Searching journal content for Lingyun Song in author.

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  1. Method: Profiling the quantitative occupancy of myriad transcription factors across conditions by modeling chromatin accessibility data
    • Kaixuan Luo,
    • Jianling Zhong,
    • Alexias Safi,
    • Linda K. Hong,
    • Alok K. Tewari,
    • Lingyun Song,
    • Timothy E. Reddy,
    • Li Ma,
    • Gregory E. Crawford,
    • and Alexander J. Hartemink
    Genome Res. June 2022 32: 1183-1198; Published in Advance May 24, 2022, doi:10.1101/gr.272203.120
  2. Method: Human cardiac cis-regulatory elements, their cognate transcription factors, and regulatory DNA sequence variants
    • Dongwon Lee,
    • Ashish Kapoor,
    • Alexias Safi,
    • Lingyun Song,
    • Marc K. Halushka,
    • Gregory E. Crawford,
    • and Aravinda Chakravarti
    Genome Res. October 2018 28: 1577-1588; Published in Advance August 23, 2018, doi:10.1101/gr.234633.118
    OPEN ACCESS ARTICLE
  3. Research: Glucocorticoid receptor recruits to enhancers and drives activation by motif-directed binding
    • Ian C. McDowell,
    • Alejandro Barrera,
    • Anthony M. D'Ippolito,
    • Christopher M. Vockley,
    • Linda K. Hong,
    • Sarah M. Leichter,
    • Luke C. Bartelt,
    • William H. Majoros,
    • Lingyun Song,
    • Alexias Safi,
    • D. Dewran Koçak,
    • Charles A. Gersbach,
    • Alexander J. Hartemink,
    • Gregory E. Crawford,
    • Barbara E. Engelhardt,
    • and Timothy E. Reddy
    Genome Res. September 2018 28: 1272-1284; Published in Advance August 10, 2018, doi:10.1101/gr.233346.117
    OPEN ACCESS ARTICLE
  4. Research: Microbiota regulate intestinal epithelial gene expression by suppressing the transcription factor Hepatocyte nuclear factor 4 alpha
    • James M. Davison,
    • Colin R. Lickwar,
    • Lingyun Song,
    • Ghislain Breton,
    • Gregory E. Crawford,
    • and John F. Rawls
    Genome Res. July 2017 27: 1195-1206; Published in Advance April 6, 2017, doi:10.1101/gr.220111.116
    OPEN ACCESS ARTICLE
  5. Research: Genome-wide specificity of DNA binding, gene regulation, and chromatin remodeling by TALE- and CRISPR/Cas9-based transcriptional activators
    • Lauren R. Polstein,
    • Pablo Perez-Pinera,
    • D. Dewran Kocak,
    • Christopher M. Vockley,
    • Peggy Bledsoe,
    • Lingyun Song,
    • Alexias Safi,
    • Gregory E. Crawford,
    • Timothy E. Reddy,
    • and Charles A. Gersbach
    Genome Res. August 2015 25: 1158-1169; Published in Advance May 29, 2015, doi:10.1101/gr.179044.114
  6. Research: DNase-seq predicts regions of rotational nucleosome stability across diverse human cell types
    • Deborah R. Winter,
    • Lingyun Song,
    • Sayan Mukherjee,
    • Terrence S. Furey,
    • and Gregory E. Crawford
    Genome Res. July 2013 23: 1118-1129; Published in Advance May 8, 2013, doi:10.1101/gr.150482.112
  7. Research: A dynamic H3K27ac signature identifies VEGFA-stimulated endothelial enhancers and requires EP300 activity
    • Bing Zhang,
    • Daniel S. Day,
    • Joshua W. Ho,
    • Lingyun Song,
    • Jingjing Cao,
    • Danos Christodoulou,
    • Jonathan G. Seidman,
    • Gregory E. Crawford,
    • Peter J. Park,
    • and William T. Pu
    Genome Res. June 2013 23: 917-927; Published in Advance April 1, 2013, doi:10.1101/gr.149674.112
  8. Research: Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions
    • Nathan C. Sheffield,
    • Robert E. Thurman,
    • Lingyun Song,
    • Alexias Safi,
    • John A. Stamatoyannopoulos,
    • Boris Lenhard,
    • Gregory E. Crawford,
    • and Terrence S. Furey
    Genome Res. May 2013 23: 777-788; Published in Advance March 12, 2013, doi:10.1101/gr.152140.112
    OPEN ACCESS ARTICLE
  9. Research: Effects of sequence variation on differential allelic transcription factor occupancy and gene expression
    • Timothy E. Reddy,
    • Jason Gertz,
    • Florencia Pauli,
    • Katerina S. Kucera,
    • Katherine E. Varley,
    • Kimberly M. Newberry,
    • Georgi K. Marinov,
    • Ali Mortazavi,
    • Brian A. Williams,
    • Lingyun Song,
    • Gregory E. Crawford,
    • Barbara Wold,
    • Huntington F. Willard,
    • and Richard M. Myers
    Genome Res. May 2012 22: 860-869; Published in Advance February 2, 2012, doi:10.1101/gr.131201.111
  10. Research: Cell-type specific and combinatorial usage of diverse transcription factors revealed by genome-wide binding studies in multiple human cells
    • Bum-Kyu Lee,
    • Akshay A. Bhinge,
    • Anna Battenhouse,
    • Ryan M. McDaniell,
    • Zheng Liu,
    • Lingyun Song,
    • Yunyun Ni,
    • Ewan Birney,
    • Jason D. Lieb,
    • Terrence S. Furey,
    • Gregory E. Crawford,
    • and Vishwanath R. Iyer
    Genome Res. January 2012 22: 9-24; Published in Advance November 16, 2011, doi:10.1101/gr.127597.111
    OPEN ACCESS ARTICLE
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