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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
Research

The rate of de novo structural variation is increased in in vitro–produced offspring and preferentially affects the paternal genome

  • Young-Lim Lee
  • Aniek C. Bouwman
  • Chad Harland
  • Mirte Bosse
  • Gabriel Costa Monteiro Moreira
  • Roel F. Veerkamp Erik Mullaart Nadine Cambisano Martien A.M. Groenen
  • ... [+4 authors] ...,
  • Latifa Karim
  • Wouter Coppieters
  • Michel Georges
  • Carole Charlier
  • First Published October 4, 2023
Resource

An organism-wide ATAC-seq peak catalog for the bovine and its use to identify regulatory variants

  • Can Yuan
  • Lijing Tang
  • Thomas Lopdell
  • Vyacheslav A. Petrov
  • Claire Oget-Ebrad
  • Gabriel Costa Monteiro Moreira José Luis Gualdrón Duarte Arnaud Sartelet Zhangrui Cheng Mazdak Salavati D. Claire Wathes Mark A. Crowe Wouter Coppieters Mathew Littlejohn Carole Charlier Tom Druet Michel Georges Haruko Takeda Mark Crowe Niamh McLoughlin Alan Fahey Elizabeth Matthews Andreia Santoro Colin Byrne Pauline Rudd Roisin O'Flaherty Sinead Hallinan Claire Wathes Zhangrui Cheng Ali Fouladi Geoff Pollott Dirk Werling Beatriz Sanz Bernardo Mazdak Salavati Laura Buggiotti Alistair Wylie Matt Bell Conrad Ferris Mieke Vaneetvelde Kristof Hermans Geert Opsomer Sander Moerman Jenne De Koster Hannes Bogaert Jan Vandepitte Leila Vandevelde Bonny Vanranst Johanna Hoglund Susanne Dahl Klaus Ingvartsen Martin Sørensen Leslie Foldager Soren Ostergaard Janne Rothmann Mogens Krogh Else Meyer Charlotte Gaillard Jehan Ettema Tine Rousing Federica Signorelli Francesco Napolitano Bianca Moioli Alessandra Crisa Luca Buttazzoni Jennifer McClure Daragh Matthews Francis Kearney Andrew Cromie Matt McClure Shujun Zhang Xing Chen Huanchun Chen Junlong Zhao Liguo Yang Guohua Hua Chen Tan Guiqiang Wang Michel Bonneau Andrea Pompozzi Armin Pearn Arnold Evertson Linda Kosten Anders Fogh Thomas Andersen Matthew Lucy Chris Elsik Gavin Conant Jerry Taylor Nicolas Gengler Michel Georges Frederic Colinet Marilou Ramos Pamplona Hedi Hammami Catherine Bastin Haruko Takeda Aurelie Laine
  • ... [+91 authors] ...,
  • Lijing Tang
  • Martin Schulze
  • Cinzia Marchitelli
  • Sergio Palma-Vera
  • First Published September 26, 2023
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

SNP-based quantitative deconvolution of biological mixtures: application to the detection of cows with subclinical mastitis by whole-genome sequencing of tank milk

  • Wouter Coppieters
  • Latifa Karim
  • Michel Georges
  • First Published June 26, 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
Research

NGS-based reverse genetic screen for common embryonic lethal mutations compromising fertility in livestock

  • Carole Charlier
  • Wanbo Li
  • Chad Harland
  • Mathew Littlejohn
  • Wouter Coppieters
  • Frances Creagh Steve Davis Tom Druet Pierre Faux François Guillaume Latifa Karim Mike Keehan
  • ... [+7 authors] ...,
  • Naveen Kumar Kadri
  • Nico Tamma
  • Richard Spelman
  • Michel Georges
  • First Published September 19, 2016
Research

HFM1, MLH3, MSH4, MSH5, RNF212, and RNF212B affect recombination rate in cattle" > Coding and noncoding variants in HFM1, MLH3, MSH4, MSH5, RNF212, and RNF212B affect recombination rate in cattle

  • Naveen Kumar Kadri
  • Chad Harland
  • Pierre Faux
  • Nadine Cambisano
  • Latifa Karim
  • Wouter Coppieters Sébastien Fritz Erik Mullaart Denis Baurain Didier Boichard
  • ... [+5 authors] ...,
  • Richard Spelman
  • Carole Charlier
  • Michel Georges
  • Tom Druet
  • First Published August 11, 2016
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
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