Ferhat Ay
Ferhat Ay
La Jolla Institute for Immunology
Verified email at lji.org - Homepage
Title
Cited by
Cited by
Year
Identification of functional elements and regulatory circuits by Drosophila modENCODE
S Roy, J Ernst, PV Kharchenko, P Kheradpour, N Negre, ML Eaton, ...
Science 330 (6012), 1787-1797, 2010
8892010
Statistical confidence estimation for Hi-C data reveals regulatory chromatin contacts
F Ay, TL Bailey, WS Noble
Genome research 24 (6), 999-1011, 2014
3102014
A statistical approach for inferring the 3D structure of the genome
N Varoquaux, F Ay, WS Noble, JP Vert
Bioinformatics 30 (12), i26-i33, 2014
1882014
Three-dimensional modeling of the P. falciparum genome during the erythrocytic cycle reveals a strong connection between genome architecture and gene expression
F Ay, EM Bunnik, N Varoquaux, SM Bol, J Prudhomme, JP Vert, WS Noble, ...
Genome research 24 (6), 974-988, 2014
1882014
Bipartite structure of the inactive mouse X chromosome
X Deng, W Ma, V Ramani, A Hill, F Yang, F Ay, JB Berletch, CA Blau, ...
Genome biology 16 (1), 1-21, 2015
1642015
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, ...
Nature Methods, 2014
1602014
Analysis methods for studying the 3D architecture of the genome
F Ay, WS Noble
Genome Biology 16 (1), 1-15, 2015
1412015
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
Genome Research, gr. 183699.114, 2015
1372015
Integrative detection and analysis of structural variation in cancer genomes
JR Dixon, J Xu, V Dileep, Y Zhan, F Song, VT Le, GG Yardımcı, ...
Nature genetics 50 (10), 1388-1398, 2018
1312018
Predictive regulatory models in Drosophila melanogaster by integrative inference of transcriptional networks
D Marbach, S Roy, F Ay, PE Meyer, R Candeias, T Kahveci, CA Bristow, ...
Genome Research 22 (7), 1334-1349, 2012
1132012
A predictive modeling approach for cell line-specific long-range regulatory interactions
S Roy, AF Siahpirani, D Chasman, S Knaack, F Ay, R Stewart, M Wilson, ...
Nucleic acids research 43 (18), 8694-8712, 2015
872015
Identifying cis elements for spatiotemporal control of mammalian dna replication
J Sima, A Chakraborty, V Dileep, M Michalski, KN Klein, NP Holcomb, ...
Cell 176 (4), 816-830. e18, 2019
752019
SubMAP: aligning metabolic pathways with subnetwork mappings
F Ay, M Kellis, T Kahveci
Journal of Computational Biology 18 (3), 219-235, 2011
732011
Scalable steady state analysis of Boolean biological regulatory networks
F Ay, F Xu, T Kahveci
PloS one 4 (12), e7992, 2009
732009
Imbalance of regulatory and cytotoxic SARS-CoV-2-reactive CD4+ T cells in COVID-19
BJ Meckiff, C Ramírez-Suástegui, V Fajardo, SJ Chee, A Kusnadi, ...
Cell, 2020
67*2020
Comprehensive identification and analysis of human accelerated regulatory DNA
RM Gittelman, E Hun, F Ay, J Madeoy, L Pennacchio, WS Noble, ...
Genome Res 25 (9), 1245-1255, 2015
642015
Form and function of topologically associating genomic domains in budding yeast
U Eser, D Chandler-Brown, F Ay, AF Straight, Z Duan, WS Noble, ...
Proceedings of the National Academy of Sciences 114 (15), E3061-E3070, 2017
592017
Multiple dimensions of epigenetic gene regulation in the malaria parasite Plasmodium falciparum Gene regulation via histone modifications, nucleosome positioning and …
F Ay, EM Bunnik, N Varoquaux, JP Vert, WS Noble, KG Le Roch
Bioessays 37 (2), 182-194, 2015
592015
17q21 asthma-risk variants switch CTCF binding and regulate IL-2 production by T cells
BJ Schmiedel, G Seumois, D Samaniego-Castruita, J Cayford, V Schulten, ...
Nature communications 7 (1), 1-14, 2016
582016
Measuring the reproducibility and quality of Hi-C data
GG Yardımcı, H Ozadam, MEG Sauria, O Ursu, KK Yan, T Yang, ...
Genome biology 20 (1), 1-19, 2019
562019
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