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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
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
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
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
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
Research

P. falciparum genome during the erythrocytic cycle reveals a strong connection between genome architecture and gene expression" > Three-dimensional modeling of the P. falciparum genome during the erythrocytic cycle reveals a strong connection between genome architecture and gene expression

  • Ferhat Ay
  • Evelien M. Bunnik
  • Nelle Varoquaux
  • Sebastiaan M. Bol
  • Jacques Prudhomme
  • Jean-Philippe Vert
  • William Stafford Noble
  • Karine G. Le Roch
  • First Published March 26, 2014
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