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|
|Exercise: Organization and presentation of projects||Tutorial Slides 01|
|28.09.2021||Lecture: String algorithms, indexing and search|
|Exercise: Tutorial String algorithms, indexing and search|
|05.10.2021||Lecture: Indexes of linear sequences and alignment|
|Exercise: Tutorial Indexes of linear sequences and alignment / Hand out of project 1|
|12.10.2021||Lecture: Variation-aware alignment, Indexes on graphs, succinct data structures|
|Exercise: Tutorial Variation-aware alignment, Indexes on graphs, succinct data structures|
|19.10.2021||Lecture: Transcript identification and quantification|
|Exercise: Tutorial Transcript identification and quantification|
|26.10.2021||Lecture: Differential Gene expression|
|Exercise: Tutorial Differential Gene expression|
|02.11.2021||Lecture: Single Cell expression data|
|Exercise: Hand in project 1 (due 11:59pm)/ Tutorial Single Cell expression data|
|09.11.2021||Lecture: Variant calling (germline)|
|Exercise: Hand out of project 2/ Tutorial Differential Gene expression case study|
|16.11.2021||Lecture: Linking genotypic information to clinical phenotypes|
|Exercise: Project 1 presentations|
|23.11.2021||Lecture: Variant interpretation and effect prediction|
|Exercise: Tutorial Variant effect|
|30.11.2021||Lecture: Ontologies and Variant Interpretation|
|Exercise: Tutorial Variant Calling (germline)|
|07.12.2021||Lecture: Sample Exam questions Q&A (10-11am; No Lecture 11am - 12pm)|
|Exercise: Hand in project 2 (due 11.59pm)/ Tutorial Variant Calling (somatic)|
|Exercise: Tutorial Ontologies|
|21.12.2021||Lecture: Somatic Variants, Research talk, Summary of course, Q & A for exam|
|Exercise: Project 2 presentations|