Key Publications

A complete publication list is available at Google Scholar.


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Simultaneous single-cell profiling of lineages and cell types in the vertebrate brain.

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.


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The primary role of zebrafish nanog is in extraembryonic tissue.

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.


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Whole organism lineage tracing by combinatorial and cumulative genome editing.

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.


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Efficient mutagenesis by Cas9 protein-mediated oligonucleotide insertion and large-scale assessment of single-guide RNAs.

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.