Jay Shendure is an Investigator of the Howard Hughes Medical Institute, Professor of Genome Sciences at the University of Washington, Director of the Allen Discovery Center for Cell Lineage Tracing, and Scientific Director of the Brotman Baty Institute for Precision Medicine. His 2005 doctoral thesis with George Church included one of the first successful reductions to practice of next generation DNA sequencing. Dr. Shendure's research group in Seattle pioneered exome sequencing and its earliest applications to gene discovery for Mendelian disorders and autism; cell-free DNA diagnostics for cancer and reproductive medicine; massively parallel reporter assays, saturation genome editing; whole organism lineage tracing, and massively parallel molecular profiling of single cells. Dr. Shendure is the recipient of the 2012 Curt Stern Award from the American Society of Human Genetics, the 2013 FEDERAprijs, a 2013 NIH Director's Pioneer Award, the 2014 HudsonAlpha Life Sciences Prize, the 2018 Richard and Carol Hertzberg Prize for Technology Innovation, and the 2019 Richard Lounsbery Award from the National Academy of Sciences. He serves or has served as an advisor to the NIH Director, the US Precision Medicine Initiative, the National Human Genome Research Institute, the Chan-Zuckerberg Initiative and the Allen Institutes for Cell Science and Immunology. He received his MD and PhD degrees from Harvard Medical School in 2007.

Systematic reconstruction of the cellular trajectories of mammalian embryogenesis
Mammalian embryogenesis is characterized by rapid cellular proliferation and diversification. Within a few weeks, a single cell zygote gives rise to millions of cells expressing a panoply of molecular programs, including much of the diversity that will subsequently be present in adult tissues. Although intensively studied, a comprehensive delineation of the major cellular trajectories that comprise mammalian development in vivo remains elusive. Here we set out to integrate several single cell RNA-seq datasets (scRNA-seq) that collectively span mouse gastrulation and organogenesis. We define cell states at each of 19 successive stages spanning E3.5 to E13.5, heuristically connect them with their pseudo-ancestors and pseudo-descendants, and for a subset of stages, deconvolve their approximate spatial distributions. Despite being constructed through automated procedures, the resulting trajectories of mammalian embryogenesis (TOME) are largely consistent with our contemporary understanding of mammalian development. We leverage TOME to nominate transcription factors (TF) and TF motifs as key regulators of each branch point at which a new cell type emerges. Finally, to facilitate comparisons across vertebrates, we apply the same procedures to single cell datasets of zebrafish and frog embryogenesis, and nominate “cell type homologs” based on shared regulators and transcriptional states.