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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
Method

Finished bacterial genomes from shotgun sequence data

  • Filipe J. Ribeiro
  • Dariusz Przybylski
  • Shuangye Yin
  • Ted Sharpe
  • Sante Gnerre
  • Amr Abouelleil Aaron M. Berlin Anna Montmayeur Terrance P. Shea Bruce J. Walker Sarah K. Young
  • ... [+6 authors] ...,
  • Carsten Russ
  • Chad Nusbaum
  • Iain MacCallum
  • David B. Jaffe
  • First Published July 24, 2012
Method

Paired-end sequencing of Fosmid libraries by Illumina

  • Louise J.S. Williams
  • Diana G. Tabbaa
  • Na Li
  • Aaron M. Berlin
  • Terrance P. Shea
  • Iain MacCallum Michael S. Lawrence Yotam Drier Gad Getz
  • ... [+4 authors] ...,
  • Sarah K. Young
  • David B. Jaffe
  • Chad Nusbaum
  • Andreas Gnirke
  • First Published July 16, 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
Resource

Assemblathon 1: A competitive assessment of de novo short read assembly methods

  • Dent Earl
  • Keith Bradnam
  • John St. John
  • Aaron Darling
  • Dawei Lin
  • Joseph Fass Hung On Ken Yu Vince Buffalo Daniel R. Zerbino Mark Diekhans Ngan Nguyen Pramila Nuwantha Ariyaratne Wing-Kin Sung Zemin Ning Matthias Haimel Jared T. Simpson Nuno A. Fonseca İnanç Birol T. Roderick Docking Isaac Y. Ho Daniel S. Rokhsar Rayan Chikhi Dominique Lavenier Guillaume Chapuis Delphine Naquin Nicolas Maillet Michael C. Schatz David R. Kelley Adam M. Phillippy Sergey Koren Shiaw-Pyng Yang Wei Wu Wen-Chi Chou Anuj Srivastava Timothy I. Shaw J. Graham Ruby Peter Skewes-Cox Miguel Betegon Michelle T. Dimon Victor Solovyev Igor Seledtsov Petr Kosarev Denis Vorobyev Ricardo Ramirez-Gonzalez Richard Leggett Dan MacLean Fangfang Xia Ruibang Luo Zhenyu Li Yinlong Xie Binghang Liu Sante Gnerre Iain MacCallum Dariusz Przybylski Filipe J. Ribeiro Shuangye Yin Ted Sharpe Giles Hall Paul J. Kersey Richard Durbin Shaun D. Jackman Jarrod A. Chapman Xiaoqiu Huang Joseph L. DeRisi Mario Caccamo Yingrui Li David B. Jaffe
  • ... [+62 authors] ...,
  • Richard E. Green
  • David Haussler
  • Ian Korf
  • Benedict Paten
  • First Published September 16, 2011
RESOURCE

ALLPATHS: De novo assembly of whole-genome shotgun microreads

  • Jonathan Butler
  • Iain MacCallum
  • Michael Kleber
  • Ilya A. Shlyakhter
  • Matthew K. Belmonte
  • Eric S. Lander
  • Chad Nusbaum
  • David B. Jaffe
  • First Published March 13, 2008
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