<div dir="ltr"><div dir="ltr"><div class="gmail_default" style="font-size:small"><div class="gmail_default"><div class="gmail_default" style="color:rgb(80,0,80)"><font face="arial, sans-serif"><font style="color:rgb(0,0,0);vertical-align:inherit"><font style="vertical-align:inherit"><b>When:</b> </font></font><font style="vertical-align:inherit"><font style="vertical-align:inherit"><font style="color:rgb(0,0,0)"> Fri</font><span class="gmail_default" style="color:rgb(0,0,0)">day, August 16<span class="gmail_default">, </span>2024</span><font style="color:rgb(0,0,0)"> at</font><b style="color:rgb(0,0,0)"> <span style="background-color:rgb(255,255,0)"><u>11:00</u></span></b><span style="background-color:rgb(255,255,0)"><b><u><font color="#000000"> am</font></u></b><b><u><font color="#000000"> CT</font></u><font color="#000000"> </font></b></span></font></font><br></font></div><div class="gmail_default"><p style="color:rgb(80,0,80);font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;line-height:normal;margin:0px"><b><font color="#500050" face="arial, sans-serif"><br></font></b></p><p style="color:rgb(80,0,80);font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;line-height:normal;margin:0px"><font face="arial, sans-serif"><b><font color="#500050">Where: </font></b><font color="#000000">Talk will be given </font><font color="#000000" style="font-weight:bold"><u>live, in-person</u></font><font style="font-weight:bold"> </font>at<br></font></p><p class="MsoNormal" style="margin:0in;color:rgb(80,0,80);line-height:normal;background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial"><font face="arial, sans-serif"><font color="#500050"> </font><font color="#000000"> TTIC, 6045 S. Kenwood Avenue</font></font></p><p class="MsoNormal" style="margin:0in;color:rgb(80,0,80);line-height:normal;background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial"><font face="arial, sans-serif" color="#000000"> 5th Floor, Room 530<b> </b></font></p><p class="MsoNormal" style="margin:0in;color:rgb(80,0,80);line-height:normal;background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial"><font face="arial, sans-serif"><b><span style="color:black"><br></span></b></font></p><p class="MsoNormal" style="margin:0in 0in 0.0001pt;color:rgb(80,0,80);line-height:normal;background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial"><font face="arial, sans-serif"><b style="color:rgb(60,64,67);letter-spacing:0.2px">Virtually:</b><span style="color:rgb(60,64,67);letter-spacing:0.2px"> <i>via panopto: </i><a href="https://uchicago.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=63281766-98bc-4c0c-8085-b1c8000ab3d3" target="_blank"><b>livestream</b></a></span></font></p><p class="MsoNormal" style="margin:0in 0in 0.0001pt;color:rgb(80,0,80);line-height:normal;background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial"><font face="arial, sans-serif"><b style="color:rgb(60,64,67);letter-spacing:0.2px"> </b></font><b style="color:rgb(60,64,67);letter-spacing:0.2px"><font face="arial, sans-serif"> </font></b></p><p class="MsoNormal" style="margin:0in 0in 0.0001pt;line-height:normal;background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial"><font face="arial, sans-serif"><font style="color:rgb(80,0,80);vertical-align:inherit"><font style="vertical-align:inherit"><b>Who: </b> <font color="#500050"> </font><font color="#000000"><font color="#500050"> </font></font></font></font>Sagi Snir, University of Haifa</font></p></div></div><div class="gmail_default"><div dir="ltr"><div><div class="MsoNormal" align="center" style="margin:0in 0in 8pt;text-align:center;line-height:15.6933px"><hr size="3" width="100%" noshade align="center" style="color:rgb(46,116,181)"></div></div><div><p class="MsoNormal" style="margin:0in 0in 8pt;line-height:13.91px"><font face="arial, sans-serif"><b>Title:</b> Bacterial Genome Dynamics: A Random Walk Approach<br></font></p><p style="margin-bottom:12pt;margin-right:0in;margin-left:0in"><font face="arial, sans-serif"><b>Abstract</b>. 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.<br><br>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. </font></p><p style="margin-bottom:12pt;margin-right:0in;margin-left:0in"><font face="arial, sans-serif">Besides analytical results, we will also show results on real data conforming with existing biological knowledge.