Ferhat Ay

Employment

• La Jolla Institute Associate Professor
  2016 - Present

Education

• University of Florida Ph.D.
  2007 - 2011
• Middle East Technical University B.S.
  2004 - 2007
• Middle East Technical University B.S.
  2002 - 2007

Projects & Funding

Projects & funding information is unavailable.

Publications (128)

• CTCF directly binds G-quadruplex structures to regulate genome topology and gene expression
  Proceedings of the National Academy of Sciences 2026 DOI: 10.1073/pnas.2509164123
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• Nuclear speckles enable processing of RNA from GC-rich isochores.
  Cell 2026 DOI: 10.1016/j.cell.2026.01.011
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• EpiExpr: Predicting gene expression using epigenetic data and chromatin interactions
  2026 DOI: 10.64898/2026.02.06.704509
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• DiffHiChIP: Identifying differential chromatin contacts from HiChIP data
  Cell Reports Methods 2025 DOI: 10.1016/j.crmeth.2025.101214
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• 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 DOI: 10.1038/s41467-025-62205-y
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• Soffritto: a deep learning model for predicting high-resolution replication timing
  Bioinformatics 2025 DOI: 10.1093/bioinformatics/btaf231
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• Distinct interferon response patterns link to increased transposable element expression in leukocytes of systemic lupus erythematosus patients
  2025 DOI: 10.1101/2025.05.30.657099
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• Soffritto: a deep-learning model for predicting high-resolution replication timing
  2025 DOI: 10.1101/2025.01.23.634644
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• DiffHiChIP: Identifying differential chromatin contacts from HiChIP data
  2025 DOI: 10.1101/2025.01.14.633096
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• Perspective on recent developments and challenges in regulatory and systems genomics
  Bioinformatics Advances 2024 DOI: 10.1093/bioadv/vbaf106
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