Key Publications

A complete publication list is available at Google Scholar.


Recording development with single cell dynamic lineage tracing.
(link, pdf)

McKenna A, Gagnon JA. Development, 2019.

In this review, we surveyed emerging technologies used to record development in animals, with an eye to future challenges and opportunities.


Simultaneous single-cell profiling of lineages and cell types in the vertebrate brain. (link, pdf, preprint)

Raj B, Wagner DW, McKenna A, Pandey S, Klein AM, Shendure J, Gagnon JA*, Schier AF*.  Nature Biotechnology, 2018.   *co-corresponding authors

We merged single cell RNA sequencing with CRISPR-Cas lineage tracing to determine relationships between cells in a large single cell atlas of the juvenile zebrafish brain.

Detailed protocol available at Nature Protocols.

Highlighted as the Science Magazine 2018 Breakthrough of Year, in Nature Reviews Genetics, Nature Methods, and in Faculty of 1000.


The primary role of zebrafish nanog is in extraembryonic tissue. (link, pdf, preprint)

Gagnon JA, Obbad K, Schier AF. Development, 2018.

We discovered that the transcription factor Nanog is required primarily for extraembryonic tissue development, and is not required in embryonic or germ cells.

Highlighted in Development.


Whole organism lineage tracing by combinatorial and cumulative genome editing. (link, pdf, preprint)

McKenna A*, Findlay G*, Gagnon JA*, Horwitz M, Schier AF, Shendure J. Science, 2016.   * co-first authors

We developed GESTALT - a tool for lineage tracing in animals using CRISPR-Cas genome editing.

Highlighted by The Atlantic, BBC World Service, The Scientist, New Scientist, Science, Science Daily, HHMI News, Biotechniques, Harvard MCB News, Nature Reviews Genetics, Nature Biotechnology, Nature Methods, Cell Systems, Benchling, Epigenie, Faculty of 1000, and a finalist for Nature Methods Method of the Year 2017.


Efficient mutagenesis by Cas9 protein-mediated oligonucleotide insertion and large-scale assessment of single-guide RNAs. (link, pdf)

Gagnon JA, Valen E, Thyme SB, Huang P, Akhmetova L, Pauli A, Montague TG, Zimmerman S, Richter C, Schier AF. PLoS One, 2014.

We determined rules that increase CRISPR-Cas activity in zebrafish, and found biases in DNA repair outcomes.

Highlighted by and A CRISPR Blog.

A (somewhat out of date) detailed protocol is available.