<br></font></p></div><div><p style="margin-right:0in;margin-left:0in"><font face="arial, sans-serif"><b>Bio: </b>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.</font></p></div></div><div><div id="m_-7723981982256661005m_6797337172009651051m_4188090432098466858m_5027524475750679197m_-2313094795471284929m_1059997580351174862m_409819206631504756m_4484082192933670602m_-1727381471164456222m_-748841883188655251m_611962526655464537m_-2291386001826280818m_8446205837173851621m_8555462040290332708m_6451956535360448322m_-6976229087647104413m_7917979885129397482m_-5423657134431402203m_-1337599008586739890m_8237382617653311322m_-1231130334284673048m_-1282025577005441955m_-1973358356214118865m_-5815637555669013367m_1779572315514282115m_-4485402625451270420m_1520697528942856564m_5948359943660736735m_-4789039193346764527m_3599676094611771654m_8264976978369198918m_7474850050874458051m_5107577024390010371m_253820422674989860m_3983419646637522536m_-7220900540036838011gmail-:qg" role="button" aria-label="Show trimmed content" aria-expanded="false"><font face="arial, sans-serif"><b>Host: </b><a href="mailto:avrim@ttic.edu" target="_blank"><b>Avrim Blum</b></a></font></div></div><div id="m_-7723981982256661005m_6797337172009651051m_4188090432098466858m_5027524475750679197m_-2313094795471284929m_1059997580351174862m_409819206631504756m_4484082192933670602m_-1727381471164456222m_-748841883188655251m_611962526655464537m_-2291386001826280818m_8446205837173851621m_8555462040290332708m_6451956535360448322m_-6976229087647104413m_7917979885129397482m_-5423657134431402203m_-1337599008586739890m_8237382617653311322m_-1231130334284673048m_-1282025577005441955m_-1973358356214118865m_-5815637555669013367m_1779572315514282115m_-4485402625451270420m_1520697528942856564m_5948359943660736735m_-4789039193346764527m_3599676094611771654m_8264976978369198918m_7474850050874458051m_5107577024390010371m_253820422674989860m_3983419646637522536m_-7220900540036838011gmail-:qg" role="button" aria-label="Show trimmed content" aria-expanded="false"><br></div><div id="m_-7723981982256661005m_6797337172009651051m_4188090432098466858m_5027524475750679197m_-2313094795471284929m_1059997580351174862m_409819206631504756m_4484082192933670602m_-1727381471164456222m_-748841883188655251m_611962526655464537m_-2291386001826280818m_8446205837173851621m_8555462040290332708m_6451956535360448322m_-6976229087647104413m_7917979885129397482m_-5423657134431402203m_-1337599008586739890m_8237382617653311322m_-1231130334284673048m_-1282025577005441955m_-1973358356214118865m_-5815637555669013367m_1779572315514282115m_-4485402625451270420m_1520697528942856564m_5948359943660736735m_-4789039193346764527m_3599676094611771654m_8264976978369198918m_7474850050874458051m_5107577024390010371m_253820422674989860m_3983419646637522536m_-7220900540036838011gmail-:qg" role="button" aria-label="Show trimmed content" aria-expanded="false"><br></div><div id="m_-7723981982256661005m_6797337172009651051m_4188090432098466858m_5027524475750679197m_-2313094795471284929m_1059997580351174862m_409819206631504756m_4484082192933670602m_-1727381471164456222m_-748841883188655251m_611962526655464537m_-2291386001826280818m_8446205837173851621m_8555462040290332708m_6451956535360448322m_-6976229087647104413m_7917979885129397482m_-5423657134431402203m_-1337599008586739890m_8237382617653311322m_-1231130334284673048m_-1282025577005441955m_-1973358356214118865m_-5815637555669013367m_1779572315514282115m_-4485402625451270420m_1520697528942856564m_5948359943660736735m_-4789039193346764527m_3599676094611771654m_8264976978369198918m_7474850050874458051m_5107577024390010371m_253820422674989860m_3983419646637522536m_-7220900540036838011gmail-:qg" role="button" aria-label="Show trimmed content" aria-expanded="false"><br></div><div id="m_-7723981982256661005m_6797337172009651051m_4188090432098466858m_5027524475750679197m_-2313094795471284929m_1059997580351174862m_409819206631504756m_4484082192933670602m_-1727381471164456222m_-748841883188655251m_611962526655464537m_-2291386001826280818m_8446205837173851621m_8555462040290332708m_6451956535360448322m_-6976229087647104413m_7917979885129397482m_-5423657134431402203m_-1337599008586739890m_8237382617653311322m_-1231130334284673048m_-1282025577005441955m_-1973358356214118865m_-5815637555669013367m_1779572315514282115m_-4485402625451270420m_1520697528942856564m_5948359943660736735m_-4789039193346764527m_3599676094611771654m_8264976978369198918m_7474850050874458051m_5107577024390010371m_253820422674989860m_3983419646637522536m_-7220900540036838011gmail-:qg" role="button" aria-label="Show