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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
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
Research

Drosophila simulans genome provides new insights into patterns of lineage-specific divergence" > A second-generation assembly of the Drosophila simulans genome provides new insights into patterns of lineage-specific divergence

  • Tina T. Hu
  • Michael B. Eisen
  • Kevin R. Thornton
  • Peter Andolfatto
  • First Published August 30, 2012
Research

Drosophila simulans clade" > Genome sequencing reveals complex speciation in the Drosophila simulans clade

  • Daniel Garrigan
  • Sarah B. Kingan
  • Anthony J. Geneva
  • Peter Andolfatto
  • Andrew G. Clark
  • Kevin R. Thornton
  • Daven C. Presgraves
  • First Published April 13, 2012
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
Method

Multiplexed shotgun genotyping for rapid and efficient genetic mapping

  • Peter Andolfatto
  • Dan Davison
  • Deniz Erezyilmaz
  • Tina T. Hu
  • Joshua Mast
  • Tomoko Sunayama-Morita
  • David L. Stern
  • First Published January 13, 2011
LETTER

Drosophila melanogaster genome" > Hitchhiking effects of recurrent beneficial amino acid substitutions in the Drosophila melanogaster genome

  • Peter Andolfatto
  • First Published November 7, 2007
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