Ferhat Ay

Also affiliated with UC San Diego Health System, University of California San Diego, Institute of Bioinformatics

Biochemistry, Genetics and Molecular BiologyAgricultural and Biological Sciences

Pilot corpus only

This score is computed over theSindex pilot corpus and does not cover the full scientific literature. Scores are relative to papers we have ingested — papers, authors, and institutions outside the pilot are not represented. Methodology.

Top 2%percentile

3.2Author DataRank

Indexed papers

4in pilot corpus

datarank_citation_only_1hop_v6· scope data_onlyMethodology

Why this DataRank?

An author's DataRank is the sum of the DataRanks of all 4 indexed papers attributed to them. A prolific author with many moderate-impact papers can outrank one with a single high-impact paper.

Author scores recompute whenever paper DataRanks are refreshed, so this number lags the underlying paper scores by at most one batch run.

Read the full methodology →

The highest-impact dataset this researcher has shared, ranked by DataRank — the single contribution doing the most to lift their data-sharing standing.

Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE

Science(2010)10.1126/science.1198374

Top 9%

2.4DataRank

Top 9%1089 citations

Sushmita Roy, Jason Ernst, Peter V. Kharchenko, Yanxiao Zhang, Richard S. Sandstrom +172 more

Papers

Driven by 57 papers — median percentile 46. Top paper: “Predictive regulatory models in Drosophila melanogaster by integrative inference of transcriptional networks”.

Predictive regulatory models in Drosophila melanogaster by integrative inference of transcriptional networks

Genome Research(2012)10.1101/gr.127191.111

N/A

4.3DataRank · unranked

126 citations

Sushmita Roy, Ferhat Ay, Patrick E. Meyer, Rogerio Candeias, Christopher A. Bristow +2 more

Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE

Science(2010)10.1126/science.1198374

Top 9%

2.4DataRank

Top 9%1089 citations

Sushmita Roy, Jason Ernst, Peter V. Kharchenko, Yanxiao Zhang, Richard S. Sandstrom +172 more

Imbalance of Regulatory and Cytotoxic SARS-CoV-2-Reactive CD4+ T Cells in COVID-19

Cell(2020)10.1016/j.cell.2020.10.001

N/A

0.957DataRank · unranked

588 citations

Ciro Ramírez-Suástegui, Vicente Fajardo, Serena Chee, Anthony Kusnadi, Hayley Simon +10 more

Perspective on recent developments and challenges in regulatory and systems genomics

Bioinformatics Advances(2024)10.1093/bioadv/vbaf106

N/A

0.373DataRank · unranked

11 citations

Sushmita Roy, Ferhat Ay, Anthony Mathelier, Alejandra Medina-Rivera, Shaun Mahony +3 more

SubMAP: Aligning Metabolic Pathways with Subnetwork Mappings

Lecture Notes in Computer Science(2010)10.1007/978-3-642-12683-3_2

N/A

0.371DataRank · unranked

7 citations

Sharon L. R. Kardia, Ferhat Ay

ExTraMapper: exon- and transcript-level mappings for orthologous gene pairs

Bioinformatics(2021)10.1093/bioinformatics/btab393

Top 52%

0.332DataRank

Top 52%4 citations

Ferhat Ay, Ramana V. Davuluri, Abhijit Chakraborty

A multi-omics systems vaccinology resource to develop and test computational models of immunity

Cell Reports Methods(2024)10.1016/j.crmeth.2024.100731

Top 57%

0.280DataRank

Top 57%5 citations

Ferran Soldevila, Joaquin Reyna, Minori Aoki, Mikkel Mylius Rasmussen, Lisa Willemsen +18 more

Loop Catalog: a comprehensive HiChIP database of human and mouse samples

Genome biology(2025)10.1186/s13059-025-03615-5

Top 63%

0.214DataRank

Top 63%3 citations

Kyra Fetter, Romeo Ignacio, Cemil Can Ali Marandi, Aiqun Ma, Nikhil Rao +5 more

Oncogenic 3D genome conformations identify novel therapeutic targets in ependymoma

