261-5100-00L Computational Biomedicine (Autumn 2020)

Semester Autumn Semester 2020
Lecturers Gunnar Rätsch; Valentina Boeva; Natalie Davidson
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.

Course Overview

Date Topic Course Material
15.09.2020 Lecture: Introduction to the topic and patient genomics Lecture Slides 01 Lecture Video 01
Exercise: Organization and presentation of projects Tutorial Slides 01
22.09.2020 Lecture: String algorithms, indexing and search Lecture Slides 02 Lecture Video 02
Exercise: Hand out of project 1, Tutorial Tutorial Slides 02 Tutorial Video 02
Project 1 Description
29.09.2020 Lecture: Indexes of linear sequences and alignment Lecture Slides 03 Lecture Video 03
Exercise: Tutorial / Project Q & A Tutorial Slides 03 Tutorial Video 03
06.10.2020 Lecture: Variation-aware alignment, Indexes on graphs, succinct data structures Lecture Slides 04 Lecture Video 04
Exercise: Tutorial / Project Q & A Tutorial Slides 04 Tutorial Video 04
13.10.2020 Lecture: Transcript identification and quantification Lecture Slides 05 Lecture Video 05
Exercise: Tutorial / Project work Tutorial Slides 05 Tutorial Video 05
20.10.2020 Lecture: Differential Gene expression Lecture Slides 06 Lecture Video 06
Exercise: Tutorial / Project work Tutorial Slides 06 Tutorial Video 06
27.10.2020 Lecture: Single Cell expression data Lecture Slides 07 Lecture Video 07
Exercise: Tutorial / Project work Tutorial Slides 07 Tutorial Video 07
03.11.2020 Lecture: Variant calling (germline) Lecture Slides 08
Exercise: Hand in project 1 (due 11:59pm) / Tutorial and Project 2 description Tutorial Slides 08 Project 2 Description Tutorial Video 08
10.11.2020 Lecture: Linking genotypic information to clinical phenotypes Lecture Slides 09 Lecture Video 09
Exercise: Project 1 presentations Tutorial Video 09
17.11.2020 Lecture: Variant interpretation and effect prediction Lecture Slides 10 Lecture Video 10
Exercise: Tutorial Project Work Tutorial Slides 10
24.11.2020 Lecture: Ontologies and Variant Interpretation Lecture Slides 11 Lecture Video 11
Exercise: Tutorial / Project work Tutorial Slides 11 Tutorial Video 11
01.12.2020 Lecture: Sample Exam questions Q&A (10-11am; No Lecture 11am - 12pm) Sample Exam Lecture Video 12
Exercise: Tutorial / Project work Tutorial Slides 12 Tutorial Video 12
08.12.2020 No Lecture
Exercise: Hand in project 2 (due 11.59pm) / Tutorial Tutorial Slides 13 Tutorial Video 13
15.12.2020 Lecture: Somatic Variants, Research talk, Summary of course, Q & A for exam Lecture Slides 13 Lecture Video 13
Exercise: Project 2 presentations Tutorial Video 14