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Molecular Biology

D-Index
45
Citations
9491
World Ranking
2850
National Ranking
1363

Overview

Ferhat Ay is affiliated with the La Jolla Institute For Allergy & Immunology in the United States. Their research spans significant areas within biochemistry, genetics, molecular biology, medicine, and immunology and microbiology. Their publication record includes 117 contributions in Biochemistry, Genetics and Molecular Biology, 60 in Medicine, and 56 in Immunology and Microbiology.

The scientist's work covers numerous subfields such as molecular biology, immunology, cancer research, genetics, and infectious diseases. Their primary topics of investigation include genomics and chromatin dynamics, immune cell function and interaction, single-cell and spatial transcriptomics, bioinformatics and genomic networks, T-cell and B-cell immunology, epigenetics and DNA methylation, and RNA research and splicing.

Frequent co-authors collaborating with Ferhat Ay include Daniela Salgado Figueroa (21 publications), Abhijit Chakraborty (19 publications), Pandurangan Vijayanand (14 publications), Sourya Bhattacharyya (14 publications), and Joaquin Reyna (13 publications).

Most of their work has appeared in several key publication venues, particularly bioRxiv (Cold Spring Harbor Laboratory) with 25 papers, The Journal of Immunology (6 papers), Genome Biology (5 papers), Nature Communications (5 papers), and Science Immunology (4 papers).

Selected recent papers by Ferhat Ay include:

  • Imbalance of Regulatory and Cytotoxic SARS-CoV-2-Reactive CD4+ T Cells in COVID-19, 2020, Cell
  • Severely ill patients with COVID-19 display impaired exhaustion features in SARS-CoV-2-reactive CD8 + T cells, 2021, Science Immunology
  • Identifying statistically significant chromatin contacts from Hi-C data with FitHiC2, 2020, Nature Protocols
  • Mustache: multi-scale detection of chromatin loops from Hi-C and Micro-C maps using scale-space representation, 2020, Genome Biology
  • Promoter-interacting expression quantitative trait loci are enriched for functional genetic variants, 2020, Nature Genetics

Best Publications

  • Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE

    Sushmita Roy;Jason Ernst;Peter V. Kharchenko;Pouya Kheradpour

  • Statistical confidence estimation for Hi-C data reveals regulatory chromatin contacts

    Ferhat Ay;Timothy L. Bailey;William Stafford Noble

  • Integrative detection and analysis of structural variation in cancer genomes

    Jesse R. Dixon;Jie Xu;Vishnu Dileep;Ye Zhan

  • Identification of significant chromatin contacts from HiChIP data by FitHiChIP.

    Sourya Bhattacharyya;Vivek Chandra;Pandurangan Vijayanand;Pandurangan Vijayanand;Pandurangan Vijayanand;Ferhat Ay;Ferhat Ay

  • Bipartite structure of the inactive mouse X chromosome.

    Xinxian Deng;Wenxiu Ma;Vijay Ramani;Andrew Hill

  • Single-cell transcriptomic analysis of tissue-resident memory T cells in human lung cancer.

    James Clarke;James Clarke;Bharat Panwar;Ariel Madrigal;Divya Singh

  • Three-dimensional modeling of the P. falciparum genome during the erythrocytic cycle reveals a strong connection between genome architecture and gene expression

    Ferhat Ay;Evelien M. Bunnik;Nelle Varoquaux;Sebastiaan M. Bol

  • Fine-scale chromatin interaction maps reveal the cis-regulatory landscape of human lincRNA genes

    Wenxiu Ma;Ferhat Ay;Choli Lee;Gunhan Gulsoy

  • Topologically-associating domains and their long-range contacts are established during early G1 coincident with the establishment of the replication timing program

    Vishnu Dileep;Ferhat Ay;Jiao Sima;Daniel L. Vera

  • Analysis methods for studying the 3D architecture of the genome

    Ferhat Ay;Ferhat Ay;William S. Noble

  • Identifying cis Elements for Spatiotemporal Control of Mammalian DNA Replication

    Jiao Sima;Abhijit Chakraborty;Vishnu Dileep;Marco Michalski

  • Measuring the reproducibility and quality of Hi-C data

    Galip Gürkan Yardımcı;Hakan Ozadam;Michael E.G. Sauria;Oana Ursu

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

    Daniel Marbach;Sushmita Roy;Ferhat Ay;Patrick E. Meyer

  • A predictive modeling approach for cell line-specific long-range regulatory interactions

    Sushmita Roy;Alireza Fotuhi Siahpirani;Deborah Chasman;Sara Knaack

  • 17q21 asthma-risk variants switch CTCF binding and regulate IL-2 production by T cells.

    Benjamin Joachim Schmiedel;Grégory Seumois;Daniela Samaniego-Castruita;Justin Cayford

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

    Vivek Chandra;Sourya Bhattacharyya;Benjamin J. Schmiedel;Ariel Madrigal

  • Comprehensive identification and analysis of human accelerated regulatory DNA

    Rachel M. Gittelman;Enna Hun;Ferhat Ay;Jennifer Madeoy

  • Changes in genome organization of parasite-specific gene families during the Plasmodium transmission stages.

    Evelien M. Bunnik;Evelien M. Bunnik;Kate B. Cook;Nelle Varoquaux;Gayani Batugedara

  • Scalable Steady State Analysis of Boolean Biological Regulatory Networks

    Ferhat Ay;Fei Xu;Tamer Kahveci

  • Joint annotation of chromatin state and chromatin conformation reveals relationships among domain types and identifies domains of cell-type-specific expression

    Maxwell W. Libbrecht;Ferhat Ay;Michael M. Hoffman;Michael M. Hoffman;David M. Gilbert

Frequent Co-Authors

Pandurangan Vijayanand
Pandurangan Vijayanand La Jolla Institute For Allergy & Immunology
William Stafford Noble
William Stafford Noble University of Washington
Christian H. Ottensmeier
Christian H. Ottensmeier University of Southampton
Grégory Seumois
Grégory Seumois La Jolla Institute For Allergy & Immunology
Jean-Philippe Vert
Jean-Philippe Vert Google (United States)
David M. Gilbert
David M. Gilbert Florida State University
Stefan Mundlos
Stefan Mundlos Max Planck Society
Ji-Fan Hu
Ji-Fan Hu Stanford University
Karine G. Le Roch
Karine G. Le Roch University of California, Riverside
Job Dekker
Job Dekker University of Massachusetts Chan Medical School

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