trimmed content" aria-expanded="false"><br></div></div></div><div><div dir="ltr" class="gmail_signature"><div dir="ltr"><div><span style="font-family:arial,helvetica,sans-serif;font-size:x-small">Mary C. Marre</span><br></div><div><div><font face="arial, helvetica, sans-serif" size="1">Faculty Administrative Support</font></div><div><i><font face="arial, helvetica, sans-serif" color="#3d85c6" size="1"><b>Toyota Technological Institute</b></font></i></div><div><i><font face="arial, helvetica, sans-serif" color="#3d85c6" size="1">6045 S. Kenwood Avenue, Rm 517</font></i></div><div><font size="1"><i><font face="arial, helvetica, sans-serif" color="#3d85c6">Chicago, IL 60637</font></i><br></font></div><div><font size="1"><i><font face="arial, helvetica, sans-serif" color="#3d85c6">773-834-1757</font></i></font></div><div><b><i><a href="mailto:mmarre@ttic.edu" target="_blank"><font face="arial, helvetica, sans-serif" size="1">mmarre@ttic.edu</font></a></i></b></div></div></div></div></div><br></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Fri, Aug 16, 2024 at 10:00 AM Mary Marre <<a href="mailto:mmarre@ttic.edu">mmarre@ttic.edu</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div dir="ltr"><div style="font-size:small"><div><div style="color:rgb(80,0,80)"><font face="arial, sans-serif"><font style="color:rgb(0,0,0);vertical-align:inherit"><font style="vertical-align:inherit"><b>When:</b> </font></font><font style="vertical-align:inherit"><font style="vertical-align:inherit"><font style="color:rgb(0,0,0)"> Fri</font><span class="gmail_default" style="color:rgb(0,0,0)">day, August 16<span class="gmail_default">, </span>2024</span><font style="color:rgb(0,0,0)"> at</font><b style="color:rgb(0,0,0)"> <span style="background-color:rgb(255,255,0)"><u>11:00</u></span></b><span style="background-color:rgb(255,255,0)"><b><u><font color="#000000"> am</font></u></b><b><u><font color="#000000"> CT</font></u><font color="#000000"> </font></b></span></font></font><br></font></div><div><p style="color:rgb(80,0,80);font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;line-height:normal;margin:0px"><b><font color="#500050" face="arial, sans-serif"><br></font></b></p><p style="color:rgb(80,0,80);font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;line-height:normal;margin:0px"><font face="arial, sans-serif"><b><font color="#500050">Where: </font></b><font color="#000000">Talk will be given </font><font color="#000000" style="font-weight:bold"><u>live, in-person</u></font><font style="font-weight:bold"> </font>at<br></font></p><p class="MsoNormal" style="margin:0in;color:rgb(80,0,80);line-height:normal;background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial"><font face="arial, sans-serif"><font color="#500050"> </font><font color="#000000"> TTIC, 6045 S. Kenwood Avenue</font></font></p><p class="MsoNormal" style="margin:0in;color:rgb(80,0,80);line-height:normal;background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial"><font face="arial, sans-serif" color="#000000"> 5th Floor, Room 530<b> </b></font></p><p class="MsoNormal" style="margin:0in;color:rgb(80,0,80);line-height:normal;background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial"><font face="arial, sans-serif"><b><span style="color:black"><br></span></b></font></p><p class="MsoNormal" style="margin:0in 0in 0.0001pt;color:rgb(80,0,80);line-height:normal;background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial"><font face="arial, sans-serif"><b style="color:rgb(60,64,67);letter-spacing:0.2px">Virtually:</b><span style="color:rgb(60,64,67);letter-spacing:0.2px"> <i>via panopto: </i><a href="https://uchicago.