Research Square(2020)10.21203/rs.3.rs-88331/v1

N/A

0DataRank · unranked

0 citations

Aylin Camgöz, Donglim Esther Park, Owen Chapman, Jens-Martin Hübner, Abhijit Chakraborty +33 more

Severely ill patients with COVID-19 display impaired exhaustion features in SARS-CoV-2–reactive CD8 + T cells

Science Immunology(2021)10.1126/sciimmunol.abe4782

N/A

0DataRank · unranked

251 citations

Ciro Ramírez-Suástegui, Vicente Fajardo, Serena Chee, Benjamin J. Meckiff, Hayley Simon +6 more

Intratumoral follicular regulatory T cells curtail anti-PD-1 treatment efficacy

Nature Immunology(2021)10.1038/s41590-021-00958-6

N/A

0DataRank · unranked

112 citations

James Clarke, Ciro Ramírez-Suástegui, Bharat Panwar, Ariel Madrigal, Serena Chee +12 more

The tumor suppressor kinase DAPK3 drives tumor-intrinsic immunity through the STING–IFN-β pathway

Nature Immunology(2021)10.1038/s41590-021-00896-3

N/A

0DataRank · unranked

110 citations

Chan‐Wang Jerry Lio, Anaamika Campeau, Martin Steger, Ferhat Ay, Matthias Mann +4 more

COVID-19 genetic risk variants are associated with expression of multiple genes in diverse immune cell types

Nature Communications(2021)10.1038/s41467-021-26888-3

N/A

0DataRank · unranked

61 citations

Job Rocha, Cristian González-Colín, Sourya Bhattacharyya, Ariel Madrigal, Christian H. Ottensmeier +4 more

Sox2- Evf2 lncRNA-mediated mechanisms of chromosome topological control in developing forebrain

Development(2021)10.1242/dev.197202

N/A

0DataRank · unranked

19 citations

Abhijit Chakraborty, Madison Lynam, Kelsey R. Swyter, Monique Bastidas, Linden Collens +4 more

Clinical recovery of Macaca fascicularis infected with Plasmodium knowlesi

Malaria Journal(2021)10.1186/s12936-021-03925-6

N/A

0DataRank · unranked

19 citations

Chester J. Joyner, Jessica A. Brady, Jennifer Wood, Monica Cabrera-Mora, Celia L. Saney +51 more

Multi–cell type gene coexpression network analysis reveals coordinated interferon response and cross–cell type correlations in systemic lupus erythematosus

Genome Research(2021)10.1101/gr.265249.120

N/A

0DataRank · unranked

58 citations

Benjamin Joachim Schmiedel, Shu Liang, Brandie White, Enrique Rodrı́guez, Kenneth Kalunian +6 more

Third-generation sequencing revises the molecular karyotype for Toxoplasma gondii and identifies emerging copy number variants in sexual recombinants

Genome Research(2021)10.1101/gr.262816.120

N/A

0DataRank · unranked

32 citations

Aarthi Venkat, Rachel E. Bainbridge, Michael L. Reese, Karine G. Le Roch, Ferhat Ay +2 more

Single-cell eQTL analysis of activated T cell subsets reveals activation and cell type–dependent effects of disease-risk variants

Science Immunology(2022)10.1126/sciimmunol.abm2508

N/A

0DataRank · unranked

104 citations

Cristian González-Colín, Vicente Fajardo, Job Rocha, Ariel Madrigal, Ciro Ramírez-Suástegui +9 more

Intermittent PI3Kδ inhibition sustains anti-tumour immunity and curbs irAEs

Nature(2022)10.1038/s41586-022-04685-2

N/A

0DataRank · unranked

92 citations

Ciro Ramírez-Suástegui, Yingcong Li, Emma V. King, Lindsey Chudley, Jaya Thomas +37 more

dcHiC detects differential compartments across multiple Hi-C datasets

Nature Communications(2022)10.1038/s41467-022-34626-6

N/A

0DataRank · unranked

80 citations

Jeffrey Wang, Ferhat Ay, Abhijit Chakraborty

A double-negative thymocyte-specific enhancer augments Notch1 signaling to direct early T cell progenitor expansion, lineage restriction and β-selection

