Search | Genome Research

EMBL_GR_LB_July1_15

Your search for returned 7 results

Method

Examining the dynamics of three-dimensional genome organization with multitask matrix factorization

Da-Inn Lee
Sushmita Roy

First Published March 20, 2025

Method

Dynamic regulatory module networks for inference of cell type–specific transcriptional networks

Alireza Fotuhi Siahpirani
Sara Knaack
Deborah Chasman
Morten Seirup
Rupa Sridharan
Ron Stewart
James Thomson
Sushmita Roy

First Published June 15, 2022

Method

Interpretation of allele-specific chromatin accessibility using cell state–aware deep learning

Zeynep Kalender Atak
Ibrahim Ihsan Taskiran
Jonas Demeulemeester
Christopher Flerin
David Mauduit
Liesbeth Minnoye Gert Hulselmans
... [+2 authors] ...,
Valerie Christiaens
Ghanem-Elias Ghanem
Jasper Wouters
Stein Aerts

First Published April 8, 2021

Method

Cross-species analysis of enhancer logic using deep learning

Liesbeth Minnoye
Ibrahim Ihsan Taskiran
David Mauduit
Maurizio Fazio
Linde Van Aerschot
Gert Hulselmans Valerie Christiaens Samira Makhzami Monika Seltenhammer Panagiotis Karras Aline Primot Edouard Cadieu Ellen van Rooijen Jean-Christophe Marine Giorgia Egidy
... [+10 authors] ...,
Ghanem-Elias Ghanem
Leonard Zon
Jasper Wouters
Stein Aerts

First Published July 30, 2020

Method

Chromatin module inference on cellular trajectories identifies key transition points and poised epigenetic states in diverse developmental processes

Sushmita Roy
Rupa Sridharan

First Published April 19, 2017

Method

Arboretum: Reconstruction and analysis of the evolutionary history of condition-specific transcriptional modules

Sushmita Roy
Ilan Wapinski
Jenna Pfiffner
Courtney French
Amanda Socha
Jay Konieczka
... [+1 authors] ...,
Naomi Habib
Manolis Kellis
Dawn Thompson
Aviv Regev

First Published May 2, 2013

Method

Drosophila melanogaster by integrative inference of transcriptional networks" > Predictive regulatory models in Drosophila melanogaster by integrative inference of transcriptional networks

Daniel Marbach
Sushmita Roy
Ferhat Ay
Patrick E. Meyer
Rogerio Candeias
Tamer Kahveci
Christopher A. Bristow
Manolis Kellis

First Published March 28, 2012