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bioinf-l@kam.mff.cuni.cz

December 2023

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2 discussions

Lecture invitation: Efficient Search of Microbial Genomes via Phylogenetic Compression
by Petr Danecek 17 Dec '23

17 Dec '23

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.

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Lecture invitation: dynamics of macromolecules and energetics of molecular interactions
by Petr Danecek 10 Dec '23

10 Dec '23

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.

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