[Theory] NOW: 2/15 Talks at TTIC: Anton Bankevich, UC San Diego

[Mary Marre]

*When:*       Monday, February 15th at* 11:10 am CT*



*Where:*      Zoom Virtual Talk (*register in advance here
<https://uchicagogroup.zoom.us/webinar/register/WN_OjIiAnUnTDac7S-d_c7whg>*)



*Who: *        Anton Bankevich, UC San Diego



*Title:    *    Algorithmic Challenges in Long-Read Genome Assembly

*Abstract:* 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.

*Bio:* 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).

*Host: *Jinbo Xu <j3xu at ttic.edu>

Mary C. Marre
Faculty Administrative Support
*Toyota Technological Institute*
*6045 S. Kenwood Avenue*
*Room 517*
*Chicago, IL  60637*
*p:(773) 834-1757*
*f: (773) 357-6970*
*mmarre at ttic.edu <mmarre at ttic.edu>*


On Mon, Feb 15, 2021 at 10:00 AM Mary Marre <mmarre at ttic.edu> wrote:

> *When:*       Monday, February 15th at* 11:10 am CT*
>
>
>
> *Where:*      Zoom Virtual Talk (*register in advance here
> <https://uchicagogroup.zoom.us/webinar/register/WN_OjIiAnUnTDac7S-d_c7whg>*
> )
>
>
>
> *Who: *        Anton Bankevich, UC San Diego
>
>
>
> *Title:    *    Algorithmic Challenges in Long-Read Genome Assembly
>
> *Abstract:* 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.
>
> *Bio:* 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).
>
> *Host: *Jinbo Xu <j3xu at ttic.edu>
>
>
>
> Mary C. Marre
> Faculty Administrative Support
> *Toyota Technological Institute*
> *6045 S. Kenwood Avenue*
> *Room 517*
> *Chicago, IL  60637*
> *p:(773) 834-1757*
> *f: (773) 357-6970*
> *mmarre at ttic.edu <mmarre at ttic.edu>*
>
>
> On Sun, Feb 14, 2021 at 3:30 PM Mary Marre <mmarre at ttic.edu> wrote:
>
>> *When:*       Monday, February 15th at* 11:10 am CT*
>>
>>
>>
>> *Where:*      Zoom Virtual Talk (*register in advance here
>> <https://uchicagogroup.zoom.us/webinar/register/WN_OjIiAnUnTDac7S-d_c7whg>*
>> )
>>
>>
>>
>> *Who: *        Anton Bankevich, UC San Diego
>>
>>
>>
>> *Title:    *    Algorithmic Challenges in Long-Read Genome Assembly
>>
>> *Abstract:* 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.
>>
>> *Bio:* 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).
>>
>> *Host: *Jinbo Xu <j3xu at ttic.edu>
>>
>>
>>
>> Mary C. Marre
>> Faculty Administrative Support
>> *Toyota Technological Institute*
>> *6045 S. Kenwood Avenue*
>> *Room 517*
>> *Chicago, IL  60637*
>> *p:(773) 834-1757*
>> *f: (773) 357-6970*
>> *mmarre at ttic.edu <mmarre at ttic.edu>*
>>
>>
>> On Tue, Feb 9, 2021 at 7:36 PM Mary Marre <mmarre at ttic.edu> wrote:
>>
>>> *When:*       Monday, February 15th at* 11:10 am CT*
>>>
>>>
>>>
>>> *Where:*      Zoom Virtual Talk (*register in advance here
>>> <https://uchicagogroup.zoom.us/webinar/register/WN_OjIiAnUnTDac7S-d_c7whg>*
>>> )
>>>
>>>
>>>
>>> *Who: *        Anton Bankevich, UC San Diego
>>>
>>>
>>>
>>> *Title:    *    Algorithmic Challenges in Long-Read Genome Assembly
>>>
>>> *Abstract:* 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.
>>>
>>> *Bio:* 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).
>>>
>>> *Host: *Jinbo Xu <j3xu at ttic.edu>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> Mary C. Marre
>>> Faculty Administrative Support
>>> *Toyota Technological Institute*
>>> *6045 S. Kenwood Avenue*
>>> *Room 517*
>>> *Chicago, IL  60637*
>>> *p:(773) 834-1757*
>>> *f: (773) 357-6970*
>>> *mmarre at ttic.edu <mmarre at ttic.edu>*
>>>
>>
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