Analysis methods for studying the 3D architecture of the genome

Por Ay, Ferhat, Noble, William S.
Publicado no Genome Biol (2015)

Scalable Steady State Analysis of Boolean Biological Regulatory Networks

Por Ay, Ferhat, Xu, Fei, Kahveci, Tamer
Publicado em 2009

SubMAP: Aligning Metabolic Pathways with Subnetwork Mappings

Por Ay, Ferhat, Kellis, Manolis, Kahveci, Tamer
Publicado em 2011

Metabolic network alignment in large scale by network compression

Por Ay, Ferhat, Dang, Michael, Kahveci, Tamer
Publicado em 2012

A multi-task graph-clustering approach for chromosome conformation capture data sets identifies conserved modules of chromosomal interactions

Por Fotuhi Siahpirani, Alireza, Ay, Ferhat, Roy, Sushmita
Publicado no Genome Biol (2016)

Statistical confidence estimation for Hi-C data reveals regulatory chromatin contacts

Por Ay, Ferhat, Bailey, Timothy L., Noble, William Stafford
Publicado em 2014

A statistical approach for inferring the 3D structure of the genome

Por Varoquaux, Nelle, Ay, Ferhat, Noble, William Stafford, Vert, Jean-Philippe
Publicado no Bioinformatics (2014)

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

Por Dileep, Vishnu, Ay, Ferhat, Sima, Jiao, Vera, Daniel L., Noble, William S., Gilbert, David M.
Publicado no Genome Res (2015)

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

Por Libbrecht, Maxwell W., Ay, Ferhat, Hoffman, Michael M., Gilbert, David M., Bilmes, Jeffrey A., Noble, William Stafford
Publicado no Genome Res (2015)

Multiple dimensions of epigenetic gene regulation in the malaria parasite Plasmodium falciparum: Gene regulation via histone modifications, nucleosome positioning and nuclear archi...

Por Ay, Ferhat, Bunnik, Evelien M., Varoquaux, Nelle, Vert, Jean-Philippe, Noble, William Stafford, Le Roch, Karine G.
Publicado no Bioessays (2014)

A predictive modeling approach for cell line-specific long-range regulatory interactions

Por Roy, Sushmita, Siahpirani, Alireza Fotuhi, Chasman, Deborah, Knaack, Sara, Ay, Ferhat, Stewart, Ron, Wilson, Michael, Sridharan, Rupa
Publicado no Nucleic Acids Res (2015)

A predictive modeling approach for cell line-specific long-range regulatory interactions

Por Roy, Sushmita, Siahpirani, Alireza Fotuhi, Chasman, Deborah, Knaack, Sara, Ay, Ferhat, Stewart, Ron, Wilson, Michael, Sridharan, Rupa
Publicado no Nucleic Acids Res (2016)

Predictive regulatory models in Drosophila melanogaster by integrative inference of transcriptional networks

Por Marbach, Daniel, Roy, Sushmita, Ay, Ferhat, Meyer, Patrick E., Candeias, Rogerio, Kahveci, Tamer, Bristow, Christopher A., Kellis, Manolis
Publicado em 2012

Form and function of topologically associating genomic domains in budding yeast

Por Eser, Umut, Chandler-Brown, Devon, Ay, Ferhat, Straight, Aaron F., Duan, Zhijun, Noble, William Stafford, Skotheim, Jan M.
Publicado no Proc Natl Acad Sci U S A (2017)

Genomic Interaction Profiles in Breast Cancer Reveal Altered Chromatin Architecture

Por Zeitz, Michael J., Ay, Ferhat, Heidmann, Julia D., Lerner, Paula L., Noble, William S., Steelman, Brandon N., Hoffman, Andrew R.
Publicado em 2013

Implications of COMT long-range interactions on the phenotypic variability of 22q11.2 deletion syndrome

Por Zeitz, Michael J, Lerner, Paula P, Ay, Ferhat, Van Nostrand, Eric, Heidmann, Julia D, Noble, William S, Hoffman, Andrew R
Publicado em 2013

Accurate identification of centromere locations in yeast genomes using Hi-C

Por Varoquaux, Nelle, Liachko, Ivan, Ay, Ferhat, Burton, Joshua N., Shendure, Jay, Dunham, Maitreya J., Vert, Jean-Philippe, Noble, William S.
Publicado no Nucleic Acids Res (2015)

Comprehensive identification and analysis of human accelerated regulatory DNA

Por Gittelman, Rachel M., Hun, Enna, Ay, Ferhat, Madeoy, Jennifer, Pennacchio, Len, Noble, William S., Hawkins, R. David, Akey, Joshua M.
Publicado no Genome Res (2015)

Identifying multi-locus chromatin contacts in human cells using tethered multiple 3C

Por Ay, Ferhat, Vu, Thanh H, Zeitz, Michael J, Varoquaux, Nelle, Carette, Jan E, Vert, Jean-Philippe, Hoffman, Andrew R, Noble, William S
Publicado no BMC Genomics (2015)

Three-dimensional modeling of the P. falciparum genome during the erythrocytic cycle reveals a strong connection between genome architecture and gene expression

Por Ay, Ferhat, Bunnik, Evelien M., Varoquaux, Nelle, Bol, Sebastiaan M., Prudhomme, Jacques, Vert, Jean-Philippe, Noble, William Stafford, Le Roch, Karine G.
Publicado em 2014