scan adaptive immune repertoires presenting one of unique individual features of the organism.

This course is an attempt to summarize the results of immunosequencing studies published during past ten years. In this course, we will study biological basics of immunology and immunogenomics, formulate main computational problems arising in the field, and discuss state-of-the-art algorithms for their solution. Students will complete a number of homework assignments involving analysis of real sequencing data and interpretation of the results.

Prerequisites to the course:

  • Python or any other programming language

  • Confident work with command line

  • Basic knowledge of algorithms

  • Basic knowledge of English

The detailed syllabus: Russian TBA / English TBA. Slides are in English, videos are in Russian.

Schedule

(a subject of change)

Week 1. October 8th

  • Introduction to the course

  • History of immunology

  • Introduction to modern immunology

  • Generation of antibody repertoire - I

  • [slides]

Week 2. October 22nd

  • Generation of antibody repertoire - II

  • Antigen recognition

  • B cell development

  • [slides]

Week 3. October 29th

  • Repertoire sequencing (Rep-Seq) data

  • Processing Rep-Seq data

  • [slides]

  • Homework #1: computing basic characteristics of antibody repertoires

Week 4. November 5th

  • Various approaches to error-correction of antibody repertoires

  • Clonal representation of antibody repertoires

  • [slides]

Week 5. November 12th

  • Reconstruction of clonal lineages

  • Efficient algorithms for pairwise comparison of sequences

  • [slides]

  • Homework #2: clonal reconstruction of antibody repertoires

Week 6. November 19th

  • Reconstruction of clonal antibody trees

  • Definitions of CDRs and FRs

  • [slides]

Week 7. November 26th

  • Applications of clonal analysis to biomedical applications

  • Population and QTL analyses of antibody repertoires

  • [slides]

  • Homework #3: eQTL analysis of antibody repertoires

Week 8. December 3rd

  • The role of IGHV alleles in Ab responses

  • Finding novel variants of IG genes

  • Assembly of IG loci vs de novo inference of IG genes using Rep-Seq data

  • [slides]

Week 9. December 11th

  • Types of QTLs of antibody repertoires

  • Types of vertebrate antibodies

  • Studying antibody response to SARS-CoV-2

  • Chain pairing & single cell Rep-seq data; allelic inclusion

  • [slides]