[Theory] TALK NOW: 3/4 Talks at TTIC: Chirag Jain, NIH/NHGRI

[Mary Marre]

*When:*      Wednesday, March 4th at 11:00 am



*Where:*     TTIC, 6045 S. Kenwood Avenue, 5th Floor, Room 526



*Who: *       Chirag Jain, NIH/NHGRI



*Title:     *   Scalable Algorithms for Rapidly Advancing DNA Sequencing
Technologies

*Abstract:  *Genomics continues to have an immense impact in life sciences,
from elucidating fundamental genetic mechanisms to providing new keys to
understand diseases. Catalyzed by breakthroughs in genomic
technologies,high-throughput DNA sequencing has become a major generator of
data, catching up with the most prominent big-data applications such as
astronomy and social media. As a result, it has become challenging to
design scalable bioinformatics algorithms with suitable accuracy guarantees.

In the first part of my talk, I will formulate the problem of aligning a
biological sequence to a ‘pan-genome’ graph. The graph-based representation
has been touted as the new standard for human genome reference,as it can
succinctly capture human genetic variation across the globe. I will present
new complexity results and algorithms for computing an optimal sequence
alignment using such graphs. In the second part, I will present an approximate
sketch-based algorithm for mapping long noisy sequences. The proposed algorithm
is able to map sequences to the entire NCBI genome database (totaling ~1
Tbp) for the first time, enabling real-time genomic analysis. I will
also discuss
generalization of the proposed algorithms to a wider set of problems, and their
impact in tackling long-standing biological questions.

*Bio: *Dr. Jain is currently a postdoctoral fellow with Dr. Adam Phillippy
in the Genome Informatics Section at the National Institutes ofHealth
(NIH), USA. He got his doctorate in Computational Science at Georgia Tech
under the supervision of Prof. Srinivas Aluru, and bachelors in Computer
Science from IIT Delhi.  He is a recipient of the Best GPU Paper Award at
IEEE HiPC’14, Best Poster awards at RECOMB’19, CRIDC’19, IITD-Open
House’14, and Reproducibility-Initiative Award at ACM Supercomputing'16.

*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 Wed, Mar 4, 2020 at 9:56 AM Mary Marre <mmarre at ttic.edu> wrote:

