Ferhat Ay

Research interests

Publications

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

  Science Immunology · 2021 · https://doi.org/10.1126/sciimmunol.abe4782

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

  Nature Genetics · 2020 · https://doi.org/10.1038/s41588-020-00745-3

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

  Genome biology · 2020 · https://doi.org/10.1186/s13059-020-02167-0

• Identifying statistically significant chromatin contacts from Hi-C data with FitHiC2

  Nature Protocols · 2020 · https://doi.org/10.1038/s41596-019-0273-0

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

  Cell · 2020 · https://doi.org/10.1016/j.cell.2020.10.001

• Measuring the reproducibility and quality of Hi-C data

  Genome biology · 2019 · https://doi.org/10.1186/s13059-019-1658-7

• Identification of significant chromatin contacts from HiChIP data by FitHiChIP

  Nature Communications · 2019 · https://doi.org/10.1038/s41467-019-11950-y

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

  The Journal of Experimental Medicine · 2019 · https://doi.org/10.1084/jem.20190249

• Identifying cis Elements for Spatiotemporal Control of Mammalian DNA Replication

  Cell · 2018 · https://doi.org/10.1016/j.cell.2018.11.036

• Integrative detection and analysis of structural variation in cancer genomes

  Nature Genetics · 2018 · https://doi.org/10.1038/s41588-018-0195-8

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

  Nature Communications · 2018 · https://doi.org/10.1038/s41467-018-04295-5

• Bipartite structure of the inactive mouse X chromosome

  Genome biology · 2015 · https://doi.org/10.1186/s13059-015-0728-8

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

  Nucleic Acids Research · 2015 · https://doi.org/10.1093/nar/gkv865

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

  Genome Research · 2015 · https://doi.org/10.1101/gr.183699.114

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

  Genome biology · 2015 · https://doi.org/10.1186/s13059-015-0745-7

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

  Genome Research · 2014 · https://doi.org/10.1101/gr.169417.113

• A statistical approach for inferring the 3D structure of the genome

  Bioinformatics · 2014 · https://doi.org/10.1093/bioinformatics/btu268

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

  Genome Research · 2014 · https://doi.org/10.1101/gr.160374.113

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

  Nature Methods · 2014 · https://doi.org/10.1038/nmeth.3205

• Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE

  Science · 2010 · https://doi.org/10.1126/science.1198374

Current projects

No projects listed.