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=63281766-98bc-4c0c-8085-b1c8000ab3d3" target="_blank"><b>livestream</b></a></span></font></p><p class="MsoNormal" style="margin:0in 0in 0.0001pt;color:rgb(80,0,80);line-height:normal;background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial"><font face="arial, sans-serif"><b style="color:rgb(60,64,67);letter-spacing:0.2px"> </b></font><b style="color:rgb(60,64,67);letter-spacing:0.2px"><font face="arial, sans-serif"> </font></b></p><p class="MsoNormal" style="margin:0in 0in 0.0001pt;line-height:normal;background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial"><font face="arial, sans-serif"><font style="color:rgb(80,0,80);vertical-align:inherit"><font style="vertical-align:inherit"><b>Who: </b> <font color="#500050"> </font><font color="#000000"><font color="#500050"> </font></font></font></font>Sagi Snir, University of Haifa</font></p></div></div><div><div dir="ltr"><div><div class="MsoNormal" align="center" style="margin:0in 0in 8pt;text-align:center;line-height:15.6933px"><hr size="3" width="100%" noshade align="center" style="color:rgb(46,116,181)"></div></div><div><p class="MsoNormal" style="margin:0in 0in 8pt;line-height:13.91px"><font face="arial, sans-serif"><b>Title:</b> Bacterial Genome Dynamics: A Random Walk Approach<br></font></p><p style="margin-bottom:12pt;margin-right:0in;margin-left:0in"><font face="arial, sans-serif"><b>Abstract</b>. 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.<br><br>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. </font></p><p style="margin-bottom:12pt;margin-right:0in;margin-left:0in"><font face="arial, sans-serif">Besides analytical results, we will also show results on real data conforming with existing biological knowledge.<br></font></p></div><div><p style="margin-right:0in;margin-left:0in"><font face="arial, sans-serif"><b>Bio: </b>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.</font></p></div></div><div><div id="m_-7723981982256661005m_6797337172009651051m_4188090432098466858m_5027524475750679197m_-2313094795471284929m_1059997580351174862m_409819206631504756m_4484082192933670602m_-1727381471164456222m_-748841883188655251m_611962526655464537m_-2291386001826280818m_8446205837173851621m_8555462040290332708m_6451956535360448322m_-6976229087647104413m_7917979885129397482m_-5423657134431402203m_-1337599008586739890m_8237382617653311322m_-1231130334284673048m_-1282025577005441955m_-1973358356214118865m_-5815637555669013367m_1779572315514282115m_-4485402625451270420m_1520697528942856564m_5948359943660736735m_-4789039193346764527m_3599676094611771654m_8264976978369198918m_7474850050874458051m_5107577024390010371m_253820422674989860m_3983419646637522536m_-7220900540036838011gmail-:qg" role="button" aria-label="Show trimmed content" aria-expanded="false"><font face="arial, sans-serif"><b>Host: </b><a href="mailto:avrim@ttic.edu" target="_blank"><b>Avrim Blum</b></a></font></div></div><div id="m_-7723981982256661005m_6797337172009651051m_4188090432098466858m_5027524475750679197m_-2313094795471284929m_1059997580351174862m_409819206631504756m_4484082192933670602m_-1727381471164456222m_-748841883188655251m_611962526655464537m_-2291386001826280818m_8446205837173851621m_8555462040290332708m_6451956535360448322m_-6976229087647104413m_7917979885129397482m_-5423657134431402203m_-1337599008586739890m_8237382617653311322m_-1231130334284673048m_-1282025577005441955m_-1973358356214118865m_-5815637555669013367m_1779572315514282115m_-4485402625451270420m_1520697528942856564m_5948359943660736735m_-4789039193346764527m_3599676094611771654m_8264976978369198918m_7474850050874458051m_5107577024390010371m_253820422674989860m_3983419646637522536m_-7220900540036838011gmail-:qg" role="button" aria-label="Show trimmed content" aria-expanded="false"><br></div><div id="m_-7723981982256661005m_6797337172009651051m_4188090432098466858m_5027524475750679197m_-2313094795471284929m_1059997580351174862m_409819206631504756m_4484082192933670602m_-1727381471164456222m_-748841883188655251m_611962526655464537m_-2291386001826280818m_8446205837173851621m_8555462040290332708m_6451956535360448322m_-6976229087647104413m_7917979885129397482m_-5423657134431402203m_-1337599008586739890m_8237382617653311322m_-1231130334284673048m_-1282025577005441955m_-1973358356214118865m_-5815637555669013367m_1779572315514282115m_-4485402625451270420m_1520697528942856564m_5948359943660736735m_-4789039193346764527m_3599676094611771654m_8264976978369198918m_7474850050874458051m_5107577024390010371m_253820422674989860m_3983419646637522536m_-7220900540036838011gmail-:qg" role="button" aria-label="Show trimmed content" aria-expanded="false"><br></div><div