Search Results - Ferhat Ay

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  1. 1
    Identification of copy number variations and translocations in cancer cells from Hi-C data

    Identification of copy number variations and translocations in cancer cells from Hi-C data by Abhijit Chakraborty, Ferhat Ay

    Published 2017
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  2. 2
    Analysis methods for studying the 3D architecture of the genome

    Analysis methods for studying the 3D architecture of the genome by Ferhat Ay, William Stafford Noble

    Published 2015
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    Revisão
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  3. 3
    SubMAP: Aligning Metabolic Pathways with Subnetwork Mappings

    SubMAP: Aligning Metabolic Pathways with Subnetwork Mappings by Ferhat Ay, Manolis Kellis, Tamer Kahveci

    Published 2011
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  4. 4
    Scalable Steady State Analysis of Boolean Biological Regulatory Networks

    Scalable Steady State Analysis of Boolean Biological Regulatory Networks by Ferhat Ay, Fei Xu, Tamer Kahveci

    Published 2009
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  5. 5
    Identifying statistically significant chromatin contacts from Hi-C data with FitHiC2

    Identifying statistically significant chromatin contacts from Hi-C data with FitHiC2 by Arya Kaul, Sourya Bhattacharyya, Ferhat Ay

    Published 2020
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  6. 6
    dcHiC detects differential compartments across multiple Hi-C datasets

    dcHiC detects differential compartments across multiple Hi-C datasets by Abhijit Chakraborty, Jeffrey Wang, Ferhat Ay

    Published 2022
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  7. 7
    Selfish: discovery of differential chromatin interactions via a self-similarity measure

    Selfish: discovery of differential chromatin interactions via a self-similarity measure by Abbas Roayaei Ardakany, Ferhat Ay, Stefano Lonardi

    Published 2019
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  8. 8
    Statistical confidence estimation for Hi-C data reveals regulatory chromatin contacts

    Statistical confidence estimation for Hi-C data reveals regulatory chromatin contacts by Ferhat Ay, Timothy L. Bailey, William Stafford Noble

    Published 2014
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  9. 9
    Identification of significant chromatin contacts from HiChIP data by FitHiChIP

    Identification of significant chromatin contacts from HiChIP data by FitHiChIP by Sourya Bhattacharyya, Vivek Chandra, Pandurangan Vijayanand, Ferhat Ay

    Published 2019
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  10. 10
    A statistical approach for inferring the 3D structure of the genome

    A statistical approach for inferring the 3D structure of the genome by Nelle Varoquaux, Ferhat Ay, William Stafford Noble, Jean‐Philippe Vert

    Published 2014
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  11. 11
    Mustache: multi-scale detection of chromatin loops from Hi-C and Micro-C maps using scale-space representation

    Mustache: multi-scale detection of chromatin loops from Hi-C and Micro-C maps using scale-space representation by Abbas Roayaei Ardakany, Halil Tuvan Gezer, Stefano Lonardi, Ferhat Ay

    Published 2020
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  12. 12
    Topologically associating domains and their long-range contacts are established during early G1 coincident with the establishment of the replication-timing program

    Topologically associating domains and their long-range contacts are established during early G1 coincident with the establishment of the replication-timing program by Vishnu Dileep, Ferhat Ay, Jiao Sima, Daniel L. Vera, William Stafford Noble, David M. Gilbert

    Published 2015
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  13. 13
    nipalsMCIA: Flexible Multi-Block Dimensionality Reduction in R via Nonlinear Iterative Partial Least Squares

    nipalsMCIA: Flexible Multi-Block Dimensionality Reduction in R via Nonlinear Iterative Partial Least Squares by Max Mattessich, Joaquin Reyna, E Aron, Ferhat Ay, Misha E. Kilmer, Steven H. Kleinstein, Anna Konstorum

    Published 2025
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  14. 14
    Multiple dimensions of epigenetic gene regulation in the malaria parasite <i>Plasmodium falciparum</i>

    Multiple dimensions of epigenetic gene regulation in the malaria parasite <i>Plasmodium falciparum</i> by Ferhat Ay, Evelien M. Bunnik, Nelle Varoquaux, Jean‐Philippe Vert, William Stafford Noble, Karine G. Le Roch

    Published 2014
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  15. 15
    Joint annotation of chromatin state and chromatin conformation reveals relationships among domain types and identifies domains of cell-type-specific expression

    Joint annotation of chromatin state and chromatin conformation reveals relationships among domain types and identifies domains of cell-type-specific expression by Maxwell W. Libbrecht, Ferhat Ay, Michael M. Hoffman, David M. Gilbert, Jeffrey A. Bilmes, William Stafford Noble

    Published 2015
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  16. 16
    A predictive modeling approach for cell line-specific long-range regulatory interactions

    A predictive modeling approach for cell line-specific long-range regulatory interactions by Sushmita Roy, Alireza Fotuhi Siahpirani, Deborah Chasman, Sara Knaack, Ferhat Ay, Ron Stewart, Michael D. Wilson, Rupa Sridharan

    Published 2015
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  17. 17
    Predictive regulatory models in <i>Drosophila melanogaster</i> by integrative inference of transcriptional networks

    Predictive regulatory models in <i>Drosophila melanogaster</i> by integrative inference of transcriptional networks by Daniel Marbach, Sushmita Roy, Ferhat Ay, Patrick E. Meyer, Rogerio Candeias, Tamer Kahveci, Christopher A. Bristow, Manolis Kellis

    Published 2012
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  18. 18
    Form and function of topologically associating genomic domains in budding yeast

    Form and function of topologically associating genomic domains in budding yeast by Umut Eser, Devon Chandler‐Brown, Ferhat Ay, Aaron F. Straight, Zhijun Duan, William Stafford Noble, Jan M. Skotheim

    Published 2017
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  19. 19
    Identifying multi-locus chromatin contacts in human cells using tethered multiple 3C

    Identifying multi-locus chromatin contacts in human cells using tethered multiple 3C by Ferhat Ay, Thanh Vu, Μ. Zeitz, Nelle Varoquaux, Jan E. Carette, Jean‐Philippe Vert, Andrew R. Hoffman, William Stafford Noble

    Published 2015
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  20. 20
    Comprehensive identification and analysis of human accelerated regulatory DNA

    Comprehensive identification and analysis of human accelerated regulatory DNA by Rachel M. Gittelman, Enna Hun, Ferhat Ay, Jennifer Madeoy, L Pennacchio, William Stafford Noble, R. David Hawkins, Joshua M. Akey

    Published 2015
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