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F

Ferhat Ay

La Jolla Institute for Immunology

46H-index
196Paper Count
9.6KCitation Count
Published Papers 69
Publication Date
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Genomic language model for predicting enhancers and their allele-specific activity in the human genome
errBioinformatics
IF5.4
err2026-09-10
err0
errOAAI
errRekha Sathian; Pratik Dutta; Ferhat Ay; Ramana V Davuluri; null
errShare
errSave
Loss of TET function in T regulatory cells yields ex-Treg cells biased toward T follicular helper cells; causing autoimmune diseases through autoantibody production
errFrontiers in Immunology
IF5.9
err2026-03-31
err0
errOAAI
errKS Kazumasa Suzuki; LJ Leo J. Arteaga-Vazquez; BV Bruno Villalobos Reveles; LH Lot Hernández-Espinosa; IF Isaac F. López-Moyado; AO Atsushi Onodera; DS Daniela Samaniego-Castruita; FA Ferhat Ay; AL Arlet Lara-Custodio; PG Patrick G. Hogan; HS Hugo Sepulveda; AR Anjana Rao
errShare
errSave
TH17 cells converted into exTH17 cells sustain rheumatoid-like IL-17–independent inflammatory arthritis
errScience Immunology
IF16.3
err2025-11-07
err0
PREAI
errMartina Zoccheddu; Kensuke Suga; Amara Seng; Mattias N. D. Svensson; Paramita Dutta; Sanaz Panahandeh; Hadijat-Kubura Moradeke Makinde; Myungja Ro; Yizhou Wang; Hyobin Kim; Zbigniew Mikulski; Katarzyna Dobaczewska; Francesca Ingegnoli; Ruth Minsha; John F. Seagrist; Mary Carns; Kathleen Aren; Salina Dominguez; Mohammad Daud Khan; Angela Denn; Roberto Caporali; Pietro Simone Randelli; David A. McBride; Arthur M. Mandelin; Carla Marie Cuda; Zhiping Paul Wang; Jason H. Moore; Nisarg J. Shah; Kyoung Jae Won; Deborah R. Winter; Ferhat Ay; Harris Perlman; Nunzio Bottini
errShare
errSave
High interferon response signatures in SLE patient leukocytes are associated with increased transposable element expression in gene introns and intergenic regions
errMobile DNA
IF3.1
err2025-11-04
err0
errOAAI
errLeo J. Arteaga-Vazquez; Hugo Sepulveda; Bruno Villalobos Reveles; Kazumasa Suzuki; Kenneth C. Kalunian; Ferhat Ay; Mark R. Boothby; Anjana Rao
errShare
errSave
DiffHiChIP: Identifying differential chromatin contacts from HiChIP data
errCell Reports Methods
IF4.5
err2025-11-03
err0
errOAAI
errSourya Bhattacharyya; Daniela Salgado Figueroa; Katia Georgopoulos; Ferhat Ay
errShare
errSave
Single-cell transcriptomics of ventral forebrain progenitors identifies Evf2 enhancer lncRNA-enhancer gene guidance through direct RNA binding and RNP recruitment domains
errNature Communications
IF15.7
err2025-07-26
err0
errOAAI
errEdward Li; Abhijit Chakraborty; Sara J. Kohtz; Ivelisse Cajigas; Laura Hinojosa-Gonzalez; Fion Shiau; Ryan Bertossi; Robert J. Vassar; Jack A. Kessler; Ferhat Ay; Brian S. Clark; Jhumku D. Kohtz
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errSave
Soffritto: a deep learning model for predicting high-resolution replication timing
errBIOINFORMATICS
IF5.4
err2025-07-01
err1
errOAAI
errBolzan, Dante; Ay, Ferhat
errShare
errSave
Rewiring of the 3D genome during acquisition of carboplatin resistance in a triple-negative breast cancer patient-derived xenograft (vol 13, 5420, 2023)
errSCIENTIFIC REPORTS
IF3.9
err2024-12-17
err0
errOAAI
errDozmorov, Mikhail G.; Marshall, Maggie A.; Rashid, Narmeen S.; Grible, Jacqueline M.; Valentine, Aaron; Olex, Amy L.; Murthy, Kavita; Chakraborty, Abhijit; Reyna, Joaquin; Figueroa, Daniela Salgado; Hinojosa-Gonzalez, Laura; Lee, Erika Da-Inn; Baur, Brittany A.; Roy, Sushmita; Ay, Ferhat; Harrell, J. Chuck
errShare
errSave
Comparison of CD30L and OX40L Reveals CD30L as a Promising Therapeutic Target in Atopic Dermatitis
errALLERGY
IF12
err2024-11-26
err0
PREAI
errGupta, Rinkesh K.; Figueroa, Daniela Salgado; Ay, Ferhat; Causton, Benjamin; Abdollahi, Shahla; Croft, Michael
errShare
errSave
Eosinophilic esophagitis drives tissue fibroblast regenerative programs toward pathologic dysfunction
errJOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY
IF11.2
err2024-11-01
err0
PREAI
