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A general approach for identifying profile shifts in functional genomics data

Title of the event A general approach for identifying profile shifts in functional genomics data
Series CIDAS Colloquium
Organizer Campus-Institut Data Science (CIDAS)
Speaker Prof. Dr. Caroline Friedel
Speaker institution Ludwig-Maximilians-Universität München
Type of event Kolloquium
Category Forschung
Registration required Nein
Details Functional genomics assays using high-throughput sequencing (e.g. ATAC-seq, or
ChIP-seq) provide unparalleled opportunities for investigating cellular processes at
unprecedented detail. Commonly these assays are used to compare a perturbation
(e.g. infection, knockdown or inhibition of specific genes or proteins) against a control
and identify changes between these conditions. While standard differential
approaches focus on changes in read counts for specific genomic regions, we and
others showed that such perturbations can result in more complex shifts in read
distributions, such as RNA Polymerase occupancy changes due to alterations in
pausing and termination. To identify such profile shifts, we developed a general
approach, RegCFinder, based on a linear-time solution for a well-known
computational problem, the “all maximum scoring subsequences” problem. This talk
will provide an overview on the biological motivation and theoretical foundations of
RegCFinder and illustrate its applicability on examples.
Date Start: 05.12.2024, 14:15 Uhr
Ende: 05.12.2024 , 15:15 Uhr
Location Anderer Ort / Other Location
Goldschmidtstraße 1, Raum 1.130
Contact Dr. Isabelle Matthias
imatthi@gwdg.de