Publications

All Altman Ay Benedict Cheroutre Croft Crotty Einav Eschweiler Grifoni Hedrick Hogan Kawakami Kronenberg Ley Lindestam Lisdestam Arlehamn Myers Pandurangan Peters Rao Reina Saphire Schmiedel Schoenberger Sette Seumois Sharma Shresta Vijayanand Von Herrath Weiskopf

Apr 11, 2017

Proc Natl Acad Sci USA

Form and function of topologically associating genomic domains in budding yeast

Eser U, Chandler-Brown D, Ay F, Straight AF, Duan Z, Noble WS, Skotheim JM

Sep 23, 2016

PLoS Genet

Neocentromeres provide chromosome segregation accuracy and centromere clustering to multiple loci along a candida albicans chromosome

Burrack LS, Hutton HF, Matter KJ, Clancey SA, Liachko I, Plemmons AE, Saha A, Power EA, Turman B, Thevandavakkam MA, Ay F, Dunham MJ, Berman J

May 27, 2016

Genome Biol

A multitask graph-clustering approach for chomosome conformation capture data sets identifies conserved modules of chromosomal interactions

Fotuhi Siahpirani A, Ay F, Roy S

Feb 29, 2016

Nucleic Acids Res

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

Roy S, Siahpirani AF, Chasman D, Knaak S, Ay F, Stewart R, Wilson M, Sridharan R

Sep 25, 2015

Genome Research

Comprehensive identification and analysis of human accelerated regulatory DNA

RM. Gittelman, E. Hun, F. Ay, J. Madeoy, L. Pennacchio, WS. Noble, RD. Hawkins, JM. Akey

Sep 02, 2015

Genome Biology

Analysis methods for studying the 3D architecture of the genome

F. Ay, WS. Noble

Aug 25, 2015

Genome Research

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

V. Dileep, F. Ay, J. Sima, DL. Vera, WS. Noble, DM. Gilbert

Aug 07, 2015

Genome Biology

Bipartite structure of the inactive mouse X chromosome

X. Deng, W. Ma, V. Rmani, A. Hill, F. Yang, F. Ay, JB. Berletch, CA. Blau, J. Shendure, WS. Noble, CM. Disteche

Jun 23, 2015

Nucleic Acids Research

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

N. Varoquaux, I. Liachko, F. Ay, JN. Burton, J. Shendure, MJ. Dunham, JP. Vert, WS. Noble

Apr 25, 2015

Genome Research

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

MW. Libbrecht, F. Ay, MM. Hoffman, DM. Gilbert, JA. Bilmes, WS. Noble

Feb 25, 2015

BMC Genomics

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

F. Ay, TH. Vu, MJ. Zeitz, N. Varoquax, JE. Carette, JP. Vert, AR. Hoffman, WS. Noble

Dec 01, 2014

Nature Methods

Fine-scale chromatin interaction maps reveal the cis-regulatory landscape of human lincRNA genes

W. Ma, F. Ay, C. Lee, G. Gulsoy, X. Deng, S. Cook, J. Hesson, C. Cavanaugh, CB. Ware, A. Krumm, J. Shendure, CA. Blau, CM. Disteche, WS. Noble