Searching journal content for Thomas R. Gingeras in author.

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  1. Resource: A limited set of transcriptional programs define major cell types
    • Alessandra Breschi,
    • Manuel Muñoz-Aguirre,
    • Valentin Wucher,
    • Carrie A. Davis,
    • Diego Garrido-Martín,
    • Sarah Djebali,
    • Jesse Gillis,
    • Dmitri D. Pervouchine,
    • Anna Vlasova,
    • Alexander Dobin,
    • Chris Zaleski,
    • Jorg Drenkow,
    • Cassidy Danyko,
    • Alexandra Scavelli,
    • Ferran Reverter,
    • Michael P. Snyder,
    • Thomas R. Gingeras,
    • and Roderic Guigó
    Genome Res. July 2020 30: 1047-1059; Published in Advance July 29, 2020, doi:10.1101/gr.263186.120
    OPEN ACCESS ARTICLE
  2. Resource: Dynamics of microRNA expression during mouse prenatal development
    • Sorena Rahmanian,
    • Rabi Murad,
    • Alessandra Breschi,
    • Weihua Zeng,
    • Mark Mackiewicz,
    • Brian Williams,
    • Carrie A. Davis,
    • Brian Roberts,
    • Sarah Meadows,
    • Dianna Moore,
    • Diane Trout,
    • Chris Zaleski,
    • Alex Dobin,
    • Lei-Hoon Sei,
    • Jorg Drenkow,
    • Alex Scavelli,
    • Thomas R. Gingeras,
    • Barbara J. Wold,
    • Richard M. Myers,
    • Roderic Guigó,
    • and Ali Mortazavi
    Genome Res. November 2019 29: 1900-1909; Published in Advance October 23, 2019, doi:10.1101/gr.248997.119
    OPEN ACCESS ARTICLE
  3. Research: Genome-wide analysis of polymerase III–transcribed Alu elements suggests cell-type–specific enhancer function
    • Xiao-Ou Zhang,
    • Thomas R. Gingeras,
    • and Zhiping Weng
    Genome Res. September 2019 29: 1402-1414; Published in Advance August 14, 2019, doi:10.1101/gr.249789.119
  4. Research: De novo DNA demethylation and noncoding transcription define active intergenic regulatory elements
    • Felix Schlesinger,
    • Andrew D. Smith,
    • Thomas R. Gingeras,
    • Gregory J. Hannon,
    • and Emily Hodges
    Genome Res. October 2013 23: 1601-1614; Published in Advance June 28, 2013, doi:10.1101/gr.157271.113
  5. Method: High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression
    • Philippe Batut,
    • Alexander Dobin,
    • Charles Plessy,
    • Piero Carninci,
    • and Thomas R. Gingeras
    Genome Res. January 2013 23: 169-180; Published in Advance August 30, 2012, doi:10.1101/gr.139618.112
  6. Research: Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs
    • Hagen Tilgner,
    • David G. Knowles,
    • Rory Johnson,
    • Carrie A. Davis,
    • Sudipto Chakrabortty,
    • Sarah Djebali,
    • João Curado,
    • Michael Snyder,
    • Thomas R. Gingeras,
    • and Roderic Guigó
    Genome Res. September 2012 22: 1616-1625; doi:10.1101/gr.134445.111
    OPEN ACCESS ARTICLE
  7. Research: Understanding transcriptional regulation by integrative analysis of transcription factor binding data
    • Chao Cheng,
    • Roger Alexander,
    • Renqiang Min,
    • Jing Leng,
    • Kevin Y. Yip,
    • Joel Rozowsky,
    • Koon-Kiu Yan,
    • Xianjun Dong,
    • Sarah Djebali,
    • Yijun Ruan,
    • Carrie A. Davis,
    • Piero Carninci,
    • Timo Lassman,
    • Thomas R. Gingeras,
    • Roderic Guigó,
    • Ewan Birney,
    • Zhiping Weng,
    • Michael Snyder,
    • and Mark Gerstein
    Genome Res. September 2012 22: 1658-1667; doi:10.1101/gr.136838.111
    OPEN ACCESS ARTICLE
  8. Resource: The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression
    • Thomas Derrien,
    • Rory Johnson,
    • Giovanni Bussotti,
    • Andrea Tanzer,
    • Sarah Djebali,
    • Hagen Tilgner,
    • Gregory Guernec,
    • David Martin,
    • Angelika Merkel,
    • David G. Knowles,
    • Julien Lagarde,
    • Lavanya Veeravalli,
    • Xiaoan Ruan,
    • Yijun Ruan,
    • Timo Lassmann,
    • Piero Carninci,
    • James B. Brown,
    • Leonard Lipovich,
    • Jose M. Gonzalez,
    • Mark Thomas,
    • Carrie A. Davis,
    • Ramin Shiekhattar,
    • Thomas R. Gingeras,
    • Tim J. Hubbard,
    • Cedric Notredame,
    • Jennifer Harrow,
    • and Roderic Guigó
    Genome Res. September 2012 22: 1775-1789; doi:10.1101/gr.132159.111
    OPEN ACCESS ARTICLE
  9. Resource: Synthetic spike-in standards for RNA-seq experiments
    • Lichun Jiang,
    • Felix Schlesinger,
    • Carrie A. Davis,
    • Yu Zhang,
    • Renhua Li,
    • Marc Salit,
    • Thomas R. Gingeras,
    • and Brian Oliver
    Genome Res. September 2011 21: 1543-1551; Published in Advance August 4, 2011, doi:10.1101/gr.121095.111
    OPEN ACCESS ARTICLE
  10. Resource: The transcriptional diversity of 25 Drosophila cell lines
    • Lucy Cherbas,
    • Aarron Willingham,
    • Dayu Zhang,
    • Li Yang,
    • Yi Zou,
    • Brian D. Eads,
    • Joseph W. Carlson,
    • Jane M. Landolin,
    • Philipp Kapranov,
    • Jacqueline Dumais,
    • Anastasia Samsonova,
    • Jeong-Hyeon Choi,
    • Johnny Roberts,
    • Carrie A. Davis,
    • Haixu Tang,
    • Marijke J. van Baren,
    • Srinka Ghosh,
    • Alexander Dobin,
    • Kim Bell,
    • Wei Lin,
    • Laura Langton,
    • Michael O. Duff,
    • Aaron E. Tenney,
    • Chris Zaleski,
    • Michael R. Brent,
    • Roger A. Hoskins,
    • Thomas C. Kaufman,
    • Justen Andrews,
    • Brenton R. Graveley,
    • Norbert Perrimon,
    • Susan E. Celniker,
    • Thomas R. Gingeras,
    • and Peter Cherbas
    Genome Res. February 2011 21: 301-314; Published in Advance December 22, 2010, doi:10.1101/gr.112961.110
    OPEN ACCESS ARTICLE
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