Dan Wagner, PhD

Title(s)Assistant Professor, Ob/Gyn, Reproductive Sciences
SchoolSchool of Medicine
Address35 Medical Center Way, #1016
San Francisco CA 94143
ORCID ORCID Icon0000-0002-2983-635X Additional info
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    Collapse Biography 
    Collapse Education and Training
    Harvard Medical School, Boston, MAPostdoc2019Systems Biology
    MIT, Cambridge, MAPh.D2012Biology
    Haverford College, Haverford, PAB.S.2003Biology, Chemistry
    Collapse Awards and Honors
    Chan Zuckerberg Biohub2022  - 2027Biohub Investigator
    NIH/NIGMS2021  - 2026 NIH Director's New Innovator Award
    Kinship Foundation2021  - 2024Searle Scholar
    Science Magazine2018  - 20182018 Breakthrough of the Year - "Development Cell by Cell"
    NIH/NIGMS2017  - 2023K99/R00 Pathway to Independence Award
    HHMI/LSRF2015  - 2017HHMI Postdoctoral Fellowship of the Life Sciences Research Foundation (LSRF)
    MIT2005  - 2006Praecis Presidential Graduate Fellowship
    Haverford College2003  - 2003Ariel G. Lowy Prize for Biology Research
    Haverford College2002  - 2002Howard Hughes Medical Institute Interdisciplinary Scholar

    Collapse Overview 
    Collapse Overview
    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.

    Collapse Research 
    Collapse Research Activities and Funding
    Challenging and decoding the logic of cell fate feedback control in the developing zebrafish embryo
    Chan Zuckerberg Biohub 7031078Mar 1, 2022 - Mar 1, 2027
    Role: Principal Investigator
    Mapping cell fate flow and feedback control on vertebrate embryonic landscapes
    NIH DP2GM146258Sep 23, 2021 - Aug 31, 2024
    Role: Principal Investigator
    Elucidating molecular mechanisms of pattern repair in zebrafish embryos
    Searle Scholar's Program, Kinship Foundation 136867AJul 1, 2021 - Jun 30, 2024
    Role: Principal Investigator
    Mapping vertebrate differentiation hierarchies with high-throughput single cell transcriptomics
    NIH R00GM121852Jun 1, 2020 - May 31, 2023
    Role: Principal Investigator
    Mapping vertebrate differentiation hierarchies with high-throughput single cell transcriptomics
    NIH K99GM121852May 1, 2017 - Apr 30, 2019
    Role: Principal Investigator

