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Dan Wagner, PhD
Dan Wagner, PhD

Assistant Professor, Ob/Gyn & Reproductive Sciences

Research Interests

Multicellular organisms possess a remarkable capacity for the development, maintenance, and regeneration of robust tissue patterns, even while facing considerable environmental and genetic challenges. Regulation of tissue patterns and the individual cell states they comprise is critical during embryonic development; failures can lead to birth defects, developmental disorders, and/or lethality. While we currently understand many of the links connecting environmental and genetic perturbations to their ultimate effects on embryos, a significant proportion of human pregnancies still result in developmental defects or miscarriages of unknown cause. At present, we also often fail to understand why certain genetic or environmental perturbations result in failed embryogenesis in some individuals, but not in others. Feedback regulation of cell fate decisions within tissues is one strategy by which developing embryos buffer a wide range of perturbations to achieve healthy outcomes.

My research seeks to understand feedback mechanisms that underlie cell fate and tissue pattern robustness, as well as the disease states that arise when these mechanisms fail. My lab studies these mechanisms in the zebrafish (Danio rerio), a vertebrate species whose embryos bear considerable genetic and anatomical similarity to those of humans. As a model system, zebrafish embryos can be studied with a wide variety of reverse genetic, lineage-tracing, imaging, and molecular tools. My lab will additionally leverage single-cell genomics methods, including TRACERSEQ and STITCH, which I developed in my postdoc, to map quantitative relationships between cell lineage and cell state, in both healthy and perturbed contexts. Such analyses will also reveal transcriptional signatures for how all tissues of a developing embryo respond to perturbations, yielding candidate genes for targeted in vivo developmental genetic studies. We will additionally use comparative approaches to relate molecular details of feedback mechanisms discovered in zebrafish to their counterparts in humans.


Year Institution & Location Degree Field of Study
2003 Haverford College, Haverford, PA BS Systems Biology
2012 MIT, Cambridge, MA PhD Biology
2019 Harvard Medical School, Boston, MA Postdoc Systems Biology

Achievements & Recognition

2022-27 Chan Zuckerberg Biohub: Biohub Investigator
2021-2026 NIH/NIGMS: NIH Director's New Innovator Award
2021-2024 Kinship Foundation: Searle Scholar
2018 Science Magazine: 2018 Breakthrough of the Year - "Development Cell by Cell"
2017-2023 NIGH/NIGMS: K99/R00 Pathway to Independence Award
2015-2017 HHMI/LSRF: HHMI Postdoctoral Fellowship of the Life Sciences Research Foundation
2005-2006 MIT: Praecis Presidential Graduate Fellowship
2003 Haverford College: Ariel G. Lowy Prize for Biology Research
2002 Haverford College: Howard Hughes Medical Institute Interdisciplinary Scholar

Selected Publications

  • Wagner DE, Weinreb C, Collins ZM, Briggs JA, Megason SG, Klein AM; Single-cell mapping of gene expression landscapes and lineage in the zebrafish embryo.; Science (New York, N.Y.); 2018

    View in: PubMed

  • Briggs JA, Weinreb C, Wagner DE, Megason S, Peshkin L, Kirschner MW, Klein AM; The dynamics of gene expression in vertebrate embryogenesis at single-cell resolution.; Science (New York, N.Y.); 2018

    View in: PubMed

  • Raj B, Wagner DE, 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

    View in: PubMed