<div dir="ltr"><div dir="ltr"><div class="gmail_default" style="font-size:small"><div class="gmail_default"><p style="font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;line-height:normal;margin:0px"><font face="arial, sans-serif"><font style="vertical-align:inherit"><font style="vertical-align:inherit"><b>When:</b> </font></font><font style="vertical-align:inherit"><font style="vertical-align:inherit"> Monday, February 15th at<b> 11:10 am CT</b></font></font><br></font></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></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="vertical-align:inherit"><font style="vertical-align:inherit"><b>Where:</b> </font></font><font color="#000000">Zoom Virtual Talk (</font><b><font color="#0000ff"><a href="https://uchicagogroup.zoom.us/webinar/register/WN_OjIiAnUnTDac7S-d_c7whg" target="_blank">register in advance here</a></font></b><font color="#000000">)</font></font></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></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="vertical-align:inherit"><font style="vertical-align:inherit"><b>Who: </b> </font></font></font>Anton Bankevich, UC San Diego</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"><br></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"><br></p><b>Title: </b> Algorithmic Challenges in Long-Read Genome Assembly<br><br><b>Abstract:</b> Even though the first draft human genome was generated two decades ago, many important regions (such as centromeres) still represent the “terra incognita'' of genome sequencing. The recently emerged long-read DNA sequencing technologies promise to transform genome sequencing toward generating complete genomes and lead to a critical demand for fast and accurate genome assembly algorithms. They also raised novel algorithmic problems since all previously developed assembly approaches fail for long reads. These problems represent the key bottlenecks for the ongoing Big Data sequencing projects, such as the Vertebrate Genomes Project (aimed at sequencing genomes of all vertebrates) and the Human Pangenome Project (aimed at population-scale sequencing of complete human genomes). I will describe the new algorithmic challenges in genome assembly, discuss the recently developed algorithms for their solution, and show how these algorithms bring us closer to the goal of complete genome sequencing.<br> <br><b>Bio:</b> Anton Bankevich is a Postdoctoral Scholar at the Computer Science and Engineering Department at UCSD. After getting the B.S. degree in Computer Science from Saint Petersburg University, Russia in 2009, he started working on his Ph.D. in algebraic graph theory. However, after joining the Center for Algorithmic Biotechnology in Saint Petersburg in 2011, he switched to developing the SPAdes genome assembler (Bankevich et al., J. Comp. Biology, 2012) that, with over 11,000 citations to date, is now the most widely-used assembler in the world. Dr. Bankevich joined UCSD as a postdoctoral scholar after receiving his Ph.D. (2018) in Computer Science from Saint Petersburg University. His research interests cover genomics and metagenomics (with a focus on algorithms and data analysis for genome assembly) and include collaborations on the discovery of novel insecticide toxins (with Keith Turner), leaderboard metagenomics (with Rob Knight), and comparative genomics (with Stephen O’Brien).</div><div class="gmail_default"><br></div><div class="gmail_default"><b>Host: </b><a href="mailto:j3xu@ttic.edu" target="_blank">Jinbo Xu</a></div><div class="gmail_default"><br></div><div class="gmail_default"><br></div><div class="gmail_default"><br></div></div><div><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><font face="arial, helvetica, sans-serif">Mary C. Marre</font><div><font face="arial, helvetica, sans-serif">Faculty Administrative Support</font></div><div><i><font face="arial, helvetica, sans-serif" color="#3d85c6"><b>Toyota Technological Institute</b></font></i></div><div><i><font face="arial, helvetica, sans-serif" color="#3d85c6">6045 S. Kenwood Avenue</font></i></div><div><i><font face="arial, helvetica, sans-serif" color="#3d85c6">Room 517</font></i></div><div><i><font face="arial, helvetica, sans-serif" color="#3d85c6">Chicago, IL 60637</font></i></div><div><i><font face="arial, helvetica, sans-serif">p:(773) 834-1757</font></i></div><div><i><font face="arial, helvetica, sans-serif">f: (773) 357-6970</font></i></div><div><b><i><a href="mailto:mmarre@ttic.edu" target="_blank"><font face="arial, helvetica, sans-serif">mmarre@ttic.edu</font></a></i></b></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div><br></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Sun, Feb 14, 2021 at 3:30 PM 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><p style="font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;line-height:normal;margin:0px"><font face="arial, sans-serif"><font