Nature Immunology(2022)10.1038/s41590-022-01322-y

N/A

0DataRank · unranked

18 citations

Daniela Salgado Figueroa, Ferhat Ay, Bruce Morgan, Katia Georgopoulos, Mariko Kashiwagi

Lymphotoxin beta receptor signaling directly controls airway smooth muscle deregulation and asthmatic lung dysfunction

Journal of Allergy and Clinical Immunology(2022)10.1016/j.jaci.2022.11.016

N/A

0DataRank · unranked

16 citations

William B. Kiosses, Mario C. Manresa, Rinkesh Kumar Gupta, Gurupreet S. Sethi, Rana Herro +11 more

Atypical B cells consist of subsets with distinct effector functions

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.09.28.509955

N/A

0DataRank · unranked

1 citations

Gayani Batugedara, Paramita Dutta, Ashley B. Reers, Rolando Garza, Isaac Ssewanyana +7 more

Lineage-specific 3D genome organization is assembled at multiple scales by IKAROS

Cell(2023)10.1016/j.cell.2023.10.023

N/A

0DataRank · unranked

45 citations

Daniela Salgado Figueroa, Zhihong Zhang, Margaret Veselits, Sourya Bhattacharyya, Mariko Kashiwagi +5 more

3D genome mapping identifies subgroup-specific chromosome conformations and tumor-dependency genes in ependymoma

Nature Communications(2023)10.1038/s41467-023-38044-0

N/A

0DataRank · unranked

26 citations

Aylin Camgöz, Owen Chapman, Sameena Wani, Donglim Esther Park, Jens-Martin Hübner +46 more

Atypical B cells consist of subsets with distinct functional profiles

iScience(2023)10.1016/j.isci.2023.108496

N/A

0DataRank · unranked

24 citations

Gayani Batugedara, Paramita Dutta, Ashley B. Reers, Rolando Garza, Isaac Ssewanyana +7 more

Rewiring of the 3D genome during acquisition of carboplatin resistance in a triple-negative breast cancer patient-derived xenograft

Scientific Reports(2023)10.1038/s41598-023-32568-7

N/A

0DataRank · unranked

10 citations

Maggie A. Marshall, Narmeen S Rashid, Jacqueline M. Grible, Aaron D. Valentine, Amy L. Olex +11 more

Integrative Keratinocyte Responses to TWEAK with IL-13 and IL-22 Reveal Pathogenic Transcriptomes Associated with Atopic Dermatitis

Journal of Investigative Dermatology(2023)10.1016/j.jid.2023.11.009

N/A

0DataRank · unranked

4 citations

Kai Fung, Daniela Salgado Figueroa, Ferhat Ay, Michael Croft, Rinkesh Kumar Gupta

MuDCoD: multi-subject community detection in personalized dynamic gene networks from single-cell RNA sequencing

Bioinformatics(2023)10.1093/bioinformatics/btad592

N/A

0DataRank · unranked

1 citations

Shan Lu, Shuchen Yan, Ferhat Ay, Öznur Taştan, Sündüz Keleş +1 more

Brd2 is dispensable for genome compartmentalization and replication timing

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.11.17.567572

N/A

0DataRank · unranked

2 citations

Jesse L. Turner, Takayo Sasaki, Ferhat Ay, David M. Gilbert, Laura Hinojosa-Gonzalez

A systems vaccinology resource to develop and test computational models of immunity

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.08.28.555193

N/A

0DataRank · unranked

0 citations

Ferran Soldevila, Joaquin Reyna, Minori Aoki, Mikkel Mylius Rasmussen, Lisa Willemsen +18 more

Eosinophilic esophagitis drives tissue fibroblast regenerative programs toward pathologic dysfunction

Journal of Allergy and Clinical Immunology(2024)10.1016/j.jaci.2024.11.028

N/A

0DataRank · unranked

7 citations

Edsel M. Abud, Kevin Okamoto, Paramita Dutta, Austin W.T. Chiang, Haining Li +13 more

Predicting gene expression state and prioritizing putative enhancers using 5hmC signal

