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UID:232@math.technion.ac.il

DTSTART;TZID=Asia/Jerusalem:20240605T143000

DTEND;TZID=Asia/Jerusalem:20240605T152000

DTSTAMP:20250109T093742Z

URL:https://math.technion.ac.il/events/sagi-snir/

SUMMARY:Sagi Snir (Haifa) -- Bacterial Genome Dynamics: A Random Walk Appro
 ach
DESCRIPTION:Lecturer:Sagi Snir\n Location:814 Amado\n The dramatic decrease
  in time and cost for generating genetic sequence data has opened up vast 
 opportunities in molecular systematics\, one of which is the ability to de
 cipher the evolutionary history of strains of a species. Under this fine s
 ystematic 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 transfe
 r of genetic material between organisms not through lineal descent\, seem 
 to provide far richer information by affecting both gene order and gene co
 ntent. To the best of our knowledge\, no rigorous statistical modelling fo
 r GD has been suggested.\n\nHere we provide a first statistical\, two-leve
 l modeling and analysis\, for GD under a very simple operation – the Jum
 p operation. Under this framework\, at the higher level\, genome evolution
  is modeled as a random walk in the genome permutation state space. At the
  lower level\, gene neighborhood is modeled as a birth–death–immigrati
 on process affected by the genes jumping across the genome. Using this mod
 eling we can infer several innate properties for genomes evolving along a 
 tree and analytically relate the HGT rate and time to the expected random 
 variables that we define.\n\nBesides analytical results\, we will also sho
 w results on real data conforming with existing biological knowledge.\n\nT
 he talk assumes no background in Biology.\n\n&nbsp\;\n\nRelated Papers\n\n
 1) Katriel G.\, Mahanaymi U.\, Koutschan C.\, Zeilberger D.\, Steel M. and
  Snir S. 2023. Gene Transfer-based Phylogenetics: Analytical Expressions a
 nd Additivity via Birth–Death Theory\, Accepted at Systematic Biology. A
  preliminary version is available at bioarxiv\n2) Sevillya\, G.\, D. Doerr
 \, Y. Lerner\, J. Stoye\, M. Steel\, and S. Snir. 2019. Horizontal Gene Tr
 ansfer Phylogenetics: A Random Walk Approach. Molecular Biology and Evolut
 ion (MBE)37:1470–1479.\n3) Shifman\, A.\, N. Ninyo\, U. Gophna\, and S. 
 Snir. 2013. Phylo si: a new genome-wide approach for prokaryotic phylogeny
 . Nucleic acids research (NAR)42:2391–2404.\n\n&nbsp\;\n 
CATEGORIES:Combinatorics Seminar,Seminars
LOCATION:814 Amado

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