261-5100-00L Computational Biomedicine (Autumn 2021)

Semester Autumn Semester 2021
Lecturers Gunnar Rätsch; Valentina Boeva
Periodicity yearly course
Language of instruction English

The course critically reviews central problems in Biomedicine and discusses the technical foundations and solutions for these problems.

Over the past years, rapid technological advancements have transformed classical disciplines such as biology and medicine into fields of apllied data science. While the sheer amount of the collected data often makes computational approaches inevitable for analysis, it is the domain specific structure and close relation to research and clinic, that call for accurate, robust and efficient algorithms. In this course we will critically review central problems in Biomedicine and will discuss the technical foundations and solutions for these problems.

The course will consist of three topic clusters that will cover different aspects of data science problems in Biomedicine:

1) String algorithms for the efficient representation, search, comparison, composition and compression of large sets of strings, mostly originating from DNA or RNA Sequencing. This includes genome assembly, efficient index data structures for strings and graphs, alignment techniques as well as quantitative approaches.
2) Statistical models and algorithms for the assessment and functional analysis of individual genomic variations. this includes the identification of variants, prediction of functional effects, imputation and integration problems as well as the association with clinical phenotypes.
3) Models for organization and representation of large scale biomedical data. This includes ontolgy concepts, biomedical databases, sequence annotation and data compression.

Prerequisites / Notice
Data Structures & Algorithms, Introduction to Machine Learning, Statistics/Probability, Programming in Python, Unix Command Line.

Teaching Material

Lectures and Tutorials will be held fully virtual. Tuesdays 10-12 and 13-14 respectively.
The course will be given fully online via Zoom. Password can be found on Moodle.
Questions and group formation for projects will take place on Moodle.
Project development and submission will be done on Gitlab.

Course Overview

Date Topic Course Material
21.09.2021 Lecture: Introduction to the topic and patient genomics Lecture Slides 01 Lecture Video 01
Exercise: Organization and presentation of projects Tutorial Slides 01 Tutorial Video 01
28.09.2021 Lecture: String algorithms, indexing and search Lecture Slides 02 Lecture Video 02
Exercise: Tutorial String algorithms, indexing and search Tutorial Slides 02 Tutorial Video 02
05.10.2021 Lecture: Indexes of linear sequences and alignment Lecture Slides 03 Lecture Video 03
Exercise: Tutorial Indexes of linear sequences and alignment / Handout of PROJECT 1 Tutorial Slides 03 Tutorial Video 03 Project 1 Handout (Updated) Project 1 Slides
12.10.2021 Lecture: Variation-aware alignment, Indexes on graphs, succinct data structures Lecture Slides 04 Lecture Video 04
Exercise: Tutorial Variation-aware alignment, Indexes on graphs, succinct data structures Tutorial Slides 04 Tutorial Video 04
19.10.2021 Lecture: Transcript identification and quantification Lecture Slides 05 Lecture Video 05
Exercise: Tutorial Transcript identification and quantification Tutorial Slides 05 Tutorial Video 05
26.10.2021 Lecture: Differential Gene expression Lecture Slides 06 Lecture Video 06
Exercise: Tutorial Differential Gene expression Tutorial Slides 06 Tutorial Video 06
02.11.2021 Lecture: Single Cell expression data Lecture Slides 07 Lecture Video 07
Exercise: Hand in project 1 (due 11:59pm)/ Tutorial Single Cell expression data Tutorial Slides 07 Tutorial Video 07
09.11.2021 Lecture: Variant calling (germline) Lecture Slides 08 Lecture Video 08
Exercise: Hand out of project 2/ Tutorial Differential Gene expression case study Tutorial Slides 08 Tutorial Video 08 Project 2 Handout
16.11.2021 Lecture: Linking genotypic information to clinical phenotypes Lecture Slides 09 Lecture Video 09
Exercise: Project 1 presentations Tutorial Video 09
23.11.2021 Lecture: Variant interpretation and effect prediction Lecture Slides 10 Lecture Video 10
Exercise: Tutorial Variant effect Tutorial Slides 10 Tutorial Video 10
30.11.2021 No Lecture
Exercise: Tutorial Variant Calling (germline) Tutorial Slides 11 Tutorial Video 11
07.12.2021 Lecture: Somatic Variants Lecture Slides 12 Lecture Additional material 12 Lecture Video 12
Exercise: Hand in project 2 (due 11.59pm)/ Tutorial Variant Calling (somatic) Tutorial Slides 12 Tutorial Video 12
14.12.2021 Lecture: Ontologies and Variant Interpretation Lecture Slides 13 Lecture Video 13
Exercise: Tutorial Ontologies Tutorial Slides 13 Tutorial Video 13
21.12.2021 Lecture: Research talk, Summary of course, Q & A for exam
Exercise: Project 2 presentations