Immunogenomics course

Fall 2019 - Bioinformatics Institute - Saint Petersburg, Russia

Lectures:

  • Dates: November 1st, 2019 – December 12th, 2019
  • Thursdays, 8:00 am PST / 7:00 pm Saint Petersburg

Course stuff:

  • Yana Safonova, remote instructor
  • Contact: safonova.yana at gmail.com

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 / English TBA. Slides are in English, videos are in Russian.

Schedule

(a subject of change)

Week 1. November 1st

  • History of immunology
  • Introduction to modern immunology
  • Generation of antibody repertoire - I
  • [slides] [video]

Week 2. November 7th

  • Generation of antibody repertoire - II
  • Clonal development of antibodies
  • Antigen recognition
  • B cell development
  • [slides] [video]

Week 3. November 14th

  • Repertoire sequencing (Rep-seq) data
  • Protocols of Rep-seq data
  • Unique molecular identifiers (UMIs) in Rep-seq data
  • [slides] [video]

Week 4. November 21st

  • Preprocessing Rep-seq data
  • Repertoire construction problem and its quality assessment
  • Clonal analysis of antibody repertoires - I.
  • [slides] [video]
  • HW #1: Basic analysis of immunosequencing data. Deadline: Nov 29th.

Week 5. November 28th

  • Clonal analysis of antibody repertoires - II.
  • Reconstructing clonal lineages.
  • Mutability of immunoglobulins and structural regions.
  • [slides] [video]
  • HW #2. Clonal reconstruction of antibody repertoires. Deadline: Dec 6th.

Week 6. December 5th

  • The role of SHMs.
  • Definitions of CDRs.
  • Design of antibody drugs.
  • Antibodies and their analogs in various vertebrate species.
  • [slides] [video]
  • HW #3: Analysis of crystallized Ab-Ag complexes. Deadline: Dec 13th.

Week 7. December 9th

  • Population analysis of immunoglobulin genes.
  • Assembly of immunoglobulin loci.
  • De novo inference of immunoglobulin genes using Rep-seq data.
  • Application of Rep-seq data to biomedical studies.
  • [slides] [video]