> *When:*      Wednesday, March 4th at 11:00 am
>
>
>
> *Where:*     TTIC, 6045 S. Kenwood Avenue, 5th Floor, Room 526
>
>
>
> *Who: *       Chirag Jain, NIH/NHGRI
>
>
>
> *Title:     *   Scalable Algorithms for Rapidly Advancing DNA Sequencing
> Technologies
>
> *Abstract:  *Genomics continues to have an immense impact in life
> sciences, from elucidating fundamental genetic mechanisms to providing new
> keys to understand diseases. Catalyzed by breakthroughs in genomic
> technologies,high-throughput DNA sequencing has become a major generator of
> data, catching up with the most prominent big-data applications such as
> astronomy and social media. As a result, it has become challenging to
> design scalable bioinformatics algorithms with suitable accuracy guarantees.
>
> In the first part of my talk, I will formulate the problem of aligning a
> biological sequence to a ‘pan-genome’ graph. The graph-based
> representation has been touted as the new standard for human genome
> reference,as it can succinctly capture human genetic variation across the
> globe. I will present new complexity results and algorithms for computing
> an optimal sequence alignment using such graphs. In the second part, I
> will present an approximate sketch-based algorithm for mapping long noisy
> sequences. The proposed algorithm is able to map sequences to the entire
> NCBI genome database (totaling ~1 Tbp) for the first time, enabling
> real-time genomic analysis. I will also discuss generalization of the
> proposed algorithms to a wider set of problems, and their impact in
> tackling long-standing biological questions.
>
> *Bio: *Dr. Jain is currently a postdoctoral fellow with Dr. Adam
> Phillippy in the Genome Informatics Section at the National Institutes
> ofHealth (NIH), USA. He got his doctorate in Computational Science at
> Georgia Tech under the supervision of Prof. Srinivas Aluru, and bachelors
> in Computer Science from IIT Delhi.  He is a recipient of the Best GPU
> Paper Award at IEEE HiPC’14, Best Poster awards at RECOMB’19, CRIDC’19,
> IITD-Open House’14, and Reproducibility-Initiative Award at ACM
> Supercomputing'16.
>
> *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, Mar 3, 2020 at 12:42 PM Mary Marre <mmarre at ttic.edu> wrote:
>
>> *When:*      Wednesday, March 4th at 11:00 am
>>
>>
>>
>> *Where:*     TTIC, 6045 S. Kenwood Avenue, 5th Floor, Room 526
>>
>>
>>
>> *Who: *       Chirag Jain, NIH/NHGRI
>>
>>
>>
>> *Title:     *   Scalable Algorithms for Rapidly Advancing DNA Sequencing
>> Technologies
>>
>> *Abstract:  *Genomics continues to have an immense impact in life
>> sciences, from elucidating fundamental genetic mechanisms to providing new
>> keys to understand diseases. Catalyzed by breakthroughs in genomic
>> technologies,high-throughput DNA sequencing has become a major generator of
>> data, catching up with the most prominent big-data applications such as
>> astronomy and social media. As a result, it has become challenging to
>> design scalable bioinformatics algorithms with suitable accuracy guarantees.
>>
>> In the first part of my talk, I will formulate the problem of aligning a
>> biological sequence to a ‘pan-genome’ graph. The graph-based
>> representation has been touted as the new standard for human genome
>> reference,as it can succinctly capture human genetic variation across the
>> globe. I will present new complexity results and algorithms for
>> computing an optimal sequence alignment using such graphs. In the second
>> part, I will present an approximate sketch-based algorithm for mapping
>> long noisy sequences. The proposed algorithm is able to map sequences to
>> the entire NCBI genome database (totaling ~1 Tbp) for the first time,
>> enabling real-time genomic analysis. I will also discuss generalization
>> of the proposed algorithms to a wider set of problems, and their impact
>> in tackling long-standing biological questions.
>>
>> *Bio: *Dr. Jain is currently a postdoctoral fellow with Dr. Adam
>> Phillippy in the Genome Informatics Section at the National Institutes
>> ofHealth (NIH), USA. He got his doctorate in Computational Science at
>> Georgia Tech under the supervision of Prof. Srinivas Aluru, and bachelors
>> in Computer Science from IIT Delhi.  He is a recipient of the Best GPU
>> Paper Award at IEEE HiPC’14, Best Poster awards at RECOMB’19, CRIDC’19,
>> IITD-Open House’14, and Reproducibility-Initiative Award at ACM
>> Supercomputing'16.
>>
>> *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 Thu, Feb 27, 2020 at 11:54 AM Mary Marre <mmarre at ttic.edu> wrote:
>>
>>> *When:*      Wednesday, March 4th at 11:00 am
>>>
>>>
>>>
>>> *Where:*     TTIC, 6045 S. Kenwood Avenue, 5th Floor, Room 526
>>>
>>>
>>>
>>> *Who: *       Chirag Jain, NIH/NHGRI
>>>
>>>
>>>
>>> *Title:     *   Scalable Algorithms for Rapidly Advancing DNA
>>> Sequencing Technologies
>>>
>>> *Abstract:  *Genomics continues to have an immense impact in life
>>> sciences, from elucidating fundamental genetic mechanisms to providing new
>>> keys to understand diseases. Catalyzed by breakthroughs in genomic
>>> technologies,high-throughput DNA sequencing has become a major generator of
>>> data, catching up with the most prominent big-data applications such as
>>> astronomy and social media. As a result, it has become challenging to
>>> design scalable bioinformatics algorithms with suitable accuracy guarantees.
>>>
>>> In the first part of my talk, I will formulate the problem of aligning
>>> a biological sequence to a ‘pan-genome’ graph. The graph-based
>>> representation has been touted as the new standard for human genome
>>> reference,as it can succinctly capture human genetic variation across the
>>> globe. I will present new complexity results and algorithms for
>>> computing an optimal sequence alignment using such graphs. In the
>>> second part, I will present an approximate sketch-based algorithm for
>>> mapping long noisy sequences. The proposed algorithm is able to map
>>> sequences to the entire NCBI genome database (totaling ~1 Tbp) for the
>>> first time, enabling real-time genomic analysis. I will also discuss
>>> generalization of the proposed algorithms to a wider set of problems,
>>> and their impact in tackling long-standing biological questions.
>>>
>>> *Bio: *Dr. Jain is currently a postdoctoral fellow with Dr. Adam
>>> Phillippy in the Genome Informatics Section at the National Institutes
>>> ofHealth (NIH), USA. He got his doctorate in Computational Science at
>>> Georgia Tech under the supervision of Prof. Srinivas Aluru, and bachelors
>>> in Computer Science from IIT Delhi.  He is a recipient of the Best GPU
>>> Paper Award at IEEE HiPC’14, Best Poster awards at RECOMB’19, CRIDC’19,
>>> IITD-Open House’14, and Reproducibility-Initiative Award at ACM
>>> Supercomputing'16.
>>>
>>> *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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