[Theory] 8/16 TTIC Colloquium: Sagi Snir, University of Haifa

[Mary Marre via Theory]

*When:*         Friday, August 16, 2024 at* 11:00** am** CT   *


*Where:       *Talk will be given *live, in-person* at

                   TTIC, 6045 S. Kenwood Avenue

                   5th Floor, Room 530


*Virtually:*   *via panopto: **livestream*
<https://uchicago.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=63281766-98bc-4c0c-8085-b1c8000ab3d3>



*Who: *         Sagi Snir, University of Haifa
------------------------------

*Title:*          Bacterial Genome Dynamics: A Random Walk Approach

*Abstract*. 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 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. To the best of
our knowledge, no rigorous statistical modelling for GD has been suggested.

Here we provide a first statistical, two-level modeling and analysis, for
GD under a very simple operation – the Jump 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–immigration process affected by
the genes jumping across the genome. Using this modeling 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.

Besides analytical results, we will also show results on real data
conforming with existing biological knowledge.

*Bio: *Sagi Snir graduated in Computer Science from the Technion Israel,
focusing on analytical, algebraic, maximum likelihood solutions to
phylogenetics. After a postdoc in the Math and the Computer Science depts
at UC Berkeley, he returned to the University of Haifa in Israel, where he
has established the Bioinformatics program for grad students. He is now a
professor of computational evolution at the University of Haifa and the
President of the Israeli Society for Bioinformatics and Computational
Biology.
*Host: **Avrim Blum* <avrim at ttic.edu>



Mary C. Marre
Faculty Administrative Support
*Toyota Technological Institute*
*6045 S. Kenwood Avenue, Rm 517*
*Chicago, IL  60637*
*773-834-1757*
*mmarre at ttic.edu <mmarre at ttic.edu>*
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