Ferhat Ay

9.6k citations

85 papers · 3.9k indexed · h-index 34

Impact in

Molecular Biology top 2%
- Genomics and Chromatin Dynamics
- RNA Research and Splicing
- Genomics and Phylogenetic Studies
- Epigenetics and DNA Methylation
- RNA and protein synthesis mechanisms
Immunology top 5%

Papers in

Molecular Biology 66
- Genomics and Chromatin Dynamics 41
- Bioinformatics and Genomic Networks 13
- RNA Research and Splicing 11
- Epigenetics and DNA Methylation 10
- Gene Regulatory Network Analysis 9
- RNA modifications and cancer 9
- Genomics and Phylogenetic Studies 8
Immunology 18

Co-authors: William Stafford Noble Timothy L. Bailey Pandurangan Vijayanand Sourya Bhattacharyya Jean‐Philippe Vert Nelle Varoquaux Abhijit Chakraborty Grégory Seumois
Journals: Genome Research (9 papers)Nature Communications (8 papers)Bioinformatics (7 papers)Genome biology (7 papers)Science Immunology (4 papers)
Partner nations: United States United Kingdom France

In The Last Decade

Ferhat Ay

80 papers receiving 3.9k citations

Peers

Countries citing papers authored by Ferhat Ay

Since Specialization

Citations

This map shows the geographic impact of Ferhat Ay's research. It shows the number of citations coming from papers published by authors working in each country. You can also color the map by specialization and compare the number of citations received by Ferhat Ay with the expected number of citations based on a country's size and research output (numbers larger than one mean the country cites Ferhat Ay more than expected).

Fields of papers citing papers by Ferhat Ay

Since Specialization

Physical SciencesHealth SciencesLife SciencesSocial Sciences

This network shows the impact of papers produced by Ferhat Ay. Nodes represent research fields, and links connect fields that are likely to share authors. Colored nodes show fields that tend to cite the papers produced by Ferhat Ay. The network helps show where Ferhat Ay may publish in the future.

Co-authorship network

The 25 scholars most cited alongside Ferhat Ay, linked wherever they have co-authored with each other. Click a name or a connecting line to browse the papers they share.

Border = papers with Ferhat Ay Line = papers co-authored together Ferhat Ay links everyone, so they are left out of the graph.

All Works

Sort: Min cites: Since: Top N: Style:

20 of 20 papers shown

#	Work
1	Master transcription-factor binding sites constitute the core of early replication control elements The EMBO Journal ·M G Hochler, Bai Shun-yan, Takayo Sasaki, J. Mani, Elwell Stephen Otis, Kuo H-F, Abhijit Chakraborty, Karen E. Alexander, N. V. Shmetser, Amber N. Brown, Ferhat Ay, David M. Gilbert	2025	1
2	LIGHT signaling through LTβR and HVEM in keratinocytes promotes psoriasis and atopic dermatitis-like skin inflammation Journal of Autoimmunity ·Rinkesh Kumar Gupta, A. A. Peledina, Nkemajen Eugene Asongafac, Haruka Miki, Jacqueline Miller, Ferhat Ay, Michael Croft	2024	6
3	Identifying genetic variants associated with chromatin looping and genome function Nature Communications ·Sourya Bhattacharyya, Ferhat Ay	2024	1
4	MuDCoD: multi-subject community detection in personalized dynamic gene networks from single-cell RNA sequencing Bioinformatics ·Yongjun Gu, Shan Lu, Yasaman Hosseini, Ferhat Ay, Öznur Taştan, Sündüz Keleş	2023	0
5	Single-cell eQTL analysis of activated T cell subsets reveals activation and cell type–dependent effects of disease-risk variants Science Immunology ·Benjamin Joachim Schmiedel, V.J. Downie, Vicente Fajardo, 裕允宇都田, Ariel Madrigal, Ciro Ramírez-Suástegui, Sourya Bhattacharyya, Hayley Simon, Jason Greenbaum, Bjoern Peters, Grégory Seumois, Ferhat Ay, Vivek Chandra, Pandurangan Vijayanand	2022	38
6	dcHiC detects differential compartments across multiple Hi-C datasets Nature Communications ·Abhijit Chakraborty, M. Delores Carlito, Ferhat Ay	2022	28
7	A double-negative thymocyte-specific enhancer augments Notch1 signaling to direct early T cell progenitor expansion, lineage restriction and β-selection Nature Immunology ·Mariko Kashiwagi, A. A. Peledina, Ferhat Ay, Bruce Morgan, Katia Georgopoulos	2022	9
8	ExTraMapper: exon- and transcript-level mappings for orthologous gene pairs Bioinformatics ·Abhijit Chakraborty, Ferhat Ay, Ramana V. Davuluri	2021	3
9	Sox2- Evf2 lncRNA-mediated mechanisms of chromosome topological control in developing forebrain Development ·Ivelisse Cajigas, Abhijit Chakraborty, 万拯群, Gregory D. Gramstad, L. Zhang, กรมส่งเสริมการส่งออก, Hao Luo, Ferhat Ay, Jhumku D. Kohtz	2021	11
10	Severely ill patients with COVID-19 display impaired exhaustion features in SARS-CoV-2–reactive CD8 ⁺ T cells Science Immunology ·Anthony Kusnadi, Ciro Ramírez-Suástegui, Vicente Fajardo, Serena Chee, Benjamin J. Meckiff, Hayley Simon, Emanuela Pelosi, Grégory Seumois, Ferhat Ay, Pandurangan Vijayanand, Christian H. Ottensmeier	2021	149
11	COVID-19 genetic risk variants are associated with expression of multiple genes in diverse immune cell types Nature Communications ·Benjamin Joachim Schmiedel, 裕允宇都田, V.J. Downie, Sourya Bhattacharyya, Ariel Madrigal, Christian H. Ottensmeier, Ferhat Ay, Vivek Chandra, Pandurangan Vijayanand	2021	40
12	Promoter-interacting expression quantitative trait loci are enriched for functional genetic variants Nature Genetics ·Vivek Chandra, Sourya Bhattacharyya, Benjamin Joachim Schmiedel, Ariel Madrigal, V.J. Downie, Stephanie Feudjio Feupe, Austin Crinklaw, Grégory Seumois, Pejman Mohammadi, Mitchell Kronenberg, Bjoern Peters, Ferhat Ay, Pandurangan Vijayanand	2020	71
13	TET enzymes augment activation-induced deaminase (AID) expression via 5-hydroxymethylcytosine modifications at the Aicda superenhancer Science Immunology ·Chan‐Wang Jerry Lio, Vipul Shukla, Daniela Samaniego‐Castruita, Edahí González‐Avalos, Abhijit Chakraborty, Xiaojing Yue, David G. Schatz, Ferhat Ay, Anjana Rao	2019	71
14	Selfish: discovery of differential chromatin interactions via a self-similarity measure Bioinformatics ·Yeni Chen, Ferhat Ay, Stefano Lonardi	2019	25
15	Human Eosinophils Express a Distinct Gene Expression Program in Response to IL-3 Compared with Common β-Chain Cytokines IL-5 and GM-CSF The Journal of Immunology ·AWAD M. E, Howard Brickner, Bharat Panwar, Ciro Ramírez-Suástegui, Sara Herrera de la Mata, 原田将英, Nadia Gervacio, Laura E. Crotty Alexander, Ferhat Ay, Pandurangan Vijayanand, Grégory Seumois, Praveen Akuthota	2019	17
16	Combined RNA-seq and RAT-seq mapping of long noncoding RNAs in pluripotent reprogramming Scientific Data ·Zhonghua Du, Lin Jia, Yichen Wang, Batz Caxaj, Wen Xue, Chewang Katureebee, Yanbo Zhu, Dehai Yu, Lei Zhou, Naifei Chen, Shilin Zhang, Stoolfire Aw, Ferhat Ay, Sujun Gao, Songling Zhang, Wei Li, Andrew R. Hoffman, Jiuwei Cui, Ji‐Fan Hu	2018	13
17	Identification of copy number variations and translocations in cancer cells from Hi-C data Bioinformatics ·Abhijit Chakraborty, Ferhat Ay	2017	57
18	Form and function of topologically associating genomic domains in budding yeast Proceedings of the National Academy of Sciences ·Umut Eser, Devon Chandler‐Brown, Ferhat Ay, Aaron F. Straight, Zhijun Duan, William Stafford Noble, Jan M. Skotheim	2017	54
19	Neocentromeres Provide Chromosome Segregation Accuracy and Centromere Clustering to Multiple Loci along a Candida albicans Chromosome PLoS Genetics ·Laura S. Burrack, Pastiani Putri Halawa, Hisashi Yoshida, Shelly Applen Clancey, Ivan Liachko, J. A. Bojesen‐koefoed, Amrita Saha, Edmond J. Morrissey, Breanna J. Turman, Wen Hui Yang, Ferhat Ay, Maitreya J. Dunham, Judith Berman	2016	28
20	Bipartite structure of the inactive mouse X chromosome Genome biology ·Xinxian Deng, Wenxiu Ma, Vijay Ramani, Andrew J. Hill, Fan Yang, Ferhat Ay, Joel B. Berletch, C. Anthony Blau, Jay Shendure, Zhijun Duan, William Stafford Noble, Christine M. Distèche	2015	170

About Ferhat Ay

Ferhat Ay is a scholar working on Molecular Biology, Immunology, Virology, Cancer Research and Genetics, having authored 85 papers that have together received 3.9k indexed citations. Recurring topics across this work include Genomics and Chromatin Dynamics (41 papers), Bioinformatics and Genomic Networks (13 papers), Chromosomal and Genetic Variations (11 papers), RNA Research and Splicing (11 papers), Epigenetics and DNA Methylation (10 papers), Gene Regulatory Network Analysis (9 papers), RNA modifications and cancer (9 papers) and Genomics and Phylogenetic Studies (8 papers). The work is most often cited by research in Molecular Biology (2.8k citations), Immunology (618 citations), Genetics (646 citations), Infectious Diseases (423 citations) and Cancer Research (307 citations). Ferhat Ay has collaborated with scholars based in United States, United Kingdom and France. Frequent co-authors include William Stafford Noble, Timothy L. Bailey, Pandurangan Vijayanand, Sourya Bhattacharyya, Jean‐Philippe Vert, Nelle Varoquaux, Abhijit Chakraborty, Grégory Seumois, Tamer Kahveci and Ciro Ramírez-Suástegui. Their work appears in journals such as Genome Research, Nature Communications, Bioinformatics, Genome biology and Science Immunology.

Rankless uses publication and citation data sourced from OpenAlex, an open and comprehensive bibliographic database. While OpenAlex provides broad and valuable coverage of the global research landscape, it—like all bibliographic datasets—has inherent limitations. These include incomplete records, variations in author disambiguation, differences in journal indexing, and delays in data updates. As a result, some metrics and network relationships displayed in Rankless may not fully capture the entirety of a scholar's output or impact.

Explore authors with similar magnitude of impact