Dan Wagner, PhD

Photo of 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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    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 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 Research 
    Collapse Featured Publications
    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

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    Collapse Bibliographic 
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    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.
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    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. Intracellular pH dynamics promotes zebrafish larval tail regeneration. Dev Biol. 2026 Jul 08; 538:80-94. Chou-Freed C, Prinz CK, Margaryan A, Theriot JA, Wagner DE, Barber DL. PMID: 42419445.
      View in: PubMed   Mentions:    Fields:    
    2. Dynamic Reprogramming of PDGFRA-Expressing Stromal Cells Facilitates WNT-Driven Transformation by Promoting a Fetal-Like State in the Intestinal Epithelium. Cancer Res. 2026 Jun 01; 86(11):2606-2622. Pellon-Cardenas O, Rout P, Hassan S, Fokas E, Patel I, Patel J, Qiu X, He P, Nussbaum O, Wu A, Kumar R, Akther M, Logerfo A, Wu S, Wagner D, Boffelli D, Walton KD, Tong K, Iqbal J, Xiao R, Chen L, Spence JR, Bessman NJ, Manieri E, Shivdasani RA, Verzi MP. PMID: 41784677; PMCID: PMC13160386.
      View in: PubMed   Mentions:    Fields:    Translation:AnimalsCells
    3. Author Correction: In vitro characterization of the human segmentation clock. Nature. 2026 Jun; 654(8118):E13. 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: 42191906.
      View in: PubMed   Mentions:    Fields:    
    4. BMP signaling during gastrulation pre-patterns the dorsal spinal cord. bioRxiv. 2026 May 20. Greenfeld H, Wagner DE. PMID: 42239102; PMCID: PMC13228635.
      View in: PubMed   Mentions:
    5. Intracellular pH dynamics promotes zebrafish larval tail regeneration. bioRxiv. 2026 May 15. Chou-Freed C, Prinz CK, Margaryan A, Theriot JA, Wagner DE, Barber DL. PMID: 42182211; PMCID: PMC13193012.
      View in: PubMed   Mentions:
    6. ZMAP: A single-cell meta-atlas of zebrafish embryonic development reveals a consensus hierarchy of cell identities. bioRxiv. 2026 Mar 24. Aponte-Santiago NA, Su Y, Wagner DE. PMID: 41928926; PMCID: PMC13041850.
      View in: PubMed   Mentions:
    7. Mouse placentae generated by in vitro fertilization exhibit altered gene expression, activated hypoxia responses, and reduced fitness†. Biol Reprod. 2026 01 11; 114(1):70-83. Oqani RK, Maltepe E, Rinaudo P, Wagner DE. PMID: 40874534; PMCID: PMC12808545.
      View in: PubMed   Mentions: 1     Fields:    Translation:Animals
    8. Comprehensive profiling of migratory primordial germ cells reveals niche-specific differences in non-canonical Wnt and Nodal-Lefty signaling in anterior vs posterior migrants. Elife. 2025 Nov 19; 14. Jaszczak RG, Zussman JW, Wagner DE, Laird DJ. PMID: 41259237; PMCID: PMC12629596.
      View in: PubMed   Mentions: 2     Fields:    Translation:AnimalsCells
    9. Evaluating Selective Quality Control in Mammalian Oogenesis: Evidence and Opportunities. Annu Rev Genet. 2025 11; 59(1):237-270. Zussman JW, Skinner DJ, Wagner DE, Shvartsman SY, Laird DJ. PMID: 40780962; PMCID: PMC12510338.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansAnimalsCells
    10. Two parallel lineage-committed progenitors contribute to the developing brain. bioRxiv. 2025 Jul 05. Dundes CE, Jokhai RT, Ahsan H, Kang RS, Salomon-Shulman REA, Rajan A, Kim YS, Stanton LJ, Xu C, Do S, McDonald BD, López JMA, Urrutia HA, Greenfeld H, Wong A, Qu Y, Petkovic AS, Miao Y, Garcia KC, Monje M, Wagner DE, Bronner ME, Lowe CJ, Loh KM. PMID: 40631129; PMCID: PMC12236623.
      View in: PubMed   Mentions:
    11. Comprehensive profiling of migratory primordial germ cells reveals niche-specific differences in non-canonical Wnt and Nodal-Lefty signaling in anterior vs posterior migrants. bioRxiv. 2025 Jun 02. Jaszczak RG, Zussman JW, Wagner DE, Laird DJ. PMID: 39257761; PMCID: PMC11383659.
      View in: PubMed   Mentions:
    12. 1-866-QUIT-YES: How the Illinois Tobacco Quitline Reached Priority Audiences Through Mass Media. Tob Use Insights. 2025; 18:1179173X251335197. Jackson DD, Goldman T, Wagner DE, Redke E, DeVito G, Younker L. PMID: 40353047; PMCID: PMC12062607.
