261-5112-00L
Algorithms and Data Structures for Population Scale Genomics
Semester
Autumn Semester 2021
Lecturers
to be announced
Periodicity
yearly recurring course
Course
Does not take place this semester.
Language of instruction
English
Comment
Number of participants limited to 30.
Courses
Number
Title
Hours
Lecturers
261-5112-00 G
Algorithms and Data Structures for Population Scale Genomics
Does not take place this semester. Course will be offered again in FS 2022.
2 hrs
to be announced
Catalogue data
Abstract
Research in Biology and Medicine have been transformed into disciplines of applied data science over the past years. Not only size and inherentcomplexity of the data but also requirements on data privacy and complexity of search and access pose a wealth of new research questions.
Learning objective
This interactive course will explore the latest research on algorithms and data structures for population scale genomics applications and give insights into both the technical basis as well as the domain questions motivating it.
Content
Over the duration of the semester, the course will cover three main topics. Each of the topics will consist of 70-80% lecture content and 20-30% seminar content. 1) Algorithms and data structures for text and graph compression. Motivated through applications in compressive genomics, the course will cover succinct indexing schemes for strings, trees and general graphs, compression schemes for binary matrices as well as the efficient representation of haplotypes and genomic variants. 2) Stochastic data structures and algorithms for approximate representation of strings and graphs as well as sets in general. This includes winnowing schemes and minimizers, sketching techniques, (minimal perfect) hashing and approximate membership query data structures. 3) Data structures supporting encryption and data privacy. As an extension to data structures discussed in the earlier topics, this will include secure indexing using homomorphic encryption as well as design for secure storage and distribution of data.
Performance assessment
Performance assessment information (valid until the course unit is held again)
Performance assessment as a semester course
ECTS credits
3 credits
Examiners
Type
session examination
Language of examination
English
Repetition
The performance assessment is only offered in the session after the course unit. Repetition only possible after re-enrolling.
Mode of examination
oral 20 minutes
This information can be updated until the beginning of the semester; information on the examination timetable is binding.