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

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.

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