Skip to content

Main Navigation

James Gagnon

Assistant Professor of Biological Sciences

Gagnon Photo

B.S. Worcester Polytechnic Institute

Ph.D. Brown University



James Gagnon's Lab Page

James Gagnon's PubMed Literature Search

James Gagnon's Google Scholar

James Gagnon's Twitter

Molecular Biology Program

Developmental Biology, Genetics, Genomics, Stem Cells


Our lab studies vertebrate development 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 using CRISPR genome editing and single-cell RNA sequencing to record lineage trees with unprecedented scale and granularity.

Our lab studies variability in the vertebrate lineage tree - how it is compensated for and how it can lead to individuality. We are 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 brain and in the germ line, as animals grow and age. Our lab addresses these topics using genome engineering, sequencing and synthetic biology in the zebrafish, a great model of vertebrate biology.

We also have a variety of side projects driven by curiosity! Approaching classic mysteries of biology with new ideas and methods is our specialty. If you are curious about the intersection of biology, engineering and math, let’s talk.


Selected Publications

  1. McKenna A, Gagnon JA. Recording development with single cell dynamic lineage tracing. Development 2019 146:dev169730 PMID: 31249005
  2. 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. Nature Biotechnology 2018 36:442-450 PMID: 29608178
  3.  Gagnon JA, Obbad K, Schier AF. The primary role of zebrafish nanog is in extra-embryonic tissue. Development 2018 145:dev147793 PMID: 29180571
  4. 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 PMID: 27229144
  5. 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 PMID: 24873830
  6. 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 PMID: 24861617
  7. Gagnon JA, Kreiling JA, Powrie EA, Wood TR, Mowry KL. Directional transport is mediated by a Dynein-dependent step in an RNA localization pathway. PLoS Biol. 2013 11:e1001551 PMID: 23637574

* Equal contribution

to page top

Last Updated: 10/1/20