Ferhat Ay
Ferhat Ay
Associate Professor, La Jolla Institute for Immunology
Verified email at - Homepage
Cited by
Cited by
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
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
Statistical confidence estimation for Hi-C data reveals regulatory chromatin contacts
F Ay, TL Bailey, WS Noble
Genome research 24 (6), 999-1011, 2014
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
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
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
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
Severely ill COVID-19 patients display impaired exhaustion features in SARS-CoV-2-reactive CD8+ T cells
A Kusnadi, C Ramírez-Suástegui, V Fajardo, SJ Chee, BJ Meckiff, ...
Science Immunology 6 (55), 2021
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
Single-cell transcriptomic analysis of tissue-resident memory T cells in human lung cancer
J Clarke, B Panwar, A Madrigal, D Singh, R Gujar, O Wood, SJ Chee, ...
Journal of Experimental Medicine 216 (9), 2128-2149, 2019
Analysis methods for studying the 3D architecture of the genome
F Ay, WS Noble
Genome Biology 16 (1), 1-15, 2015
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
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
Identification of significant chromatin contacts from HiChIP data by FitHiChIP
S Bhattacharyya, V Chandra, P Vijayanand, F Ay
Nature communications 10 (1), 4221, 2019
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
Identifying statistically significant chromatin contacts from Hi-C data with FitHiC2
A Kaul, S Bhattacharyya, F Ay
Nature Protocols 15 (3), 991-1012, 2020
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
Mustache: multi-scale detection of chromatin loops from Hi-C and Micro-C maps using scale-space representation
A Roayaei Ardakany, HT Gezer, S Lonardi, F Ay
Genome Biology 21, 2020
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), 13426, 2016
Measuring the reproducibility and quality of Hi-C data
GG Yardımcı, H Ozadam, MEG Sauria, O Ursu, KK Yan, T Yang, ...
Genome biology 20, 1-19, 2019
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