[Theory] REMINDER: 3/17 Talks at TTIC: Ahmed Abbas, The Jackson Laboratory (JAX)

[Mary Marre]

*When:*      Wednesday, March 17th at* 11:10 am CT*



*Where:*     Zoom Virtual Talk (*register in advance here
<https://uchicagogroup.zoom.us/webinar/register/WN_03lG-UTPT8KjMqd0AL1wtQ>*)



*Who: *       Ahmed Abbas, The Jackson Laboratory (JAX)


*Title:*        Integrating Hi-C and FISHdata for Modeling of the 3D
Organization of Chromosomes

*Abstract:* The new advances in various experimental techniques that
provide complementary information about the spatial conformations of
chromosomes have inspired researchers to develop computational methods to
fully exploit the merits of individual data sources and combine them to
improve the modeling of chromosome structure. Here we propose GEM-FISH, a
method for reconstructing the3D models of chromosomes through
systematically integrating both Hi-C and FISHdata with the prior
biophysical knowledge of a polymer model. Comprehensive Tests on a set of
chromosomes, for which both Hi-C and FISH data are available,demonstrate
that GEM-FISH can outperform previous chromosome structure modeling methods
and accurately capture the higher order spatial features of chromosome
conformations. Moreover, our reconstructed 3D models of chromosomes
revealed interesting patterns of spatial distributions of super-enhancers
which can provide useful insights into understanding the functional roles
of these super-enhancers in gene regulation.

*Biography:*  Ahmed Abbas is a postdoctoral associate at The Jackson
Laboratory for Genomic Medicine. He received his Master's degree in
Computer Science from Ain Shams University, Egypt, in 2010. Then, he joined
King Abdullah University for Science and Technology (KAUST) as a Ph.D.
student and received his Ph.D. degree in 2015. During his Ph.D. study, he
worked on developing new methods to solve key open problems in automated
NMR protein structure determination. He did his first postdoctoral training
at the Institute of Interdisciplinary Information Sciences (IIIS), Tsinghua
University. During his training at Tsinghua University, he worked on a
project on three-dimensional chromosome modeling through the integration of
Hi-C and FISH data and published his work in Nature Communications. He
joined The Jackson Laboratory for Genomic Medicine in 2019, and his main
research at Jax is on developing computational methods for scATAC-seq data
denoising and single-cell data analysis in general.


*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 16, 2021 at 4:11 PM Mary Marre <mmarre at ttic.edu> wrote:

> *When:*      Wednesday, March 17th at* 11:10 am CT*
>
>
>
> *Where:*     Zoom Virtual Talk (*register in advance here
> <https://uchicagogroup.zoom.us/webinar/register/WN_03lG-UTPT8KjMqd0AL1wtQ>*
> )
>
>
>
> *Who: *       Ahmed Abbas, The Jackson Laboratory (JAX)
>
>
> *Title:*        Integrating Hi-C and FISHdata for Modeling of the 3D
> Organization of Chromosomes
>
> *Abstract:* The new advances in various experimental techniques that
> provide complementary information about the spatial conformations of
> chromosomes have inspired researchers to develop computational methods to
> fully exploit the merits of individual data sources and combine them to
> improve the modeling of chromosome structure. Here we propose GEM-FISH, a
> method for reconstructing the3D models of chromosomes through
> systematically integrating both Hi-C and FISHdata with the prior
> biophysical knowledge of a polymer model. Comprehensive Tests on a set of
> chromosomes, for which both Hi-C and FISH data are available,demonstrate
> that GEM-FISH can outperform previous chromosome structure modeling methods
> and accurately capture the higher order spatial features of chromosome
> conformations. Moreover, our reconstructed 3D models of chromosomes
> revealed interesting patterns of spatial distributions of super-enhancers
> which can provide useful insights into understanding the functional roles
> of these super-enhancers in gene regulation.
>
> *Biography:*  Ahmed Abbas is a postdoctoral associate at The Jackson
> Laboratory for Genomic Medicine. He received his Master's degree in
> Computer Science from Ain Shams University, Egypt, in 2010. Then, he joined
> King Abdullah University for Science and Technology (KAUST) as a Ph.D.
> student and received his Ph.D. degree in 2015. During his Ph.D. study, he
> worked on developing new methods to solve key open problems in automated
> NMR protein structure determination. He did his first postdoctoral training
> at the Institute of Interdisciplinary Information Sciences (IIIS), Tsinghua
> University. During his training at Tsinghua University, he worked on a
> project on three-dimensional chromosome modeling through the integration of
> Hi-C and FISH data and published his work in Nature Communications. He
> joined The Jackson Laboratory for Genomic Medicine in 2019, and his main
> research at Jax is on developing computational methods for scATAC-seq data
> denoising and single-cell data analysis in general.
>
>
> *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 10, 2021 at 8:31 PM Mary Marre <mmarre at ttic.edu> wrote:
>
>> *When:*      Wednesday, March 17th at* 11:10 am CT*
>>
>>
>>
>> *Where:*     Zoom Virtual Talk (*register in advance here
>> <https://uchicagogroup.zoom.us/webinar/register/WN_03lG-UTPT8KjMqd0AL1wtQ>*
>> )
>>
>>
>>
>> *Who: *       Ahmed Abbas, The Jackson Laboratory (JAX)
>>
>>
>> *Title:*        Integrating Hi-C and FISHdata for Modeling of the 3D
>> Organization of Chromosomes
>>
>> *Abstract:* The new advances in various experimental techniques that
>> provide complementary information about the spatial conformations of
>> chromosomes have inspired researchers to develop computational methods to
>> fully exploit the merits of individual data sources and combine them to
>> improve the modeling of chromosome structure. Here we propose GEM-FISH, a
>> method for reconstructing the3D models of chromosomes through
>> systematically integrating both Hi-C and FISHdata with the prior
>> biophysical knowledge of a polymer model. Comprehensive Tests on a set of
>> chromosomes, for which both Hi-C and FISH data are available,demonstrate
>> that GEM-FISH can outperform previous chromosome structure modeling methods
>> and accurately capture the higher order spatial features of chromosome
>> conformations. Moreover, our reconstructed 3D models of chromosomes
>> revealed interesting patterns of spatial distributions of super-enhancers
>> which can provide useful insights into understanding the functional roles
>> of these super-enhancers in gene regulation.
>>
>> *Biography:*  Ahmed Abbas is a postdoctoral associate at The Jackson
>> Laboratory for Genomic Medicine. He received his Master's degree in
>> Computer Science from Ain Shams University, Egypt, in 2010. Then, he joined
>> King Abdullah University for Science and Technology (KAUST) as a Ph.D.
>> student and received his Ph.D. degree in 2015. During his Ph.D. study, he
>> worked on developing new methods to solve key open problems in automated
>> NMR protein structure determination. He did his first postdoctoral training
>> at the Institute of Interdisciplinary Information Sciences (IIIS), Tsinghua
>> University. During his training at Tsinghua University, he worked on a
>> project on three-dimensional chromosome modeling through the integration of
>> Hi-C and FISH data and published his work in Nature Communications. He
>> joined The Jackson Laboratory for Genomic Medicine in 2019, and his main
>> research at Jax is on developing computational methods for scATAC-seq data
>> denoising and single-cell data analysis in general.
>>
>> *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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