    Collapse ORNG Applications 
    Collapse Featured Publications

    Collapse Featured Content 
    Collapse Twitter

    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
    Newest   |   Oldest   |   Most Cited   |   Most Discussed   |   Timeline   |   Field Summary   |   Plain Text
    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Pluripotency of a founding field: rebranding developmental biology. Development. 2024 Feb 01; 151(3). Rogers CD, Amemiya C, Arur S, Babonis L, Barresi M, Bartlett M, Behringer R, Benham-Pyle B, Bergmann D, Blackman B, Brown CT, Browne B, Camacho J, Chabu CY, Chow I, Cleaver O, Cool J, Dennis MY, Dickinson AJ, Di Talia S, Frank M, Gillmor S, Haag ES, Hariharan I, Harland R, Husbands A, Jerome-Majewska L, Koenig K, Labonne C, Layden M, Lowe C, Mani M, Martik M, McKown K, Moens C, Mosimann C, Onyenedum J, Reed R, Rivera A, Rokhsar D, Royer L, Rutaganira F, Shahan R, Sinha N, Swalla B, Van Norman JM, Wagner DE, Wikramanayake A, Zebell S, Brady SM. PMID: 38345109; PMCID: PMC10986740.
      View in: PubMed   Mentions:    Fields:    
    2. Graded BMP signaling within intestinal crypt architecture directs self-organization of the Wnt-secreting stem cell niche. Cell Stem Cell. 2023; 4(30):433-449. View Publication.
    3. Graded BMP signaling within intestinal crypt architecture directs self-organization of the Wnt-secreting stem cell niche. Cell Stem Cell. 2023 04 06; 30(4):433-449.e8. Kraiczy J, McCarthy N, Malagola E, Tie G, Madha S, Boffelli D, Wagner DE, Wang TC, Shivdasani RA. PMID: 37028407; PMCID: PMC10134073.
      View in: PubMed   Mentions: 6     Fields:    Translation:AnimalsCells
    4. Triangulating spatial relationships from single-cell interaction maps. Nat Methods. 2021 08; 18(8):867-869. Wagner DE. PMID: 34272537.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    5. Lineage tracing meets single-cell omics: opportunities and challenges. Nat Rev Genet. 2020 07; 21(7):410-427. Wagner DE, Klein AM. PMID: 32235876; PMCID: PMC7307462.
      View in: PubMed   Mentions: 182     Fields:    Translation:HumansAnimalsCells
    6. The emergence of transcriptional identity in somatosensory neurons. Nature. 2020 01; 577(7790):392-398. Sharma N, Flaherty K, Lezgiyeva K, Wagner DE, Klein AM, Ginty DD. PMID: 31915380; PMCID: PMC7307422.
      View in: PubMed   Mentions: 144     Fields:    Translation:AnimalsCells
    7. In vitro characterization of the human segmentation clock. Nature. 2020 04; 580(7801):113-118. Diaz-Cuadros M, Wagner DE, Budjan C, Hubaud A, Tarazona OA, Donelly S, Michaut A, Al Tanoury Z, Yoshioka-Kobayashi K, Niino Y, Kageyama R, Miyawaki A, Touboul J, Pourquié O. PMID: 31915384; PMCID: PMC7336868.
      View in: PubMed   Mentions: 72     Fields:    Translation:HumansAnimalsCells
    8. A small set of conserved genes, including sp5 and Hox, are activated by Wnt signaling in the posterior of planarians and acoels. PLoS Genet. 2019 10; 15(10):e1008401. Tewari AG, Owen JH, Petersen CP, Wagner DE, Reddien PW. PMID: 31626630; PMCID: PMC6821139.
      View in: PubMed   Mentions: 12     Fields:    Translation:AnimalsCells
    9. Single-cell mapping of gene expression landscapes and lineage in the zebrafish embryo. Science. 2018 06 01; 360(6392):981-987. Wagner DE, Weinreb C, Collins ZM, Briggs JA, Megason SG, Klein AM. PMID: 29700229; PMCID: PMC6083445.
      View in: PubMed   Mentions: 314     Fields:    Translation:Animals
    10. The dynamics of gene expression in vertebrate embryogenesis at single-cell resolution. Science. 2018 06 01; 360(6392). Briggs JA, Weinreb C, Wagner DE, Megason S, Peshkin L, Kirschner MW, Klein AM. PMID: 29700227; PMCID: PMC6038144.
      View in: PubMed   Mentions: 223     Fields:    Translation:AnimalsCells
    11. Simultaneous single-cell profiling of lineages and cell types in the vertebrate brain. Nat Biotechnol. 2018 06; 36(5):442-450. Raj B, Wagner DE, McKenna A, Pandey S, Klein AM, Shendure J, Gagnon JA, Schier AF. PMID: 29608178; PMCID: PMC5938111.
      View in: PubMed   Mentions: 239     Fields:    Translation:HumansAnimalsCells
    12. Clonal Analysis of Planarian Stem Cells by Subtotal Irradiation and Single-Cell Transplantation. Methods Mol Biol. 2018; 1774:479-495. Wang IE, Wagner DE, Reddien PW. PMID: 29916173.
      View in: PubMed   Mentions: 6     Fields:    Translation:AnimalsCells
    13. Genetic screening enters the single-cell era. Nat Methods. 2017 02 28; 14(3):237-238. Wagner DE, Klein AM. PMID: 28245215.
      View in: PubMed   Mentions: 6     Fields:    
    14. teashirt is required for head-versus-tail regeneration polarity in planarians. Development. 2015 Mar 15; 142(6):1062-72. Owen JH, Wagner DE, Chen CC, Petersen CP, Reddien PW. PMID: 25725068; PMCID: PMC4360178.
      View in: PubMed   Mentions: 18     Fields:    Translation:AnimalsCells
    15. Single-cell analysis reveals functionally distinct classes within the planarian stem cell compartment. Cell Stem Cell. 2014 Sep 04; 15(3):326-339. van Wolfswinkel JC, Wagner DE, Reddien PW. PMID: 25017721; PMCID: PMC4171737.
      View in: PubMed   Mentions: 134     Fields:    Translation:AnimalsCells
    16. Muscle cells provide instructions for planarian regeneration. Cell Rep. 2013 Aug 29; 4(4):633-41. Witchley JN, Mayer M, Wagner DE, Owen JH, Reddien PW. PMID: 23954785; PMCID: PMC4101538.
      View in: PubMed   Mentions: 119     Fields:    Translation:AnimalsCells
    17. Genetic regulators of a pluripotent adult stem cell system in planarians identified by RNAi and clonal analysis. Cell Stem Cell. 2012 Mar 02; 10(3):299-311. Wagner DE, Ho JJ, Reddien PW. PMID: 22385657; PMCID: PMC3338251.
      View in: PubMed   Mentions: 99     Fields:    Translation:AnimalsCells
    18. Clonogenic neoblasts are pluripotent adult stem cells that underlie planarian regeneration. Science. 2011 May 13; 332(6031):811-6. Wagner DE, Wang IE, Reddien PW. PMID: 21566185; PMCID: PMC3338249.
      View in: PubMed   Mentions: 268     Fields:    Translation:AnimalsCells
    19. Toward the development of peptide nanofilaments and nanoropes as smart materials. Proc Natl Acad Sci U S A. 2005 Sep 06; 102(36):12656-61. Wagner DE, Phillips CL, Ali WM, Nybakken GE, Crawford ED, Schwab AD, Smith WF, Fairman R. PMID: 16129839; PMCID: PMC1193539.
      View in: PubMed   Mentions: 19     Fields:    Translation:Cells
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