Publications

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

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

Fotuhi Siahpirani A, Ay F, Roy S

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

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

Analysis methods for studying the 3D architecture of the genome

F. Ay, WS. Noble

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

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

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

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

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

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

Multiple dimensions of epigenetic gene regulation in the malaria parasite Plasmodium falciparum

F. Ay, EM. Bunnik, N. Varoquax, JP. Vert, WS. Noble, KG. Le Roch