id="m_-7723981982256661005m_6797337172009651051m_4188090432098466858m_5027524475750679197m_-2313094795471284929m_1059997580351174862m_409819206631504756m_4484082192933670602m_-1727381471164456222m_-748841883188655251m_611962526655464537m_-2291386001826280818m_8446205837173851621m_8555462040290332708m_6451956535360448322m_-6976229087647104413m_7917979885129397482m_-5423657134431402203m_-1337599008586739890m_8237382617653311322m_-1231130334284673048m_-1282025577005441955m_-1973358356214118865m_-5815637555669013367m_1779572315514282115m_-4485402625451270420m_1520697528942856564m_5948359943660736735m_-4789039193346764527m_3599676094611771654m_8264976978369198918m_7474850050874458051m_5107577024390010371m_253820422674989860m_3983419646637522536m_-7220900540036838011gmail-:qg" role="button" aria-label="Show trimmed content" aria-expanded="false"><br></div></div></div><div><div dir="ltr" class="gmail_signature"><div dir="ltr"><div><span style="font-family:arial,helvetica,sans-serif;font-size:x-small">Mary C. Marre</span><br></div><div><div><font face="arial, helvetica, sans-serif" size="1">Faculty Administrative Support</font></div><div><i><font face="arial, helvetica, sans-serif" color="#3d85c6" size="1"><b>Toyota Technological Institute</b></font></i></div><div><i><font face="arial, helvetica, sans-serif" color="#3d85c6" size="1">6045 S. Kenwood Avenue, Rm 517</font></i></div><div><font size="1"><i><font face="arial, helvetica, sans-serif" color="#3d85c6">Chicago, IL 60637</font></i><br></font></div><div><font size="1"><i><font face="arial, helvetica, sans-serif" color="#3d85c6">773-834-1757</font></i></font></div><div><b><i><a href="mailto:mmarre@ttic.edu" target="_blank"><font face="arial, helvetica, sans-serif" size="1">mmarre@ttic.edu</font></a></i></b></div></div></div></div></div><br></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Thu, Aug 15, 2024 at 2:09 PM Mary Marre <<a href="mailto:mmarre@ttic.edu" target="_blank">mmarre@ttic.edu</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div dir="ltr"><div style="font-size:small"><div><div style="color:rgb(80,0,80)"><font face="arial, sans-serif"><font style="color:rgb(0,0,0);vertical-align:inherit"><font style="vertical-align:inherit"><b>When:</b> </font></font><font style="vertical-align:inherit"><font style="vertical-align:inherit"><font style="color:rgb(0,0,0)"> Fri</font><span class="gmail_default" style="color:rgb(0,0,0)">day, August 16<span class="gmail_default">, </span>2024</span><font style="color:rgb(0,0,0)"> at</font><b style="color:rgb(0,0,0)"> <span style="background-color:rgb(255,255,0)"><u>11:00</u></span></b><span style="background-color:rgb(255,255,0)"><b><u><font color="#000000"> am</font></u></b><b><u><font color="#000000"> CT</font></u><font color="#000000"> </font></b></span></font></font><br></font></div><div><p style="color:rgb(80,0,80);font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;line-height:normal;margin:0px"><b><font color="#500050" face="arial, sans-serif"><br></font></b></p><p style="color:rgb(80,0,80);font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;line-height:normal;margin:0px"><font face="arial, sans-serif"><b><font color="#500050">Where: </font></b><font color="#000000">Talk will be given </font><font color="#000000" style="font-weight:bold"><u>live, in-person</u></font><font style="font-weight:bold"> </font>at<br></font></p><p class="MsoNormal" style="margin:0in;color:rgb(80,0,80);line-height:normal;background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial"><font face="arial, sans-serif"><font color="#500050"> </font><font color="#000000"> TTIC, 6045 S. Kenwood Avenue</font></font></p><p class="MsoNormal" style="margin:0in;color:rgb(80,0,80);line-height:normal;background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial"><font face="arial, sans-serif" color="#000000"> 5th Floor, Room 530<b> </b></font></p><p class="MsoNormal" style="margin:0in;color:rgb(80,0,80);line-height:normal;background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial"><font face="arial, sans-serif"><b><span style="color:black"><br></span></b></font></p><p class="MsoNormal" style="margin:0in 0in 0.0001pt;color:rgb(80,0,80);line-height:normal;background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial"><font face="arial, sans-serif"><b style="color:rgb(60,64,67);letter-spacing:0.2px">Virtually:</b><span style="color:rgb(60,64,67);letter-spacing:0.2px"> <i>via panopto: </i><a href="https://uchicago.