• Member, Center for Genomic Medicine
  • Member, Allen Discovery Center for Cell Lineage Tracing
  • Mario R. Capecchi Endowed Chair in Biology, Biology
  • Member, Henry Eyring Center for Cell & Genome Science
  • Assistant Professor, Biology


  • Wee CL & Nikitchenko M, Wang WC, Luks-Morgan SJ, Song E, Gagnon JA, Randlett O, Bianco IH, Lacoste AMB, Glushenkova E, Barrios JP, Schier AF, Kunes S, Engert F, Douglass AD (2019). Zebrafish oxytocin neurons drive nocifensive behavior by activating brainstem premotor targets. Nature Neuroscience. Vol. 22, 1477-1492. Published, 09/2019.
  • McKenna A & Gagnon JA. (2019). Recording development with single cell dynamic lineage tracing. Development. Vol. 146. Published, 06/2019.
  • Labun K, & Guo X, Chavez A, Church G, Gagnon JA, Valen E. (2019). Accurate analysis of genuine CRISPR editing events with ampliCan. Genome Research. Vol. 5, 843-847. Published, 05/2019.
  • Montague TM, Gagnon JA, Schier AF. Conserved regulation of Nodal-mediated left-right patterning in zebrafish and mouse. Development 2018 dev171090. Published, 11/2018.
  • Raj B, Gagnon JA, Schier AF. Large-scale reconstruction of cell lineages using single-cell readout of transcriptomes and CRISPR-Cas9 barcodes by scGESTALT. Nature Protocols 2018 13:2685-2713. Published, 10/2018.
  • 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. Published, 03/2018.
  • Gagnon JA, Obbad K, Schier AF. The primary role of zebrafish nanog is in extra-embryonic tissue. Development 2018 145:dev147793. Published, 01/2018.
  • Freifeld L, et al. 2017 Expansion microscopy of zebrafish for neuroscience and developmental biology studies. Proceedings of the National Academy of Sciences 114 (50), E10799-E10808. Published, 12/12/2017.
  • Rogers KW, Lord ND, Gagnon JA, Pauli A, Zimmerman S, Aksel DC. 2017. Nodal patterning without Lefty inhibitory feedback is functional but fragile. eLife 6. Published, 12/07/2017.
  • Norris ML, Pauli A, Gagnon JA, Lord ND, Rogers KW, Mosimann C, Zon LI, Schier AF. 2017. Toddler signaling regulates mesodermal cell migration downstream of Nodal signaling. eLife 6. Published, 11/09/2017.
  • Gagnon JA. Pigmentation loss after injection of Cas9 or Cpf1 RNPs into zebrafish embryos. Figshare 2017 https://doi.org/10.6084/m9.figshare.5633452. Published, 11/2017.
  • Ciocanel MV, Kreiling JA, Gagnon JA, Mowry KL, Sandstede B. 2017. Analysis of Active Transport by Fluorescence Recovery after Photobleaching. Biophysical Journal 112 (8), 1714-1725. Published, 04/25/2017.
  • Labun K, Montague TG, Gagnon JA, Thyme SB, Valen E. 2016. CHOPCHOP v2: a web tool for the next generation of CRISPR genome engineering. Nucleic acids research 44 (W1), W272-W276. Published, 05/16/2016.
  • Powrie EA, Ciocanel V, Kreiling JA, Gagnon JA, Sandstede B, Mowry KL. 2016. Using in vivo imaging to measure RNA mobility in Xenopus laevis oocytes. Methods 98, 60-65. Published, 04/01/2016.
  • 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. Published, 01/01/2016.
  • Merkle FT, Neuhausser WM, Santos D, Valen E, Gagnon JA, Maas K, Sandoe J, Schier AF, Eggan, K. 2015.Efficient CRISPR-Cas9-mediated generation of knockin human pluripotent stem cells lacking undesired mutations at the targeted locus. Cell reports 11 (6), 875-883. Published, 05/12/2015.
  • Liu J, Merkle FT, Gandhi AV, Gagnon JA, Woods IG, Chiu CN, Shimogori T, Schier AF, Prober, DA. 2015. Evolutionarily conserved regulation of hypocretin neuron specification by Lhx9. Development 142 (6), 1113-1124. Published, 03/15/2015.
  • 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. Published, 05/29/2014.
  • 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. Published, 05/26/2014.
  • Pauli A, et al. 2014. Toddler: an embryonic signal that promotes cell movement via Apelin receptors. Science 343 (6172), 1248636. Published, 02/14/2014.
  • 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. Published, 04/30/2013.
  • Gagnon JA, Mowry KL. 2011. Molecular motors: directing traffic during RNA localization. Critical reviews in biochemistry and molecular biology 46 (3), 229-239. Published, 04/11/2011.
  • Gagnon JA, Mowry KL. 2011. Visualization of mRNA localization in Xenopus oocytes. RNA Detection and Visualization: Methods and Protocols, 71-82. Published, 03/02/2011.
  • Gagnon JA, Mowry KL. 2010. Visualizing RNA localization in Xenopus oocytes. Journal of visualized experiments: JoVE. Published, 06/14/2010.
  • Gagnon JA, Mowry KL. 2009. VISIONS: the art of science. Molecular reproduction and development 76 (12), 1115-1115. Published, 10/15/2009.
  • Messitt TJ, Gagnon JA, Kreiling JA, Pratt CA, Yoon YJ, Mowry KL. 2008. Multiple Kinesin Motors Coordinate Cytoplasmic RNA Transport on a Subpopulation of Microtubules in Xenopus Oocytes. Developmental cell 15 (3), 426-436. Published, 09/16/2008.
  • Lewis RA, Gagnon JA, Mowry KL. 2008. PTB/hnRNP I is required for RNP remodeling during RNA localization in Xenopus oocytes. Molecular and cellular biology 28 (2), 678-686. Published, 11/26/2007.
  • Lohmueller J, et al. 2007. Progress toward construction and modelling of a tri-stable toggle switch in E. coli. IET Synthetic Biology 1 (1), 25-28. Published, 06/01/2007.
  • Lohmueller J, et al. 2007. Progress toward the construction of a tri-stable genetic toggle switch in E. coli. BMC Systems Biology 1 (1), P39. Published, 05/08/2007.
  • Lengner CJ, Steinman HA, Gagnon JA, TW Smith, JE Henderson, Kream BE, Stein GS, Lian JB, & Jones SN. 2006. Osteoblast differentiation and skeletal developmnt are regulatred by Mdm2-p53 signalling. J Cell Biol 172 (6), 909-921. Published, 03/13/2006.
  • Lengner CJ, Stemman HA, Gagnon JA, Kream BE, Stein GS, Lian JB, Jones SN. 2004. Activity of the Mdm2 oncogene supports Runx2 expression and osteoblast differentiation during embryonic skeletogenesis. JOURNAL OF BONE AND MINERAL RESEARCH 19, S5-S5. Published, 10/01/2004.

