261-5100-00L Computational Biomedicine (Autumn 2021)
|Semester||Autumn Semester 2021|
|Lecturers||Gunnar Rätsch; Valentina Boeva|
|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.
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.
|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|
|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|