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=63281766-98bc-4c0c-8085-b1c8000ab3d3" target="_blank"><b>livestream</b></a></span></font></p><p class="MsoNormal" style="margin:0in 0in 0.0001pt;color:rgb(80,0,80);line-height:normal;background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial"><font face="arial, sans-serif"><b style="color:rgb(60,64,67);letter-spacing:0.2px"> </b></font><b style="color:rgb(60,64,67);letter-spacing:0.2px"><font face="arial, sans-serif"> </font></b></p><p class="MsoNormal" style="margin:0in 0in 0.0001pt;line-height:normal;background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial"><font face="arial, sans-serif"><font style="color:rgb(80,0,80);vertical-align:inherit"><font style="vertical-align:inherit"><b>Who: </b> <font color="#500050"> </font><font color="#000000"><font color="#500050"> </font></font></font></font>Sagi Snir, University of Haifa</font></p></div></div><div><div dir="ltr"><div><div class="MsoNormal" align="center" style="margin:0in 0in 8pt;text-align:center;line-height:15.6933px"><hr size="3" width="100%" noshade align="center" style="color:rgb(46,116,181)"></div></div><div><p class="MsoNormal" style="margin:0in 0in 8pt;line-height:13.91px"><font face="arial, sans-serif"><b>Title:</b> Bacterial Genome Dynamics: A Random Walk Approach<br></font></p><p style="margin-bottom:12pt;margin-right:0in;margin-left:0in"><font face="arial, sans-serif"><b>Abstract</b>. 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.<br><br>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. </font></p><p style="margin-bottom:12pt;margin-right:0in;margin-left:0in"><font face="arial, sans-serif">Besides analytical results, we will also show results on real data conforming with existing biological knowledge.<br></font></p></div><div><p style="margin-right:0in;margin-left:0in"><font face="arial, sans-serif"><b>Bio: </b>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.</font></p></div></div><div><div id="m_-7723981982256661005m_6797337172009651051m_4188090432098466858m_5027524475750679197m_-2313094795471284929m_1059997580351174862m_409819206631504756m_4484082192933670602m_-1727381471164456222m_-748841883188655251m_611962526655464537m_-2291386001826280818m_8446205837173851621m_8555462040290332708m_6451956535360448322m_-6976229087647104413m_7917979885129397482m_-5423657134431402203m_-1337599008586739890m_8237382617653311322m_-1231130334284673048m_-1282025577005441955m_-1973358356214118865m_-5815637555669013367m_1779572315514282115m_-4485402625451270420m_1520697528942856564m_5948359943660736735m_-4789039193346764527m_3599676094611771654m_8264976978369198918m_7474850050874458051m_5107577024390010371m_253820422674989860m_3983419646637522536m_-7220900540036838011gmail-:qg" role="button" aria-label="Show trimmed content" aria-expanded="false"><font face="arial, sans-serif"><b>Host: </b><a href="mailto:avrim@ttic.edu" target="_blank"><b>Avrim Blum</b></a></font></div></div><br></div><div><br></div><div><br></div></div><div><div dir="ltr" class="gmail_signature"><div dir="ltr"><div><span style="font-family:arial,helvetica,sans-serif;font-size:x-small">Mary C. Marre</span><br></div><div><div><font face="arial, helvetica, sans-serif" size="1">Faculty Administrative Support</font></div><div><i><font face="arial, helvetica, sans-serif" color="#3d85c6" size="1"><b>Toyota Technological Institute</b></font></i></div><div><i><font face="arial, helvetica, sans-serif" color="#3d85c6" size="1">6045 S. Kenwood Avenue, Rm 517</font></i></div><div><font size="1"><i><font face="arial, helvetica, sans-serif" color="#3d85c6">Chicago, IL 60637</font></i><br></font></div><div><font size="1"><i><font face="arial, helvetica, sans-serif" color="#3d85c6">773-834-1757</font></i></font></div><div><b><i><a href="mailto:mmarre@ttic.edu" target="_blank"><font face="arial, helvetica, sans-serif" size="1">mmarre@ttic.edu</font></a></i></b></div></div></div></div></div><br></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Fri, Aug 9, 2024 at 11:42 PM Mary Marre <<a href="mailto:mmarre@ttic.edu" target="_blank">mmarre@ttic.edu</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div><div><div style="color:rgb(80,0,80)"><font face="arial, sans-serif"><font style="color:rgb(0,0,0);vertical-align:inherit"><font style="vertical-align:inherit"><b>When:</b> </font></font><font style="vertical-align:inherit"><font style="vertical-align:inherit"><font style="color:rgb(0,0,0)"> Fri</font><span