Searching journal content for Ferhat Ay in author.

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  1. Research: 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,
    • and Jon P. Boyle
    Genome Res. May 2021 31: 834-851; Published in Advance April 27, 2021, doi:10.1101/gr.262816.120
    OPEN ACCESS ARTICLE
  2. 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,
    • Rachel Soloff,
    • Gregory Seumois,
    • Pandurangan Vijayanand,
    • and Ferhat Ay
    Genome Res. April 2021 31: 659-676; Published in Advance March 5, 2021, doi:10.1101/gr.265249.120
  3. 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,
    • Wei Li,
    • Andrew R. Hoffman,
    • Ji-Fan Hu,
    • and Jiuwei Cui
    Genome Res. September 2019 29: 1521-1532; Published in Advance July 17, 2019, doi:10.1101/gr.244996.118
    OPEN ACCESS ARTICLE
  4. 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,
    • and David M. Gilbert
    Genome Res. September 2019 29: 1415-1428; Published in Advance August 21, 2019, doi:10.1101/gr.247049.118
  5. 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,
    • and Joshua M. Akey
    Genome Res. September 2015 25: 1245-1255; Published in Advance June 23, 2015, doi:10.1101/gr.192591.115
  6. 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,
    • and David M. Gilbert
    Genome Res. August 2015 25: 1104-1113; Published in Advance May 20, 2015, doi:10.1101/gr.183699.114
  7. 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,
    • and William Stafford Noble
    Genome Res. April 2015 25: 544-557; Published in Advance February 12, 2015, doi:10.1101/gr.184341.114
  8. Research: 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,
    • and Karine G. Le Roch
    Genome Res. June 2014 24: 974-988; Published in Advance March 26, 2014, doi:10.1101/gr.169417.113
  9. Method: Statistical confidence estimation for Hi-C data reveals regulatory chromatin contacts
    • Ferhat Ay,
    • Timothy L. Bailey,
    • and William Stafford Noble
    Genome Res. June 2014 24: 999-1011; Published in Advance February 5, 2014, doi:10.1101/gr.160374.113
  10. Method: 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,
    • and Manolis Kellis
    Genome Res. July 2012 22: 1334-1349; Published in Advance March 28, 2012, doi:10.1101/gr.127191.111
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