Dear all,
the next seminar will take place on Wednesday, please see the details
below. We look forward to seeing you all!
Title: Efficient Search of Microbial Genomes via Phylogenetic Compression
Speaker: Karel Břinda (INRIA)
Date and time: Wednesday 20/12/2023 - 17:20
Location: MFF UK, Malostranské nám. 25, lecture hall S3 (3rd floor)
https://bioinformatics.cuni.cz/seminar/
Best wishes,
Petr Danecek
-------------------------------
*Karel Břinda (INRIA)
/Efficient Search of Microbial Genomes via Phylogenetic Compression/*
Comprehensive collections approaching millions of sequenced genomes have
become central information sources in the life sciences. However, the
rapid growth of these collections makes it effectively impossible to
search these data using tools such as BLAST and its successors. In this
talk, we will present a new technique called phylogenetic compression,
which uses evolutionary history to guide compression and efficiently
search large collections of microbial genomes using existing algorithms
and data structures. We will show that, when applied to modern diverse
collections approaching millions of genomes, lossless phylogenetic
compression improves the compression ratios of assemblies, de Bruijn
graphs, and k-mer indexes by one to two orders of magnitude.
Additionally, we will present a pipeline for a BLAST-like search over
these phylogeny-compressed reference data, and demonstrate it can align
genes, plasmids, or entire sequencing experiments against all sequenced
bacteria until 2019 on ordinary desktop computers within a few hours.
Phylogenetic compression has broad applications in computational biology
and may provide a fundamental design principle for future genomics
infrastructure.
Dear all,
the next seminar will take place on *Tuesday*, please see the details
below. We look forward to seeing you all!
Title: Probing the dynamics of macromolecules and energetics of
molecular interactions with high-performance, fast and accessible
computational methods
Speaker: Rafael Najmanovich (University of Montreal)
Date and time: *Tuesday 12/12/2023 - 10:40am*
Location: *PřF UK, Viničná 7, room 311 (3rd floor)*
https://bioinformatics.cuni.cz/seminar/ [bioinformatics.cuni.cz]
Best wishes,
Petr Danecek
-------------------------------
*Probing the dynamics of macromolecules and energetics of molecular
interactions with high-performance, fast and accessible computational
methods*
*/Rafael Najmanovich (University of Montreal)/*
In this talk I will discuss recent methods developed within our group
for ultra-massive virtual screening, protein engineering and
understanding macromolecular dynamics all based on basic simple
biophysical principles leading to fas, accessible and high-performing
computational methods with examples of their application in the study of
GPCRs, SARS-CoV-2 and Ebola.