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 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]