Genome biology(2024)10.1186/s13059-024-03273-z

N/A

0DataRank · unranked

13 citations

Atsushi Onodera, Daniela Samaniego‐Castruita, Anjana Rao, Ferhat Ay, Edahí González‐Avalos

LIGHT signaling through LTβR and HVEM in keratinocytes promotes psoriasis and atopic dermatitis-like skin inflammation

Journal of Autoimmunity(2024)10.1016/j.jaut.2024.103177

N/A

0DataRank · unranked

10 citations

Daniela Salgado Figueroa, Kai Fung, Haruka Miki, Jacqueline Miller, Ferhat Ay +2 more

Identifying genetic variants associated with chromatin looping and genome function

Nature Communications(2024)10.1038/s41467-024-52296-4

N/A

0DataRank · unranked

6 citations

Ferhat Ay, Sourya Bhattacharyya

nipalsMCIA : flexible multi-block dimensionality reduction in R via nonlinear iterative partial least squares

Bioinformatics(2024)10.1093/bioinformatics/btaf015

N/A

0DataRank · unranked

2 citations

Joaquin Reyna, E Aron, Ferhat Ay, Misha E. Kilmer, Steven H. Kleinstein +2 more

nipalsMCIA: Flexible Multi-Block Dimensionality Reduction in R via Non-linear Iterative Partial Least Squares

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.06.07.597819

N/A

0DataRank · unranked

1 citations

Joaquin Reyna, E Aron, Ferhat Ay, Misha E. Kilmer, Steven H. Kleinstein +2 more

Putting computational models of immunity to the test - an invited challenge to predict B. pertussis vaccination outcomes

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.09.04.611290

N/A

0DataRank · unranked

1 citations

Lisa Willemsen, Michael C. Anderson, Minori Aoki, Saonli Basu, Julie G. Burel +54 more

Chromatin structure and var2csa – a tango in regulation of var gene expression in the human malaria parasite, Plasmodium falciparum ?

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.02.13.580059

N/A

0DataRank · unranked

0 citations

Xu Zhang, Abhijit Chakraborty, Abbas Roayaei Ardakany, Jacques Prudhomme, Ferhat Ay +3 more

Perspective on recent developments and challenges in regulatory and systems genomics

arXiv (Cornell University)(2024)10.48550/arxiv.2411.04363

N/A

0DataRank · unranked

0 citations

Sushmita Roy, Ferhat Ay, Anthony Mathelier, Alejandra Medina-Rivera, Shaun Mahony +3 more

Author Correction: Rewiring of the 3D genome during acquisition of carboplatin resistance in a triple-negative breast cancer patient-derived xenograft

Scientific Reports(2024)10.1038/s41598-024-82374-y

N/A

0DataRank · unranked

0 citations

Maggie A. Marshall, Narmeen S Rashid, Jacqueline M. Grible, Aaron D. Valentine, Amy L. Olex +11 more

T H 17 cells converted into exT H 17 cells sustain rheumatoid-like IL-17–independent inflammatory arthritis

Science Immunology(2025)10.1126/sciimmunol.adm7800

N/A

0DataRank · unranked

6 citations

Kensuke Suga, Amara Seng, Mattias N. D. Svensson, Paramita Dutta, Sanaz Panahandeh +28 more

Master transcription-factor binding sites constitute the core of early replication control elements

The EMBO Journal(2025)10.1038/s44318-025-00501-5

N/A

0DataRank · unranked

5 citations

Laura Hinojosa-Gonzalez, Takayo Sasaki, Satoshi Uchino, Athanasios E Vouzas, Mariella S Soto +7 more

Single-cell transcriptomics of ventral forebrain progenitors identifies Evf2 enhancer lncRNA-enhancer gene guidance through direct RNA binding and RNP recruitment domains

Nature Communications(2025)10.1038/s41467-025-62205-y

N/A

0DataRank · unranked

4 citations

Abhijit Chakraborty, Sara J. Kohtz, Ivelisse Cajigas, Laura Hinojosa-Gonzalez, Fion Shiau +7 more

Putting computational models of immunity to the test—An invited challenge to predict B.pertussis vaccination responses

