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Faculty & Research


Patrick Cahan

Department Affiliation Primary: Biomedical Engineering
RankAssistant Professor
Phone Numbers
School of Medicine Address733 N. Broadway
MRB 653
Baltimore MD 21287
Link to Lab Homepage
Patrick Cahan

Research Topic: Engineering stem cell fate

Gene regulatory networks (GRNs) govern the cell’s transcriptional output both at steady state and in response to perturbations, and thus act as major molecular determinants of cell-type identity. The long-term aims of my research program are:

1. to develop computational and experimental tools to map mammalian GRNs,

2. to better understand how canonical signaling pathways modulate and are 
    modulated by transiently established GRNs in the developing embryo, and

3. to characterize how cell type specific GRNs are rewired during tumorigenesis and

Towards these ends, we work across several disciplines including molecular and developmental biology, manipulation of pluripotent stem cells, population based and single-cell genomics, and computational and network biology. The outcomes of my research program will include improving the fidelity of directed differentiation to mesendodermal lineages (for purposes of disease modeling, drug screening, and regenerative medicine), the generation of fundamental insights into the interactions between GRNs, signaling pathways, and cell fate decisions, and improved models of human tumors.



​Bian Q, Cahan P. Computational Tools for Stem Cell Biology. Trends in Biotechnology. 2016 Jun. 10.1016/j.tibtech.2016.05.010.
PubMed Abstract

Kumar RM*, Cahan P*, Shalek A, Satija R, DaleyKeyser A, Li H, Zhang J, Pardee K, Gennert D, Trombetta JJ, Ferrante TC, Regev A, Daley GQ, and Collins JJ. Deconstructing transcriptional heterogeneity in pluripotent stem cells. Nature. 2014 Dec 4;516(7529):56–61.
PubMed Abstract

Cahan P*, Li H*, Morris SA*, Lummertz da Rocha E, Daley GQ, Collins JJ. CellNet: Network Biology Applied to Stem Cell Engineering. Cell. 2014 Aug 14;158(4):903–15.
PubMed Abstract

Morris SA*, Cahan P*, Li H*, Zhao AM, San Roman AK, Shivdasani RA, Collins JJ, Daley GQ. Dissecting Engineered Cell Types and Enhancing Cell Fate Conversion via CellNet. Cell. 2014 Aug 14;158(4):889–902.
PubMed Abstract

Cahan P, Daley GQ. Origins and implications of pluripotent stem cell variability and heterogeneity. (2013). Nature Reviews Molecular Cell Biology 14:357–68.
PubMed Abstract

McKinney-Freeman S*, Cahan P*, Li H*, Lacadie SA, Huang HT, Curran M, Loewer S, Naveiras O, Kathrein KL, Konantz M, Langdon EM, Lengerke C, Zon LI, Collins JJ, Daley GQ. The transcriptional landscape of hematopoietic stem cell ontogeny. Cell Stem Cell. 2012 Nov 2;11(5):701–14.
PubMed Abstract

Cahan P, Li Y, Izumi M, Graubert TA. The impact of copy number variation on local gene expression in mouse hematopoietic stem and progenitor cells. Nature Genetics. 2009 Apr;41(4):430–7.
PubMed Abstract

*Denotes equal contribution