Research Statement

Vertebrate lineage and cell fate choice, cell signaling, genome engineering.


  • High-Throughput Dense Reconstruction of Cell Lineages conference – Janelia Research Campus (VA). Invited Talk/Keynote, Presented, 01/2019.
  • Zebrafish Cancer Research Interest Group meeting – Boston (MA). Invited Talk/Keynote, Presented, 01/2019.
  • Bioscience Symposium – University of Utah (UT). Invited Talk/Keynote, Presented, 01/2019.
  • Department of Biological Sciences, University of Pittsburgh (PA). Invited Talk/Keynote, Presented, 01/2019.
  • Zebrafish for Precision/Personal Medicine conference – Toronto (ON). Invited Talk/Keynote, Presented, 01/2019.
  • Zebrafish Disease Models 12 conference – Boston (MA). Invited Talk/Keynote, Presented, 01/2019.
  • Dept Neurobiology & Anatomy – University of Utah (UT). Invited Talk/Keynote, Presented, 01/2019.
  • Huntsman Cancer Institute – University of Utah (UT). Invited Talk/Keynote, Presented, 01/2019.
  • Math/Bio Seminar Series – University of Utah (UT). Invited Talk/Keynote, Presented, 01/2018.
  • College of Science Junior Faculty Luncheon – University of Utah (UT). Invited Talk/Keynote, Presented, 01/2018.
  • School of Biological Sciences Retreat – University of Utah (UT). Invited Talk/Keynote, Presented, 01/2018.
  • Zebrafish Interest Group – University of Utah (UT). Invited Talk/Keynote, Presented, 01/2018.
  • Triangle Zebrafish Symposium - Duke University (NC). Other, Presented, 01/2018.