261-5100-00L Computational Biomedicine (Autumn 2019)

Semester Autumn Semester 2019
Lecturers Gunnar Rätsch; Valentina Boeva; Natalie Davidson
Periodicity yearly course
Language of instruction English

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

Objective
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.

Content
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.

Location

The lecture will be held at ETH in LEE E 101 (link to location) and CAB G 56 (link to location). Tuesdays 10-12 (LEE E 101) and 13-14 (CAB G 56).

Course Overview

Date Topic Course Material
17.09.2019 Lecture: Introduction to the topic and patient genomics Lecture Slides 01
Exercise: Organization and presentation of projects Exercise Slides 01
24.09.2019 Lecture: String algorithms, indexing and search Lecture Slides 02
Exercise: Hand out of project 1, Tutorial Project 1 Description
01.10.2019 Lecture: Indexes of linear sequences and alignment Lecture Slides 03
Exercise: Tutorial / Project work Exercise Slides 03
08.10.2019 Lecture: Variation-aware alignment, Indexes on graphs, succinct data structures Lecture Slides 04
Exercise: Tutorial / Project work Exercise Slides 04
15.10.2019 Lecture: Transcript identification and quantification Lecture Slides 05
Exercise: Tutorial / Project work Exercise Slides 05
22.10.2019 Lecture: Differential Gene expression Lecture Slides 06
Exercise: Tutorial / Project work Exercise Slides 06
29.10.2019 Lecture: Single Cell expression data Lecture Slides 07
Exercise: Tutorial / Project work Exercise Slides 07
05.11.2019 Lecture: Variant calling (germline) Lecture Slides 08 (with annotations)
Exercise: Hand in project 1 (due 11:59pm) / Project 1 presentations
12.11.2019 Lecture: Linking genotypic information to clinical phenotypes Lecture Slides 09
Exercise: Project 1 presentations
19.11.2019 Lecture: Variant interpretation and effect prediction Lecture Slides 10
Exercise: Hand out of project 2, Tutorial Project 2 Description
26.11.2019 Lecture: Ontologies and Variant Interpretation
Exercise: Tutorial / Project work
03.12.2019 Lecture: Somatic Variant calling and Tumor Heterogeneity
Exercise: Tutorial / Project work
10.12.2019 No Lecture
Exercise: Hand in project 2 / Project 2 presentations
17.12.2019 Lecture: Repetition and Outlook
Exercise: Project 2 presentations