class="gmail_default" style="color:rgb(0,0,0)">day, August 16<span class="gmail_default">, </span>2024</span><font style="color:rgb(0,0,0)"> at</font><b style="color:rgb(0,0,0)"> <span style="background-color:rgb(255,255,0)"><u>11:00</u></span></b><span style="background-color:rgb(255,255,0)"><b><u><font color="#000000"> am</font></u></b><b><u><font color="#000000"> CT</font></u><font color="#000000"> </font></b></span></font></font><br></font></div><div><p style="color:rgb(80,0,80);font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;line-height:normal;margin:0px"><b><font color="#500050" face="arial, sans-serif"><br></font></b></p><p style="color:rgb(80,0,80);font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;line-height:normal;margin:0px"><font face="arial, sans-serif"><b><font color="#500050">Where: </font></b><font color="#000000">Talk will be given </font><font color="#000000" style="font-weight:bold"><u>live, in-person</u></font><font style="font-weight:bold"> </font>at<br></font></p><p class="MsoNormal" style="margin:0in;color:rgb(80,0,80);line-height:normal;background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial"><font face="arial, sans-serif"><font color="#500050"> </font><font color="#000000"> TTIC, 6045 S. Kenwood Avenue</font></font></p><p class="MsoNormal" style="margin:0in;color:rgb(80,0,80);line-height:normal;background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial"><font face="arial, sans-serif" color="#000000"> 5th Floor, Room 530<b> </b></font></p><p class="MsoNormal" style="margin:0in;color:rgb(80,0,80);line-height:normal;background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial"><font face="arial, sans-serif"><b><span style="color:black"><br></span></b></font></p><p class="MsoNormal" style="margin:0in 0in 0.0001pt;color:rgb(80,0,80);line-height:normal;background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial"><font face="arial, sans-serif"><b style="color:rgb(60,64,67);letter-spacing:0.2px">Virtually:</b><span style="color:rgb(60,64,67);letter-spacing:0.2px"> <i>via panopto: </i><a href="https://uchicago.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=63281766-98bc-4c0c-8085-b1c8000ab3d3" target="_blank"><b>livestream</b></a></span></font></p><p class="MsoNormal" style="margin:0in 0in 0.0001pt;color:rgb(80,0,80);line-height:normal;background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial"><font face="arial, sans-serif"><b style="color:rgb(60,64,67);letter-spacing:0.2px"> </b></font><b style="color:rgb(60,64,67);letter-spacing:0.2px"><font face="arial, sans-serif"> </font></b></p><p class="MsoNormal" style="margin:0in 0in 0.0001pt;line-height:normal;background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial"><font face="arial, sans-serif"><font style="color:rgb(80,0,80);vertical-align:inherit"><font style="vertical-align:inherit"><b>Who: </b> <font color="#500050"> </font><font color="#000000"><font color="#500050"> </font></font></font></font>Sagi Snir, University of Haifa</font></p></div></div><div><div dir="ltr"><div><div class="MsoNormal" align="center" style="margin:0in 0in 8pt;text-align:center;line-height:15.6933px"><hr size="3" width="100%" noshade align="center" style="color:rgb(46,116,181)"></div></div><div><p class="MsoNormal" style="margin:0in 0in 8pt;line-height:13.91px"><font face="arial, sans-serif"><b>Title:</b> Bacterial Genome
Dynamics: A Random Walk Approach<br></font></p><p style="margin-bottom:12pt;margin-right:0in;margin-left:0in"><font face="arial, sans-serif"><b>Abstract</b>. 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.<br><br>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. </font></p><p style="margin-bottom:12pt;margin-right:0in;margin-left:0in"><font face="arial, sans-serif">Besides analytical results, we will also show results on real data conforming with existing biological knowledge.<br></font></p></div><div><p style="margin-right:0in;margin-left:0in"><font face="arial, sans-serif"><b>Bio: </b>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.