style="vertical-align:inherit"><font style="vertical-align:inherit"><b>When:</b> </font></font><font style="vertical-align:inherit"><font style="vertical-align:inherit"> Monday, February 15th at<b> 11:10 am CT</b></font></font><br></font></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></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="vertical-align:inherit"><font style="vertical-align:inherit"><b>Where:</b> </font></font><font color="#000000">Zoom Virtual Talk (</font><b><font color="#0000ff"><a href="https://uchicagogroup.zoom.us/webinar/register/WN_OjIiAnUnTDac7S-d_c7whg" target="_blank">register in advance here</a></font></b><font color="#000000">)</font></font></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></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="vertical-align:inherit"><font style="vertical-align:inherit"><b>Who: </b> </font></font></font>Anton Bankevich, UC San Diego</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"><br></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"><br></p><b>Title: </b> Algorithmic Challenges in Long-Read Genome Assembly<br><br><b>Abstract:</b> Even though the first draft human genome was generated two decades ago, many important regions (such as centromeres) still represent the “terra incognita'' of genome sequencing. The recently emerged long-read DNA sequencing technologies promise to transform genome sequencing toward generating complete genomes and lead to a critical demand for fast and accurate genome assembly algorithms. They also raised novel algorithmic problems since all previously developed assembly approaches fail for long reads. These problems represent the key bottlenecks for the ongoing Big Data sequencing projects, such as the Vertebrate Genomes Project (aimed at sequencing genomes of all vertebrates) and the Human Pangenome Project (aimed at population-scale sequencing of complete human genomes). I will describe the new algorithmic challenges in genome assembly, discuss the recently developed algorithms for their solution, and show how these algorithms bring us closer to the goal of complete genome sequencing.<br> <br><b>Bio:</b> Anton Bankevich is a Postdoctoral Scholar at the Computer Science and Engineering Department at UCSD. After getting the B.S. degree in Computer Science from Saint Petersburg University, Russia in 2009, he started working on his Ph.D. in algebraic graph theory. However, after joining the Center for Algorithmic Biotechnology in Saint Petersburg in 2011, he switched to developing the SPAdes genome assembler (Bankevich et al., J. Comp. Biology, 2012) that, with over 11,000 citations to date, is now the most widely-used assembler in the world. Dr. Bankevich joined UCSD as a postdoctoral scholar after receiving his Ph.D. (2018) in Computer Science from Saint Petersburg University. His research interests cover genomics and metagenomics (with a focus on algorithms and data analysis for genome assembly) and include collaborations on the discovery of novel insecticide toxins (with Keith Turner), leaderboard metagenomics (with Rob Knight), and comparative genomics (with Stephen O’Brien).</div><div><br></div><div><b>Host: </b><a href="mailto:j3xu@ttic.edu" target="_blank">Jinbo Xu</a></div><div><br></div><div><br><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"><br></p></div></div><div><div dir="ltr"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><font face="arial, helvetica, sans-serif">Mary C. Marre</font><div><font face="arial, helvetica, sans-serif">Faculty Administrative Support</font></div><div><i><font face="arial, helvetica, sans-serif" color="#3d85c6"><b>Toyota Technological Institute</b></font></i></div><div><i><font face="arial, helvetica, sans-serif" color="#3d85c6">6045 S. Kenwood Avenue</font></i></div><div><i><font face="arial, helvetica, sans-serif" color="#3d85c6">Room 517</font></i></div><div><i><font face="arial, helvetica, sans-serif" color="#3d85c6">Chicago, IL 60637</font></i></div><div><i><font face="arial, helvetica, sans-serif">p:(773) 834-1757</font></i></div><div><i><font face="arial, helvetica, sans-serif">f: (773) 357-6970</font></i></div><div><b><i><a href="mailto:mmarre@ttic.edu" target="_blank"><font face="arial, helvetica, sans-serif">mmarre@ttic.edu</font></a></i></b></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div><br></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Tue, Feb 9, 2021 at 7:36 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><p style="font-size:small;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;line-height:normal;margin:0px"><font face="arial, sans-serif"><font style="vertical-align:inherit"><font style="vertical-align:inherit"><b>When:</b> </font></font><font style="vertical-align:inherit"><font style="vertical-align:inherit"> Monday, February 15th at<b> 11:10 am CT</b></font></font><br></font></p><p