Search Results - Benjamin P. Berman

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  1. 1
    Demystifying the secret mission of enhancers: linking distal regulatory elements to target genes

    Demystifying the secret mission of enhancers: linking distal regulatory elements to target genes by Lijing Yao, Benjamin P. Berman, Peggy Farnham

    Published 2015
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  2. 2
    Functional annotation of colon cancer risk SNPs

    Functional annotation of colon cancer risk SNPs by Lijing Yao, Yu Gyoung Tak, Benjamin P. Berman, Peggy Farnham

    Published 2014
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  3. 3
    Bis-SNP: Combined DNA methylation and SNP calling for Bisulfite-seq data

    Bis-SNP: Combined DNA methylation and SNP calling for Bisulfite-seq data by Yaping Liu, Kimberly D. Siegmund, Peter W. Laird, Benjamin P. Berman

    Published 2012
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  4. 4
    Inferring regulatory element landscapes and transcription factor networks from cancer methylomes

    Inferring regulatory element landscapes and transcription factor networks from cancer methylomes by Lijing Yao, Hui Shen, Peter W. Laird, Peggy Farnham, Benjamin P. Berman

    Published 2015
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  5. 5
    FunciSNP: an R/bioconductor tool integrating functional non-coding data sets with genetic association studies to identify candidate regulatory SNPs

    FunciSNP: an R/bioconductor tool integrating functional non-coding data sets with genetic association studies to identify candidate regulatory SNPs by Simon G. Coetzee, Suhn K. Rhie, Benjamin P. Berman, Gerhard A. Coetzee, Houtan Noushmehr

    Published 2012
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  6. 6
    GENT-33. EPIGENETIC ALTERATIONS AT INTERGENIC REGIONS ASSOCIATED WITH PROGRESSION IN A SUBSET OF IDH MUTANT GLIOMAS

    GENT-33. EPIGENETIC ALTERATIONS AT INTERGENIC REGIONS ASSOCIATED WITH PROGRESSION IN A SUBSET OF IDH MUTANT GLIOMAS by Thaís S. Sabedot, Tathiane M. Malta, Michele Ceccarelli, Huy Dihn, Benjamin P. Berman, Houtan Noushmehr

    Published 2016
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  7. 7
    Global loss of DNA methylation uncovers intronic enhancers in genes showing expression changes

    Global loss of DNA methylation uncovers intronic enhancers in genes showing expression changes by Adam Blattler, Lijing Yao, Heather Witt, Yu Guo, Charles M. Nicolet, Benjamin P. Berman, Peggy Farnham

    Published 2014
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  8. 8
    Genome-wide mapping of nucleosome positioning and DNA methylation within individual DNA molecules

    Genome-wide mapping of nucleosome positioning and DNA methylation within individual DNA molecules by Theresa K. Kelly, Yaping Liu, Fides D. Lay, Gangning Liang, Benjamin P. Berman, Peter A. Jones

    Published 2012
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  9. 9
    TCGAbiolinksGUI: A graphical user interface to analyze GDC cancer molecular and clinical data

    TCGAbiolinksGUI: A graphical user interface to analyze GDC cancer molecular and clinical data by Tiago C. Silva, Antonio Colaprico, Catharina Olsen, Gianluca Bontempi, Michele Ceccarelli, Benjamin P. Berman, Houtan Noushmehr

    Published 2017
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  10. 10
    Global analysis of patterns of gene expression during Drosophila embryogenesis

    Global analysis of patterns of gene expression during Drosophila embryogenesis by Pavel Tomančák, Benjamin P. Berman, Amy Beaton, Richard Weiszmann, Elaine Kwan, Volker Hartenstein, S Celniker, Gerald M. Rubin

    Published 2007
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  11. 11
    The role of DNA methylation in directing the functional organization of the cancer epigenome

    The role of DNA methylation in directing the functional organization of the cancer epigenome by Fides D. Lay, Yaping Liu, Theresa K. Kelly, Heather Witt, Peggy Farnham, Peter A. Jones, Benjamin P. Berman

    Published 2015
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  12. 12
    H2A.Z Maintenance during Mitosis Reveals Nucleosome Shifting on Mitotically Silenced Genes

    H2A.Z Maintenance during Mitosis Reveals Nucleosome Shifting on Mitotically Silenced Genes by Theresa K. Kelly, Tina Branscombe Miranda, Gangning Liang, Benjamin P. Berman, Joy Lin, Amos Tanay, Peter A. Jones

    Published 2010
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  13. 13
    Gender-specific postnatal demethylation and establishment of epigenetic memory

    Gender-specific postnatal demethylation and establishment of epigenetic memory by Yitzhak Reizel, Adam Spiro, Ofra Sabag, Yael Skversky‐Blocq, Merav Hecht, Ilana Keshet, Benjamin P. Berman, Howard Cedar

    Published 2015
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  14. 14
    Dynamic Nucleosome-Depleted Regions at Androgen Receptor Enhancers in the Absence of Ligand in Prostate Cancer Cells

    Dynamic Nucleosome-Depleted Regions at Androgen Receptor Enhancers in the Absence of Ligand in Prostate Cancer Cells by Claudia Andreu‐Vieyra, John Lai, Benjamin P. Berman, Baruch Frenkel, Jia Li, Peter A. Jones, Gerhard A. Coetzee

    Published 2011
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  15. 15
    Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura.

    Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobs... by Benjamin P. Berman, Barret D. Pfeiffer, Todd Laverty, Steven L. Salzberg, Gerald M. Rubin, Michael B. Eisen, S Celniker

    Published 2004
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  16. 16
    Exosomal MicroRNA Transfer Into Macrophages Mediates Cellular Postconditioning

    Exosomal MicroRNA Transfer Into Macrophages Mediates Cellular Postconditioning by Geoffrey de Couto, Romain Gallet, Linda Cambier, Ervin Jaghatspanyan, Nupur Makkar, James Dawkins, Benjamin P. Berman, Eduardo Marbán

    Published 2017
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  17. 17
    Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the <i>Drosophila</i> genome

    Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the <i>Drosophila</i> genome by Benjamin P. Berman, Yutaka Nibu, Barret D. Pfeiffer, Pavel Tomančák, S Celniker, Michael Levine, Gerald M. Rubin, Michael B. Eisen

    Published 2002
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  18. 18
    TCGAbiolinksGUI: A graphical user interface to analyze cancer molecular and clinical data

    TCGAbiolinksGUI: A graphical user interface to analyze cancer molecular and clinical data by Tiago C. Silva, Antonio Colaprico, Catharina Olsen, Tathiane M. Malta, Gianluca Bontempi, Michele Ceccarelli, Benjamin P. Berman, Houtan Noushmehr

    Published 2018
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  19. 19
    DNA methylation loss in late-replicating domains is linked to mitotic cell division

    DNA methylation loss in late-replicating domains is linked to mitotic cell division by Wanding Zhou, Huy Q. Dinh, Zachary Ramjan, Daniel J. Weisenberger, Charles M. Nicolet, Hui Shen, Peter W. Laird, Benjamin P. Berman

    Published 2018
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  20. 20
    ELMER v.2: an R/Bioconductor package to reconstruct gene regulatory networks from DNA methylation and transcriptome profiles

    ELMER v.2: an R/Bioconductor package to reconstruct gene regulatory networks from DNA methylation and transcriptome profiles by Tiago C. Silva, Simon G. Coetzee, Nicole Gull, Lijing Yao, Dennis J. Hazelett, Houtan Noushmehr, De‐Chen Lin, Benjamin P. Berman

    Published 2018
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