errJumabay, Medet; Abud, Edsel M.; Okamoto, Kevin; Dutta, Paramita; Chiang, Austin W. T.; Li, Haining; Manresa, Mario C.; Zhu, Yanfang P.; Frederick, Dana; Kurten, Richard; Croker, Ben; Lewis, Nathan E.; Kennedy, Joshua L.; Dohil, Ranjan; Croft, Michael; Ay, Ferhat; Wechsler, Joshua B.; Aceves, Seema S.
errShare
errSave
Identifying genetic variants associated with chromatin looping and genome function
errNATURE COMMUNICATIONS
IF15.7
err2024-09-18
err0
errOAAI
errBhattacharyya, Sourya; Ay, Ferhat
errShare
errSave
Predicting gene expression state and prioritizing putative enhancers using 5hmC signal
errGENOME BIOLOGY
IF9.4
err2024-06-03
err0
errOAAI
errGonzalez-Avalos, Edahi; Onodera, Atsushi; Samaniego-Castruita, Daniela; Rao, Anjana; Ay, Ferhat
errShare
errSave
Integrative Keratinocyte Responses to TWEAK with IL-13 and IL-22 Reveal Pathogenic Transcriptomes Associated with Atopic Dermatitis
errJOURNAL OF INVESTIGATIVE DERMATOLOGY
IF5.7
err2024-05-01
err0
PREAI
errGupta, Rinkesh K.; Fung, Kai; Figueroa, Daniela Salgado; Ay, Ferhat; Croft, Michael
errShare
errSave
LIGHT signaling through LTβR and HVEM in keratinocytes promotes psoriasis and atopic dermatitis-like skin inflammation
errJOURNAL OF AUTOIMMUNITY
IF7
err2024-04-01
err5
PREAI
errGupta, Rinkesh K.; Figueroa, Daniela Salgado; Fung, Kai; Miki, Haruka; Miller, Jacqueline; Ay, Ferhat; Croft, Michael
errShare
errSave
A multi-omics systems vaccinology resource to develop and test computational models of immunity
errCELL REPORTS METHODS
IF4.5
err2024-03-01
err0
errOAAI
errShinde, Pramod; Soldevila, Ferran; Reyna, Joaquin; Aoki, Minori; Rasmussen, Mikkel; Willemsen, Lisa; Kojima, Mari; Ha, Brendan; Greenbaum, Jason A.; Overton, James A.; Guzman-Orozco, Hector; Nili, Somayeh; Orfield, Shelby; Gygi, Jeremy P.; Antunes, Ricardo da Silva; Sette, Alessandro; Grant, Barry; Olsen, Lars Ronn; Konstorum, Anna; Guan, Leying; Ay, Ferhat; Kleinstein, Steven H.; Peters, Bjoern
errShare
errSave
Rewiring of the 3D genome during acquisition of carboplatin resistance in a triple-negative breast cancer patient-derived xenograft (vol 13, 5420, 2023)
errSCIENTIFIC REPORTS
IF3.9
err2023-05-09
err0
errOAAI
errDozmorov, Mikhail G.; Marshall, Maggie A.; Rashid, Narmeen S.; Grible, Jacqueline M.; Valentine, Aaron; Olex, Amy L.; Murthy, Kavita; Chakraborty, Abhijit; Reyna, Joaquin; Figueroa, Daniela Salgado; Hinojosa-Gonzalez, Laura; Da-Inn Lee, Erika; Baur, Brittany A.; Roy, Sushmita; Ay, Ferhat; Harrell, J. Chuck
errShare
errSave
Rewiring of the 3D genome during acquisition of carboplatin resistance in a triple-negative breast cancer patient-derived xenograft
errSCIENTIFIC REPORTS
IF3.9
err2023-04-03
err5
errOAAI
errDozmorov, Mikhail G.; Marshall, Maggie A.; Rashid, Narmeen S.; Grible, Jacqueline M.; Valentine, Aaron; Olex, Amy L.; Murthy, Kavita; Chakraborty, Abhijit; Reyna, Joaquin; Figueroa, Daniela Salgado; Hinojosa-Gonzalez, Laura; Da-Inn Lee, Erika; Baur, Brittany A.; Roy, Sushmita; Ay, Ferhat; Harrell, J. Chuck
errShare
errSave
Lymphotoxin beta receptor signaling directly controls airway smooth muscle deregulation and asthmatic lung dysfunction
errJOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY
IF11.2
err2023-04-01
err6
errOAAI
errMiki, Haruka; Kiosses, William B.; Manresa, Mario C.; Gupta, Rinkesh K.; Sethi, Gurupreet S.; Herro, Rana; Antunes, Ricardo Da Silva; Dutta, Paramita; Miller, Marina; Fung, Kai; Chawla, Ashu; Dobaczewska, Katarzyna; Ay, Ferhat; Broide, David H.; Tumanov, Alexei V.; Croft, Michael
errShare
errSave
Carboplatin resistance-associated changes in the 3D chromatin landscape of a triple-negative breast cancer Patient-Derived Xenograft
errCANCER RESEARCH
IF16.6
err2023-03-01
err0
PREAI
errDozmorov, Mikhail; Marshall, Maggie; Rashid, Narmeen; Grible, Jacqueline; Valentine, Aaron D.; Olex, Amy; Murthy, Kavita; Chakraborty, Abhijit; Reyna, Joaquin; Figueroa, Daniela Salgado; Lee, Da-Inn; Baur, Brittany; Roy, Sushmita; Ay, Ferhat; Harrell, Chuck
errShare
errSave
dcHiC detects differential compartments across multiple Hi-C datasets
errNATURE COMMUNICATIONS
IF15.7
err2022-11-11
err23
errOAAI
errChakraborty, Abhijit; Wang, Jeffrey G.; Ay, Ferhat
errShare
errSave

Research Directions

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