BEGIN:VCALENDAR VERSION:2.0 PRODID:-//wp-events-plugin.com//7.2.2.1//EN TZID:Asia/Jerusalem X-WR-TIMEZONE:Asia/Jerusalem BEGIN:VEVENT UID:1222@biology.technion.ac.il DTSTART;TZID=Asia/Jerusalem:20240527T130000 DTEND;TZID=Asia/Jerusalem:20240527T140000 DTSTAMP:20240520T123708Z URL:https://biology.technion.ac.il/en/seminars/faculty-seminar-prof-sagi-s nir-harnessing-genome-dynamics-for-phylogenetic-reconstruction/ SUMMARY:Faculty Seminar - Prof. Sagi Snir-Harnessing Genome Dynamics for Ph ylogenetic Reconstruction [No Categories] DESCRIPTION:Location: Biology auditorium Prof. Sagi Snir\n Affiliation: \n Host:Dr. Dvir Aran\n Dear all\,\n\n \;\n\nExcited to open up the seco nd semester Faculty of Biology Seminar Series. The opening seminar will be given by Prof. Sagi Snir from the Department of Evolutionary and Envir onmental Biology and The Institute of Evolution\, University of Haifa and  President of the Israel Society for Bioinformatics and Computational Bio logy.\n\n \;\n\nPlace and time: Biology auditorium\, Monday 27/5 at 1 3:00.\n\n \;\n\nTitle: Harnessing Genome Dynamics for Phylogenetic Re construction\n\n \;\n\nSnir lab website: https://sagi-snir.wixsite.co m/snir-lab\n\nLooking forward to seeing you all\,\n\nDvir\n\n \;\n\nHa rnessing Genome Dynamics for Phylogenetic Reconstruction\n\nThe dramatic d ecrease in time and cost for generating genetic sequence data has opened u p vast opportunities in molecular systematics\, one of which is the abilit y to decipher the evolutionary history of strains of a species. Under this fine systematic resolution\, the standard markers are often too crude to provide a reliable phylogenetic signal. Nevertheless\, among prokaryotes\, genome dynamics (GD) in the form of horizontal gene transfer (HGT)\, the transfer of genetic material between organisms not through lineal descent\ , seem to provide far richer information by affecting both gene order and gene content.\n\nIn modern systematics\, a common practice is to assume a stochastic model describing the behavior of the system.  Such modelling i s valuable\, as it allows advanced machine learning approaches to be appli ed to the data.\n\nHere we provide a first statistical\, two-level modelin g and analysis\, for GD under a very simple operation – the Jump operati on. Using this modeling we can infer several essential  characteristics f or genomes evolving along a tree and analytically infer HGT rate and time. \n\nWe applied this model to the new version of the orthology DB EggNOG co ntaining over 4.5K taxa. To the best of our knowledge\, this is the larges t gene-order-based tree constructed and it overcomes shortcomings found in previous approaches. Constructing a GD-based tree allows to confirm and c ontrast findings based on other phylogenetic approaches\, as we show.\n\nT he talk is self-contained and assumes no mathematical background. \n\n&nb sp\;\n\nRelated Papers: \n\n Katriel\, G.\, Mahanaymi\, U.\, Brezner\, S .\, Kezel\, N.\, Koutschan\, C.\, Zeilberger\, D.\, ... &\; Snir\, S. G ene Transfer-based Phylogenetics: Analytical Expressions and Additivity vi a Birth-Death Theory. Systematic biology\, syad060.\n Sevillya\, G.\, D. Doerr\, Y. Lerner\, J. Stoye\, M. Steel\, and S. Snir. 2019. Horizontal G ene Transfer Phylogenetics: A Random Walk Approach. Molecular Biology and Evolution (MBE)37:1470–1479.\n  Shifman\, A.\, N. Ninyo\, U. Gophna\, and S. Snir. 2013. Phylo si: a new genome-wide approach for prokaryotic ph ylogeny. Nucleic acids research (NAR)42:2391–2404.\n\n \;\n\nShort B io: Sagi Snir graduated in Computer Science from the Technion Israel\, foc using on analytical\, algebraic\, maximum likelihood solutions to phylogen etics. After a postdoc in the Math and the Computer Science depts at UC Be rkeley\, he returned to the dept of Evolutionary &\; Environmental biol ogy  at the University of Haifa in Israel\, where he has established the Bioinformatics program for grad students. He is now a professor of computa tional evolution at the University of Haifa and the President of the Israe li Society for Bioinformatics and Computational Biology.\n\nHis research c ombines algorithmic approaches to problems from evolution with focus on ph ylogenetic trees and networks. He has developed the Quartet MaxCut algorit hm to combine conflicting signals between evolutionary trees and other fun damental results on maximum likelihood of trees and networks. His papers h ave been published in both pure theoretical computer science venues and pu re evolution venues.\n\nAfter his army service he traveled for two years o n a motorcycle from the tip of South America (Tierra del Fuego) to Alaska. LOCATION:Biology auditorium END:VEVENT BEGIN:VTIMEZONE TZID:Asia/Jerusalem X-LIC-LOCATION:Asia/Jerusalem BEGIN:DAYLIGHT DTSTART:20240329T030000 TZOFFSETFROM:+0200 TZOFFSETTO:+0300 TZNAME:IDT END:DAYLIGHT END:VTIMEZONE END:VCALENDAR