class="MsoNormal" style="font-size:small;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></p><p class="MsoNormal" style="font-size:small;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="vertical-align:inherit"><font style="vertical-align:inherit"><b>Where:</b> </font></font><font color="#000000">Zoom Virtual Talk (</font><b><font color="#0000ff"><a href="https://uchicagogroup.zoom.us/webinar/register/WN_OjIiAnUnTDac7S-d_c7whg" target="_blank">register in advance here</a></font></b><font color="#000000">)</font></font></p><p class="MsoNormal" style="font-size:small;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></p><p class="MsoNormal" style="font-size:small;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="vertical-align:inherit"><font style="vertical-align:inherit"><b>Who: </b> </font></font></font>Anton Bankevich, UC San Diego</p><p class="MsoNormal" style="font-size:small;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"><br></p><p class="MsoNormal" style="font-size:small;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"><br></p><b>Title: </b> Algorithmic Challenges in Long-Read Genome Assembly<br><br><b>Abstract:</b> Even though the first draft human genome was generated two decades ago, many important regions (such as centromeres) still represent the “terra incognita'' of genome sequencing. The recently emerged long-read DNA sequencing technologies promise to transform genome sequencing toward generating complete genomes and lead to a critical demand for fast and accurate genome assembly algorithms. They also raised novel algorithmic problems since all previously developed assembly approaches fail for long reads. These problems represent the key bottlenecks for the ongoing Big Data sequencing projects, such as the Vertebrate Genomes Project (aimed at sequencing genomes of all vertebrates) and the Human Pangenome Project (aimed at population-scale sequencing of complete human genomes). I will describe the new algorithmic challenges in genome assembly, discuss the recently developed algorithms for their solution, and show how these algorithms bring us closer to the goal of complete genome sequencing.<br> <br><b>Bio:</b> Anton Bankevich is a Postdoctoral Scholar at the Computer Science and Engineering Department at UCSD. After getting the B.S. degree in Computer Science from Saint Petersburg University, Russia in 2009, he started working on his Ph.D. in algebraic graph theory. However, after joining the Center for Algorithmic Biotechnology in Saint Petersburg in 2011, he switched to developing the SPAdes genome assembler (Bankevich et al., J. Comp. Biology, 2012) that, with over 11,000 citations to date, is now the most widely-used assembler in the world. Dr. Bankevich joined UCSD as a postdoctoral scholar after receiving his Ph.D. (2018) in Computer Science from Saint Petersburg University. His research interests cover genomics and metagenomics (with a focus on algorithms and data analysis for genome assembly) and include collaborations on the discovery of novel insecticide toxins (with Keith Turner), leaderboard metagenomics (with Rob Knight), and comparative genomics (with Stephen O’Brien).</div><div><br></div><div><b>Host: </b><a href="mailto:j3xu@ttic.edu" target="_blank">Jinbo Xu</a><p class="MsoNormal" style="font-size:small;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"><br></p><p class="MsoNormal" style="font-size:small;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"><br></p><p class="MsoNormal" style="font-size:small;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"><br></p><p class="MsoNormal" style="font-size:small;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"><br></p><p class="MsoNormal" style="font-size:small;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"><br></p><p class="MsoNormal" style="font-size:small;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"><br></p></div><div><div dir="ltr"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><font face="arial, helvetica, sans-serif">Mary C. Marre</font><div><font face="arial, helvetica, sans-serif">Faculty Administrative Support</font></div><div><i><font face="arial, helvetica, sans-serif" color="#3d85c6"><b>Toyota Technological Institute</b></font></i></div><div><i><font face="arial, helvetica, sans-serif" color="#3d85c6">6045 S. Kenwood Avenue</font></i></div><div><i><font face="arial, helvetica, sans-serif" color="#3d85c6">Room 517</font></i></div><div><i><font face="arial, helvetica, sans-serif" color="#3d85c6">Chicago, IL 60637</font></i></div><div><i><font face="arial, helvetica, sans-serif">p:(773) 834-1757</font></i></div><div><i><font face="arial, helvetica, sans-serif">f: (773) 357-6970</font></i></div><div><b><i><a href="mailto:mmarre@ttic.edu" target="_blank"><font face="arial, helvetica, sans-serif">mmarre@ttic.edu</font></a></i></b></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div>
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