</font></p></div></div><div><div id="m_-7723981982256661005m_6797337172009651051m_4188090432098466858m_5027524475750679197m_-2313094795471284929m_1059997580351174862m_409819206631504756m_4484082192933670602m_-1727381471164456222m_-748841883188655251m_611962526655464537m_-2291386001826280818m_8446205837173851621m_8555462040290332708m_6451956535360448322m_-6976229087647104413m_7917979885129397482m_-5423657134431402203m_-1337599008586739890m_8237382617653311322m_-1231130334284673048m_-1282025577005441955m_-1973358356214118865m_-5815637555669013367m_1779572315514282115m_-4485402625451270420m_1520697528942856564m_5948359943660736735m_-4789039193346764527m_3599676094611771654m_8264976978369198918m_7474850050874458051m_5107577024390010371m_253820422674989860m_3983419646637522536m_-7220900540036838011gmail-:qg" role="button" aria-label="Show trimmed content" aria-expanded="false"><font face="arial, sans-serif"><b>Host: </b><a href="mailto:avrim@ttic.edu" target="_blank"><b>Avrim Blum</b></a></font></div></div><div id="m_-7723981982256661005m_6797337172009651051m_4188090432098466858m_5027524475750679197m_-2313094795471284929m_1059997580351174862m_409819206631504756m_4484082192933670602m_-1727381471164456222m_-748841883188655251m_611962526655464537m_-2291386001826280818m_8446205837173851621m_8555462040290332708m_6451956535360448322m_-6976229087647104413m_7917979885129397482m_-5423657134431402203m_-1337599008586739890m_8237382617653311322m_-1231130334284673048m_-1282025577005441955m_-1973358356214118865m_-5815637555669013367m_1779572315514282115m_-4485402625451270420m_1520697528942856564m_5948359943660736735m_-4789039193346764527m_3599676094611771654m_8264976978369198918m_7474850050874458051m_5107577024390010371m_253820422674989860m_3983419646637522536m_-7220900540036838011gmail-:qg" role="button" aria-label="Show trimmed content" aria-expanded="false"><font face="arial, sans-serif"><br></font></div><div id="m_-7723981982256661005m_6797337172009651051m_4188090432098466858m_5027524475750679197m_-2313094795471284929m_1059997580351174862m_409819206631504756m_4484082192933670602m_-1727381471164456222m_-748841883188655251m_611962526655464537m_-2291386001826280818m_8446205837173851621m_8555462040290332708m_6451956535360448322m_-6976229087647104413m_7917979885129397482m_-5423657134431402203m_-1337599008586739890m_8237382617653311322m_-1231130334284673048m_-1282025577005441955m_-1973358356214118865m_-5815637555669013367m_1779572315514282115m_-4485402625451270420m_1520697528942856564m_5948359943660736735m_-4789039193346764527m_3599676094611771654m_8264976978369198918m_7474850050874458051m_5107577024390010371m_253820422674989860m_3983419646637522536m_-7220900540036838011gmail-:qg" role="button" aria-label="Show trimmed content" aria-expanded="false" style="font-size:small"><br></div><div id="m_-7723981982256661005m_6797337172009651051m_4188090432098466858m_5027524475750679197m_-2313094795471284929m_1059997580351174862m_409819206631504756m_4484082192933670602m_-1727381471164456222m_-748841883188655251m_611962526655464537m_-2291386001826280818m_8446205837173851621m_8555462040290332708m_6451956535360448322m_-6976229087647104413m_7917979885129397482m_-5423657134431402203m_-1337599008586739890m_8237382617653311322m_-1231130334284673048m_-1282025577005441955m_-1973358356214118865m_-5815637555669013367m_1779572315514282115m_-4485402625451270420m_1520697528942856564m_5948359943660736735m_-4789039193346764527m_3599676094611771654m_8264976978369198918m_7474850050874458051m_5107577024390010371m_253820422674989860m_3983419646637522536m_-7220900540036838011gmail-:qg" role="button" aria-label="Show trimmed content" aria-expanded="false" style="font-size:small"><br></div></div></div><div><div dir="ltr" class="gmail_signature"><div dir="ltr"><div><span style="font-family:arial,helvetica,sans-serif;font-size:x-small">Mary C. Marre</span><br></div><div><div><font face="arial, helvetica, sans-serif" size="1">Faculty Administrative Support</font></div><div><i><font face="arial, helvetica, sans-serif" color="#3d85c6" size="1"><b>Toyota Technological Institute</b></font></i></div><div><i><font face="arial, helvetica, sans-serif" color="#3d85c6" size="1">6045 S. Kenwood Avenue, Rm 517</font></i></div><div><font size="1"><i><font face="arial, helvetica, sans-serif" color="#3d85c6">Chicago, IL 60637</font></i><br></font></div><div><font size="1"><i><font face="arial, helvetica, sans-serif" color="#3d85c6">773-834-1757</font></i></font></div><div><b><i><a href="mailto:mmarre@ttic.edu" target="_blank"><font face="arial, helvetica, sans-serif" size="1">mmarre@ttic.edu</font></a></i></b></div></div></div></div></div></div>
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