Patrick Cahan, Ph.D., M.S.

Headshot of Patrick Cahan
  • Associate Professor of Biomedical Engineering

Research Interests

Stem Cell Engineering; Computational Biology; Single Cell Genomics more


Patrick Cahan received a B.S. in Computer Science from University of Maryland, Baltimore County, a M.S. in Genomics and Bioinformatics at George Washington University, and a Ph.D. in Computational Biology from Washington University in St. Louis. His postdoctoral training at Harvard Medical School and Boston Children’s Hospital focused on the development and experimental validation of computational methods to assess and improve engineered cells, such as those resulting from directed differentiation of pluripotent stem cells. more


  • Associate Professor of Biomedical Engineering
  • Assistant Professor of Molecular Biology and Genetics

Departments / Divisions



  • M.S.; George Washington University (District of Columbia) (2004)
  • B.S.; University of Maryland (Baltimore County) (Maryland) (2000)
  • Ph.D.; Washington University in St. Louis (Missouri) (2009)

Research & Publications


We focus on stem cell biology and cell fate engineering, with an emphasis on the development and diseases of the synovial joint. We invent computational tools to improve our understanding of development and to improve our ability to engineer cell fate and function, and we experimentally validate and apply these tools.

Lab Website: Cahan Laboratory

Selected Publications

View all on PubMed

Cahan P, Treutlein B. A conversation with ChatGPT on the role of computational systems biology in stem cell research. Stem Cell Reports. 22023 Jan 10;18(1):1-2 PMID: 36630899

Su EY*, Spangler A*,Bian Q, Kasamoto JY, Cahan P. Reconstruction of dynamic regulatory networks reveals signaling-induced topology changes associated with germ layer specification. Stem Cell Reports. 2022 Jan 10 PMID: 35090587

Peng D*, Gleyzer R*, Tai WH, Kumar P, Bian Q, Isaacs B, Rocha EL, Cai S, DiNapoli K, Huang FW, Cahan P. Evaluating the transcriptional fidelity of cancer models. Genome Medicine 2021 Apr 13;73. PMID: 33926541

Bian Q, Cheng YH, Wilson JP, Su EY, Kim DQ, Yoo S, Blackshaw S, Cahan P. A single cell transcriptional atlas of early synovial joint development. Development. 2020 June 20;147(14):dev185777 PMID: 32580935

Tan Y and Cahan P. SingleCellNet: A Computational Tool to Classify Single Cell RNA-Seq Data Across Platforms and Across Species. Cell Systems. 2019 Jul 17. pii: S2405-4712(19)30199-1. PMID: 31377170

Academic Affiliations & Courses

Courses and Syllabi

  • Computational Stem Cell Biology (580.447/647 (see
    Johns Hopkins University

Activities & Honors


  • Discovery Innovation Award, The Johns Hopkins University School of Medicine, 2017
  • Johns Hopkins Catalyst Award, Johns Hopkins University, 2022
  • Rising Star BMES Cellular and Molecular Bioengineering, Biomedical Engineering Society, 2019

Videos & Media

Recent News Articles and Media Coverage

Study Adds to Evidence That Most Cancer Cells Grown in a Dish Have Little in Common Genetically with Cancer Cells in People Newsroom (June 17, 2021)

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