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Research

Multi-species analysis of inflammatory response elements reveals ancient and lineage-specific contributions of transposable elements to NF-kB binding

Liangxi Wang
Tiegh Taylor
Kumaragurubaran Rathnakumar
Nadiya Khyzha
Minggao Liang
Azad Alizada Laura F. Campitelli Sara E. Pour Zain M. Patel Lina Antounians Ian C. Tobias Huayun Hou Timothy R. Hughes
... [+8 authors] ...,
Sushmita Roy
Jennifer A. Mitchell
Jason E. Fish
Michael D. Wilson

First Published June 6, 2025

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

Research

Yeast genetic interaction screen of human genes associated with amyotrophic lateral sclerosis: identification of MAP2K5 kinase as a potential drug target

Myungjin Jo
Ah Young Chung
Nozomu Yachie
Minchul Seo
Hyejin Jeon
Youngpyo Nam Yeojin Seo Eunmi Kim Quan Zhong
... [+4 authors] ...,
Marc Vidal
Hae Chul Park
Frederick P. Roth
Kyoungho Suk

First Published June 8, 2017

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

Research

Diurnal regulation of RNA polymerase III transcription is under the control of both the feeding–fasting response and the circadian clock

François Mange
Viviane Praz
Eugenia Migliavacca
Ian M. Willis
Frédéric Schütz
Nouria Hernandez Nouria Hernandez Mauro Delorenzi Bart Deplancke Béatrice Desvergne Nicolas Guex Winship Herr Felix Naef Jacques Rougemont Ueli Schibler Teemu Andersin Pascal Cousin Federica Gilardi Fabienne Lammers François Mange Dominic Villeneuve Fabrice David Roberto Fabbretti Philippe Jacquet Irina Krier Dmitry Kuznetsov Marion Leleu Robin Liechti Olivier Martin Eugenia Migliavacca Aurélien Naldi Viviane Praz
... [+27 authors] ...,
Leonor Rib
Jonathan Sobel
Volker Vlegel
Ioannis Xenarios

First Published March 24, 2017

Method

An extended set of yeast-based functional assays accurately identifies human disease mutations

Song Sun
Fan Yang
Guihong Tan
Michael Costanzo
Rose Oughtred
Jodi Hirschman Chandra L. Theesfeld Pritpal Bansal Nidhi Sahni Song Yi Analyn Yu Tanya Tyagi Cathy Tie David E. Hill Marc Vidal
... [+10 authors] ...,
Brenda J. Andrews
Charles Boone
Kara Dolinski
Frederick P. Roth

First Published March 14, 2016

Method

Quantifying ChIP-seq data: a spiking method providing an internal reference for sample-to-sample normalization

Nicolas Bonhoure
Gergana Bounova
David Bernasconi
Viviane Praz
Fabienne Lammers
Donatella Canella Ian M. Willis Winship Herr Nouria Hernandez Mauro Delorenzi Nouria Hernandez Mauro Delorenzi Bart Deplancke Béatrice Desvergne Nicolas Guex Winship Herr Felix Naef Jacques Rougemont Ueli Schibler Teemu Andersin Pascal Cousin Federica Gilardi Pascal Gos Fabienne Lammers Sunil Raghav Dominic Villeneuve Roberto Fabbretti Volker Vlegel Ioannis Xenarios Eugenia Migliavacca Viviane Praz Fabrice David Yohan Jarosz Dmitry Kuznetsov Robin Liechti Olivier Martin Julien Delafontaine Julia Cajan Kyle Gustafson Irina Krier Marion Leleu Nacho Molina
... [+37 authors] ...,
Aurélien Naldi
Leonor Rib
Laura Symul
Gergana Bounova

First Published April 7, 2014

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

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Your search for returned 31 results

Research

Multi-species analysis of inflammatory response elements reveals ancient and lineage-specific contributions of transposable elements to NF-kB binding

Method

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

Method

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

Research

Yeast genetic interaction screen of human genes associated with amyotrophic lateral sclerosis: identification of MAP2K5 kinase as a potential drug target

Method

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

Research

Diurnal regulation of RNA polymerase III transcription is under the control of both the feeding–fasting response and the circadian clock

Method

An extended set of yeast-based functional assays accurately identifies human disease mutations

Method

Quantifying ChIP-seq data: a spiking method providing an internal reference for sample-to-sample normalization

Method

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

Method

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

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