      View in: PubMed   Mentions:
    13. Generating Campaign Awareness With Digital Media: Exploring Factors Associated With Awareness of and Receptivity to FDA's Fresh Empire Tobacco Prevention Campaign. Nicotine Tob Res. 2025 Apr 22; 27(5):864-872. Henes A, Curry L, Farrelly M, Guillory J, Crichton A, Saunders M, MacMonegle A, Mekos D, Zhao X, Nonnemaker J, Guo M, Wagner DE. PMID: 39565279.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    14. Neural plate pre-patterning enables specification of intermediate neural progenitors in the spinal cord. bioRxiv. 2025 Jan 10. Nandagopal S, Cha A, Jia BZ, Liao H, Comenho C, Lahav G, Wagner DE, Tsai TY, Megason SG. PMID: 39829904; PMCID: PMC11741283.
      View in: PubMed   Mentions:
    15. Discrimination, identity connectedness and tobacco use in a sample of sexual and gender minority young adults. Tob Control. 2024 11 10; 33(e2):e143-e150. Budenz A, Gaber J, Crankshaw E, Malterud A, Peterson EB, Wagner DE, Sanders EC. PMID: 36601779.
      View in: PubMed   Mentions: 4     Fields:    Translation:Humans
    16. Pluripotency of a founding field: rebranding developmental biology. Development. 2024 02 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: 1     Fields:    
    17. Factors Associated with Use of Cigars, Little Cigars, Cigarillos, and Blunts among Hip Hop Youth in the United States. Am J Health Behav. 2023 Aug; 47(4):851-869. Curry LE, Guillory J, Henes A, Saunders M, MacMonegle A, Nonnemaker J, Mekos D, Vigorita MW, McDonald E, Wagner DE, Sanders EC. PMID: 42343894; PMCID: PMC13289666.
      View in: PubMed   Mentions:    Fields:    
    18. 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.
    19. Swap Up Your Meal: A Mass Media Nutrition Education Campaign for Oklahoma Teens. Int J Environ Res Public Health. 2022 08 16; 19(16). Wagner DE, Seneres G, Jones E, Brodersen KA, Whitsitt-Paulson S. PMID: 36011746; PMCID: PMC9408208.
      View in: PubMed   Mentions: 3     Fields:    Translation:Humans
    20. Unpacking Cigar Product Familiarity and Terminology among Black and Hispanic Youth: It's All about Blunts. Int J Environ Res Public Health. 2022 02 01; 19(3). Jackson DD, Sanders EC, Barry M, Wagner DE, Vigorita MW, Navarro MA. PMID: 35162711; PMCID: PMC8834713.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansAnimals
    21. 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
    22. 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: 320     Fields:    Translation:HumansAnimalsCells
    23. Who Uses Tobacco Products? Using Peer Crowd Segmentation to Identify Youth at Risk for Cigarettes, Cigar Products, Hookah, and E-Cigarettes. Subst Use Misuse. 2020; 55(7):1045-1053. Stalgaitis CA, Navarro MA, Wagner DE, Walker MW. PMID: 32024418.
      View in: PubMed   Mentions: 5     Fields:    Translation:Humans
    24. 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: 256     Fields:    Translation:AnimalsCells
    25. 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: 105     Fields:    Translation:HumansAnimalsCells
    26. 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: 24     Fields:    Translation:AnimalsCells
    27. Youth peer crowds and risk of cigarette use: The effects of dual peer crowd identification among hip hop youth. Addict Behav Rep. 2019 Dec; 10:100204. Navarro MA, Stalgaitis CA, Walker MW, Wagner DE. PMID: 31388555; PMCID: PMC6675938.
      View in: PubMed   Mentions: 3  
    28. Understanding Adversity and Peer Crowds to Prevent Youth Health Risks. Am J Health Behav. 2019 07 01; 43(4):767-780. Stalgaitis CA, Wagner DE, Djakaria M, Jordan JW. PMID: 31239019.
      View in: PubMed   Mentions: 4     Fields:    Translation:Humans
    29. 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: 416     Fields:    Translation:Animals
    30. 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: 283     Fields:    Translation:AnimalsCells
    31. 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: 328     Fields:    Translation:HumansAnimalsCells
    32. The Hip Hop peer crowd: An opportunity for intervention to reduce tobacco use among at-risk youth. Addict Behav. 2018 07; 82:28-34. Walker MW, Navarro MA, Hoffman L, Wagner DE, Stalgaitis CA, Jordan JW. PMID: 29477904; PMCID: PMC12990986.
      View in: PubMed   Mentions: 17     Fields:    Translation:Humans
    33. 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: 9     Fields:    Translation:AnimalsCells
    34. 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: 7     Fields:    
    35. Why Peer Crowds Matter: Incorporating Youth Subcultures and Values in Health Education Campaigns. Am J Public Health. 2017 Mar; 107(3):389-395. Moran MB, Walker MW, Alexander TN, Jordan JW, Wagner DE. PMID: 28103067; PMCID: PMC5296684.
      View in: PubMed   Mentions: 36     Fields:    Translation:Humans
    36. 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: 22     Fields:    Translation:AnimalsCells
    37. 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: 166     Fields:    Translation:AnimalsCells
    38. 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: 146     Fields:    Translation:AnimalsCells
    39. 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: 116     Fields:    Translation:AnimalsCells
    40. 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: 321     Fields:    Translation:AnimalsCells
    41. 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: 21     Fields:    Translation:Cells
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