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Research

Toxoplasma gondii and identifies emerging copy number variants in sexual recombinants" > Third-generation sequencing revises the molecular karyotype for Toxoplasma gondii and identifies emerging copy number variants in sexual recombinants

  • Jing Xia
  • Aarthi Venkat
  • Rachel E. Bainbridge
  • Michael L. Reese
  • Karine G. Le Roch
  • Ferhat Ay
  • Jon P. Boyle
  • First Published April 27, 2021
Method

Multi–cell type gene coexpression network analysis reveals coordinated interferon response and cross–cell type correlations in systemic lupus erythematosus

  • Bharat Panwar
  • Benjamin J. Schmiedel
  • Shu Liang
  • Brandie White
  • Enrique Rodriguez
  • Kenneth Kalunian Andrew J. McKnight
  • ... [+2 authors] ...,
  • Rachel Soloff
  • Gregory Seumois
  • Pandurangan Vijayanand
  • Ferhat Ay
  • First Published March 5, 2021
Research

Replication timing networks reveal a link between transcription regulatory circuits and replication timing control

  • Juan Carlos Rivera-Mulia
  • Sebo Kim
  • Haitham Gabr
  • Abhijit Chakraborty
  • Ferhat Ay
  • Tamer Kahveci
  • David M. Gilbert
  • First Published August 21, 2019
Method

Profiling the long noncoding RNA interaction network in the regulatory elements of target genes by chromatin in situ reverse transcription sequencing

  • Shilin Zhang
  • Yichen Wang
  • Lin Jia
  • Xue Wen
  • Zhonghua Du
  • Cong Wang Yajing Hao Dehai Yu Lei Zhou Naifei Chen Jingcheng Chen Huiling Chen Hui Zhang Ilkay Celik Günhan Gülsoy Jianjun Luo Baoming Qin Xueling Cui Zhonghui Liu Songling Zhang Miguel A. Esteban Ferhat Ay Wei Xu Runsheng Chen
  • ... [+19 authors] ...,
  • Wei Li
  • Andrew R. Hoffman
  • Ji-Fan Hu
  • Jiuwei Cui
  • First Published July 17, 2019
Method

Genome-wide chemical mutagenesis screens allow unbiased saturation of the cancer genome and identification of drug resistance mutations

  • Jonathan S. Brammeld
  • Mia Petljak
  • Inigo Martincorena
  • Steven P. Williams
  • Luz Garcia Alonso
  • Alba Dalmases Beatriz Bellosillo Carla Daniela Robles-Espinoza Stacey Price Syd Barthorpe Patrick Tarpey Constantine Alifrangis Graham Bignell Joana Vidal Jamie Young Lucy Stebbings Kathryn Beal Michael R. Stratton Julio Saez-Rodriguez
  • ... [+14 authors] ...,
  • Mathew Garnett
  • Clara Montagut
  • Francesco Iorio
  • Ultan McDermott
  • First Published February 8, 2017
Corrigendum

Corrigendum: Frequent somatic transfer of mitochondrial DNA into the nuclear genome of human cancer cells

  • Young Seok Ju
  • Jose M.C. Tubio
  • William Mifsud
  • Beiyuan Fu
  • Helen R. Davies
  • Manasa Ramakrishna Yilong Li Lucy Yates Gunes Gundem Patrick S. Tarpey Sam Behjati Elli Papaemmanuil Sancha Martin Anthony Fullam Moritz Gerstung Jyoti Nangalia Anthony R. Green Carlos Caldas Åke Borg Andrew Tutt Ming Ta Michael Lee Laura J. van't Veer Benita K.T. Tan Samuel Aparicio Paul N. Span John W.M. Martens Stian Knappskog Anne Vincent-Salomon Anne-Lise Børresen-Dale Jórunn Erla Eyfjörd Ola Myklebost Adrienne M. Flanagan Christopher Foster David E. Neal Colin Cooper Rosalind Eeles G. Steven Bova Sunil R. Lakhani Christine Desmedt Gilles Thomas Andrea L. Richardson Colin A. Purdie Alastair M. Thompson Ultan McDermott
  • ... [+39 authors] ...,
  • Fengtang Yang
  • Serena Nik-Zainal
  • Peter J. Campbell
  • Michael R. Stratton
  • First Published May 2, 2016
Research

Comprehensive identification and analysis of human accelerated regulatory DNA

  • Rachel M. Gittelman
  • Enna Hun
  • Ferhat Ay
  • Jennifer Madeoy
  • Len Pennacchio
  • William S. Noble
  • R. David Hawkins
  • Joshua M. Akey
  • First Published June 23, 2015
Research

Topologically associating domains and their long-range contacts are established during early G1 coincident with the establishment of the replication-timing program

  • Vishnu Dileep
  • Ferhat Ay
  • Jiao Sima
  • Daniel L. Vera
  • William S. Noble
  • David M. Gilbert
  • First Published May 20, 2015
Research

Frequent somatic transfer of mitochondrial DNA into the nuclear genome of human cancer cells

  • Young Seok Ju
  • Jose M.C. Tubio
  • William Mifsud
  • Beiyuan Fu
  • Helen R. Davies
  • Manasa Ramakrishna Yilong Li Lucy Yates Gunes Gundem Patrick S. Tarpey Sam Behjati Elli Papaemmanuil Sancha Martin Anthony Fullam Moritz Gerstung Jyoti Nangalia Anthony R. Green Carlos Caldas Åke Borg Andrew Tutt Ming Ta Michael Lee Laura J. van't Veer Benita K.T. Tan Samuel Aparicio Paul N. Span John W.M. Martens Stian Knappskog Anne Vincent-Salomon Anne-Lise Børresen-Dale Jórunn Erla Eyfjörd Ola Myklebost Adrienne M. Flanagan Christopher Foster David E. Neal Colin Cooper Rosalind Eeles G. Steven Bova Sunil R. Lakhani Christine Desmedt Gilles Thomas Andrea L. Richardson Colin A. Purdie Alastair M. Thompson Ultan McDermott
  • ... [+39 authors] ...,
  • Fengtang Yang
  • Serena Nik-Zainal
  • Peter J. Campbell
  • Michael R. Stratton
  • First Published May 11, 2015
Method

Joint annotation of chromatin state and chromatin conformation reveals relationships among domain types and identifies domains of cell-type-specific expression

  • Maxwell W. Libbrecht
  • Ferhat Ay
  • Michael M. Hoffman
  • David M. Gilbert
  • Jeffrey A. Bilmes
  • William Stafford Noble
  • First Published February 12, 2015
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