PLoS Computational Biology(2025)10.1371/journal.pcbi.1012927

N/A

0DataRank · unranked

1 citations

Lisa Willemsen, Michael C. Anderson, Minori Aoki, Saonli Basu, Julie G. Burel +54 more

Soffritto: a deep learning model for predicting high-resolution replication timing

Bioinformatics(2025)10.1093/bioinformatics/btaf231

N/A

0DataRank · unranked

1 citations

Ferhat Ay, Dante Bolzan

Loss of TET function in T regulatory cells yields ex-Treg cells biased toward T follicular helper cells, causing autoimmune diseases through autoantibody production

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.08.29.673187

N/A

0DataRank · unranked

1 citations

Leo Josue Arteaga Vazquez, Bruno Villalobos Reveles, Lot Hernández-Espinosa, Isaac F. López-Moyado, Atsushi Onodera +7 more

Distinct interferon response patterns link to increased transposable element expression in leukocytes of systemic lupus erythematosus patients

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.05.30.657099

N/A

0DataRank · unranked

0 citations

Hugo Sepúlveda, Bruno Villalobos Reveles, Kazumasa Suzuki, Kenneth Kalunian, Ferhat Ay +3 more

DiffHiChIP: Identifying differential chromatin contacts from HiChIP data

Cell Reports Methods(2025)10.1016/j.crmeth.2025.101214

N/A

0DataRank · unranked

0 citations

Daniela Salgado Figueroa, Katia Georgopoulos, Ferhat Ay, Sourya Bhattacharyya

High interferon response signatures in SLE patient leukocytes are associated with increased transposable element expression in gene introns and intergenic regions

Mobile DNA(2025)10.1186/s13100-025-00377-6

N/A

0DataRank · unranked

0 citations

Hugo Sepúlveda, Bruno Villalobos Reveles, Kazumasa Suzuki, Kenneth Kalunian, Ferhat Ay +3 more

Mustache: multi-scale detection of chromatin loops from Hi-C and Micro-C maps using scale-space representation

Genome biology(2020)10.1186/s13059-020-02167-0

N/A

0DataRank · unranked

266 citations

Halil Tuvan Gezer, Stefano Lonardi, Ferhat Ay, Abbas Roayaei Ardakany

Promoter-interacting expression quantitative trait loci are enriched for functional genetic variants

Nature Genetics(2020)10.1038/s41588-020-00745-3

N/A

0DataRank · unranked

131 citations

Sourya Bhattacharyya, Benjamin Joachim Schmiedel, Ariel Madrigal, Cristian González-Colín, Stephanie Feudjio Feupe +8 more

COVID-19 genetic risk variants are associated with expression of multiple genes in diverse immune cell types

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.12.01.407429

N/A

0DataRank · unranked

15 citations

Vivek Chandra, Job Rocha, Cristian González-Colín, Sourya Bhattacharyya, Ariel Madrigal +4 more

CD4 + follicular helper-like T cells are key players in anti-tumor immunity

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.01.08.898346

N/A

0DataRank · unranked

13 citations

AP Ganesan, Bharat Panwar, Simon Eschweiler, Christopher J. Hanley, Ariel Madrigal +18 more

Mustache: Multi-scale Detection of Chromatin Loops from Hi-C and Micro-C Maps using Scale-Space Representation

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.02.24.963579

N/A

0DataRank · unranked

13 citations

Halil Tuvan Gezer, Stefano Lonardi, Ferhat Ay, Abbas Roayaei Ardakany

Severely ill COVID-19 patients display augmented functional properties in SARS-CoV-2-reactive CD8 + T cells

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.07.09.194027

N/A

0DataRank · unranked

10 citations

Ciro Ramírez-Suástegui, Vicente Fajardo, Serena Chee, Benjamin J. Meckiff, Hayley Simon +6 more

Integrative transcriptomic analysis of SLE reveals IFN-driven cross-talk between immune cells

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.04.27.065227

N/A

0DataRank · unranked

2 citations

Benjamin Joachim Schmiedel, Shu Liang, Brandie White, Enrique Rodrı́guez, Kenneth Kalunian +6 more

Ferhat Ay

Indexed papers

Top data-sharing exemplar

Papers