[Theory] REMINDER: 3/21 Talks at TTIC at 2pm!: Kristoffer Sahlin, Pennsylvania State University

[Mary Marre]

*When: *   Thursday, March 21st at *2:00 pm*

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

Who:       Kristoffer Sahlin, Pennsylvania State University

*Title:* Accelerating biological discovery with scalable and accurate
algorithms

*Abstract:*
In our cells, DNA and RNA holds information to answer questions about our
evolution, diseases, and traits. We are now able to assay this sequence
information at large scale using various high throughput sequencing
techniques. The rapid advances in sequencing technologies are allowing
molecular biologists to answer yet more complex questions about the
information encoded in our cells. However, these technological advances
require parallel advances in bioinformatic algorithms. Today, the lack of
fast and accurate tools is the bottleneck that stands between raw data and
biological discovery. Two ways to reduce the time spent on going from data
to answers are to improve runtime or accuracy of bioinformatic algorithms,
both of which are best solved through algorithmic design. In this talk, I
will outline some of the common bioinformatic problems encountered in
biological projects concerned with genome and transcriptome sequence
analysis, and I will present my research on algorithms to reduce the
computational bottleneck. I will first discuss how a simple model that I
designed bridged the gap between speed and accuracy in algorithms for
genomic problems such as genome assembly and structural variation
detection. I will then continue to describe my recent and ongoing work on
transcriptomics, focusing on reconstructing transcripts from long and noisy
reads.

Host: Jinbo Xu <j3xu at ttic.edu>



Mary C. Marre
Administrative Assistant
*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 20, 2019 at 4:52 PM Mary Marre <mmarre at ttic.edu> wrote:

> *When: *   Thursday, March 21st at *2:00 pm*
>
> Where:    TTIC, 6045 S Kenwood Avenue, 5th Floor, Room 526
>
> Who:       Kristoffer Sahlin, Pennsylvania State University
>
> *Title:* Accelerating biological discovery with scalable and accurate
> algorithms
>
> *Abstract:*
> In our cells, DNA and RNA holds information to answer questions about our
> evolution, diseases, and traits. We are now able to assay this sequence
> information at large scale using various high throughput sequencing
> techniques. The rapid advances in sequencing technologies are allowing
> molecular biologists to answer yet more complex questions about the
> information encoded in our cells. However, these technological advances
> require parallel advances in bioinformatic algorithms. Today, the lack of
> fast and accurate tools is the bottleneck that stands between raw data and
> biological discovery. Two ways to reduce the time spent on going from data
> to answers are to improve runtime or accuracy of bioinformatic algorithms,
> both of which are best solved through algorithmic design. In this talk, I
> will outline some of the common bioinformatic problems encountered in
> biological projects concerned with genome and transcriptome sequence
> analysis, and I will present my research on algorithms to reduce the
> computational bottleneck. I will first discuss how a simple model that I
> designed bridged the gap between speed and accuracy in algorithms for
> genomic problems such as genome assembly and structural variation
> detection. I will then continue to describe my recent and ongoing work on
> transcriptomics, focusing on reconstructing transcripts from long and noisy
> reads.
>
> Host: Jinbo Xu <j3xu at ttic.edu>
>
>
>
>
>
>
> Mary C. Marre
> Administrative Assistant
> *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 Sat, Mar 16, 2019 at 1:31 PM Mary Marre <mmarre at ttic.edu> wrote:
>
>> *When: *   Thursday, March 21st at *2:00 pm*
>>
>> Where:    TTIC, 6045 S Kenwood Avenue, 5th Floor, Room 526
>>
>> Who:       Kristoffer Sahlin, Pennsylvania State University
>>
>> *Title:* Accelerating biological discovery with scalable and accurate
>> algorithms
>>
>> *Abstract:*
>> In our cells, DNA and RNA holds information to answer questions about our
>> evolution, diseases, and traits. We are now able to assay this sequence
>> information at large scale using various high throughput sequencing
>> techniques. The rapid advances in sequencing technologies are allowing
>> molecular biologists to answer yet more complex questions about the
>> information encoded in our cells. However, these technological advances
>> require parallel advances in bioinformatic algorithms. Today, the lack of
>> fast and accurate tools is the bottleneck that stands between raw data and
>> biological discovery. Two ways to reduce the time spent on going from data
>> to answers are to improve runtime or accuracy of bioinformatic algorithms,
>> both of which are best solved through algorithmic design. In this talk, I
>> will outline some of the common bioinformatic problems encountered in
>> biological projects concerned with genome and transcriptome sequence
>> analysis, and I will present my research on algorithms to reduce the
>> computational bottleneck. I will first discuss how a simple model that I
>> designed bridged the gap between speed and accuracy in algorithms for
>> genomic problems such as genome assembly and structural variation
>> detection. I will then continue to describe my recent and ongoing work on
>> transcriptomics, focusing on reconstructing transcripts from long and noisy
>> reads.
>>
>> Host: Jinbo Xu <j3xu at ttic.edu>
>>
>>
>>
>>
>> Mary C. Marre
>> Administrative Assistant
>> *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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