James Gagnon

Assistant Professor of Biology

Gagnon Photo

B.S. Worcester Polytechnic Institute

Ph.D. Brown University




James Gagnon's Lab Page

James Gagnon's PubMed Literature Search


Molecular Biology Program

Developmental Biology, Genetics, Genomics


Our lab tries to understand vertebrate embryogenesis and adult tissue homeostasis through the lens of the lineage tree. The lineage tree is the branching structure of cell divisions that describes relationships between all cells in the adult animal, and connects these cells to their ancestor cells in the embryo. We have developed tools to record this lineage tree, with unprecedented scale and granularity, using genome editing and sequencing.

Our lab studies variability in the vertebrate lineage tree - how it is compensated for and how it can lead to individuality. Our lab is interested in cell signaling pathways, and how they influence cell fate choice at critical branch points within the tree. Finally, our lab researches how stem cells contribute to tissue maintenance and regeneration, particularly in the blood and in the germ line. Our lab addresses these topics using genome engineering, sequencing and synthetic biology in the zebrafish, a great model of vertebrate biology.


Selected Publications

  1. Raj B, Wagner DW, McKenna A, Pandey S, Klein AM, Shendure J, Gagnon JA*, Schier AF*. Simultaneous single-cell profiling of lineages and cell types in the vertebrate brain by scGESTALT. Under review. Preprint available at bioRxiv
  2. Gagnon JA, Obbad K, Schier AF. The primary role of zebrafish nanog is in extraembryonic tissue. Development, in press.  Preprint available at bioRxiv
  3. McKenna A*, Findlay G*, Gagnon JA*, Horwitz M, Schier AF, Shendure J. Whole organism lineage tracing by combinatorial and cumulative genome editing. Science 2016 353:aaf7907
  4. Gagnon JA, Valen E, Thyme SB, Huang P, Akhmetova L, Pauli A, Montague TG, Zimmerman S, Richter C, Schier AF. Efficient mutagenesis by Cas9 protein-mediated oligonucleotide insertion and large-scale assessment of single-guide RNAs. PLoS One 2014 9:e98186
  5. Montague TG*, Cruz JM*, Gagnon JA, Church GM, Valen E. CHOPCHOP: a CRISPR/Cas9 and TALEN web tool for genome editing. Nucleic Acids Res. 2014 42:W401-7

* Equal contribution

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Last Updated: 1/7/18