Publications

Full list on Pubmed and Google Scholar

2026

Couturier H, Greenfeld H, Zussman JW, Wagner DE. Spatially restricted bmp16 in an extra-embryonic syncytium promotes dorsoventral patterning. bioRxiv 2026.10.05.756835; https://doi.org/10.64898/2026.10.05.756835

Aponte-Santiago NA, Suren N, Su Y, Halanych CN, Matubrew MN, Song E, Swinburne IA, Matus DQ, Wagner DE. Evaluation of eef1a1l1 expression stability and promoter-driven reporter activity during zebrafish development. MicroPubl Biol. 2026 Sep 14;2026:10.17912/micropub.biology.002410. doi: 10.17912/micropub.biology.002410. PMID: 42819765; PMCID: PMC13624862.

Jokhai RT, Dundes CE, Ahsan HS, Kang RS, Salomon-Shulman REA, Rajan A, Kim YS, Stanton LJ, Xu C, Do S, McDonald BD, Andrade López JM, Urrutia HA, Greenfeld H, Wong A, Qu Y, Petkovic AS, Miao Y, Garcia KC, Monje M, Wagner DE, Bronner ME, Lowe CJ, Loh KM. Two parallel neural ectoderm progenitors contribute to the developing brain. Nat Neurosci. 2026 Sep 18. doi: 10.1038/s41593-026-02433-7. Epub ahead of print. PMID: 42760324.

Chou-Freed C, Prinz CK, Margaryan A, Theriot JA, Wagner DE, Barber DL. Intracellular pH dynamics promotes zebrafish larval tail regeneration. Dev Biol. 2026 Oct;538:80-94. doi: 10.1016/j.ydbio.2026.07.004. Epub 2026 Jul 8. PMID: 42419445.

Aponte-Santiago NA, Su Y, Wagner DE. ZMAP: A single-cell meta-atlas of zebrafish embryonic development reveals a consensus hierarchy of cell identities. bioRxiv. 2026 Mar 24. PMID: 41928926. PMCID: PMC13041850

Greenfeld H, Wagner DE. BMP signaling during gastrulation pre-patterns the dorsal spinal cord. bioRxiv. 2026 May 18. https://doi.org/10.64898/2026.05.18.726076 PMID: 42239102. PMCID: PMC13228635.

Chen CP, Wagner DE. Dynamic polyadenylation safeguards developmental trajectories during paused embryogenesis. bioRxiv. 2026. https://doi.org/10.64898/2026.05.18.726068

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, K. D., Tong, K., Iqbal, J., Verzi, M. P. (2026). Dynamic reprogramming of PDGFRA-expressing stromal cells facilitates WNT-driven transformation by promoting a fetal-like state in the intestinal epithelium. Cancer Research. https://doi.org/10.1158/0008-5472.CAN-25-0101

Oqani RK, Maltepe E, Rinaudo P, Wagner DE. Mouse placentae generated by in vitro fertilization exhibit altered gene expression, activated hypoxia responses, and reduced fitness. Biol Reprod. 2026 Jan 11; 114(1):70-83. PMID: 40874534. PMCID: PMC12808545

2025

Zussman JW, Skinner DJ, Wagner DE, Shvartsman SY, Laird DJ. Evaluating Selective Quality Control in Mammalian Oogenesis: Evidence and Opportunities. Annu Rev Genet. 2025 11; 59(1):237-270. PMID: 40780962. PMCID: PMC12510338

Jaszczak RG, Zussman JW, Wagner DE, Laird DJ. 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. PMID: 41259237. PMCID: PMC12629596.

Nandagopal S, Cha A, Jia BZ, Liao H, Comenho C, Lahav G, Wagner DE, Tsai TY, Megason SG. Neural plate pre-patterning enables specification of intermediate neural progenitors in the spinal cord. bioRxiv. 2025 Jan 10. PMID: 39829904. PMCID: PMC11741283.

2024

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.  Pluripotency of a founding field: rebranding developmental biology. Development. 2024 Feb 01; 151(3).  PMID: 38345109; PMCID: PMC10986740.

2023

Kraiczy J, McCarthy N, Malagola E, Tie G, Madha S, Boffelli D, Wagner DE, Wang TC, Shivdasani RA. 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.

2020

In this review, we discuss the differences between a gene expression trajectory and a cell lineage, and modern experimental methods for integrating these two complimentary aspects of cellular history.

In this review, we discuss the differences between a gene expression trajectory and a cell lineage, and modern experimental methods for integrating these two complimentary aspects of cellular history.

Wagner DE* and Klein AM*. Lineage tracing meets single-cell omics: opportunities and challenges. Nature Reviews Genetics 2020; doi.org/10.1038/s41576-020-0223-2 [PUBMED] [PDF]

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. In vitro characterization of the human segmentation clock. Nature 2020. doi.org/10.1038/s41586-019-1885-9. [PUBMED] [Nature News & Views]

Single-cell transcriptomics-based classification of cells differentiated in vitro, using reference states from the E9.5 mouse embryo.

Single-cell transcriptomics-based classification of cells differentiated in vitro, using reference states from the E9.5 mouse embryo.

Sharma N, Flaherty K, Lezgiyeva K, Wagner DE, Klein A, Ginty DD. The emergence of transcriptional identity in somatosensory neurons. Nature 2020; Jan 577(7790): 392-398. doi: 10.1038/s41586-019-1900-1. [PUBMED]

Gene expression trajectories for somatosensory neurons, constructed using the STITCH algorithm.

Gene expression trajectories for somatosensory neurons, constructed using the STITCH algorithm.

2019

Tewari AG, Owen JH, Petersen CP, Wagner DE, Reddien PW. 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; 15(10):e1008401. [PUBMED]

2018

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 2018; 360(6392):981-987. [PUBMED] [PDF] [Science Preview] [Nature Highlight] [Science Perspective by Richard Harland] [2018 Science Breakthrough of the Year] [Science Video Walkthrough]

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 2018; 360(6392). [PUBMED] [PDF]

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; 36(5):442-450. [PUBMED]

2015

Genetic perturbations alter the positional identity of regenerating tissues (microfluidic transcriptional profiling + principal component analysis). D.Wagner, 2015.

Genetic perturbations alter the positional identity of regenerating tissues (microfluidic transcriptional profiling + principal component analysis). D.Wagner, 2015.

[* co-first authors] Owen JH*, Wagner DE*, Petersen CP, Reddien PW. teashirt is required for antero-posterior polarity regeneration in planarians. Development 2015; 146(6):1062-1072. [PUBMED] [PDF]

2014

[* co-first authors] van Wolfswinkel JC*, Wagner DE*, Reddien PW. Single-cell analysis reveals functionally distinct classes within the planarian stem cell compartment. Cell Stem Cell 2014; 15:326-339. [PUBMED] [PDF]

Recently born BrdU+ cells (magenta) in the planarian epidermis. D.Wagner, 2014.

Recently born BrdU+ cells (magenta) in the planarian epidermis. D.Wagner, 2014.

Two classes of mitotic stem cells (magenta & green) were identified in planarians using a first-generation single-cell transcriptomics method. D.Wagner, 2014.

Two classes of mitotic stem cells (magenta & green) were identified in planarians using a first-generation single-cell transcriptomics method. D.Wagner, 2014.

2013

Patterning genes that drive regeneration polarity decisions (magenta) are expressed predominantly in muscle cell bodies (green). D.Wagner, 2013.

Patterning genes that drive regeneration polarity decisions (magenta) are expressed predominantly in muscle cell bodies (green). D.Wagner, 2013.

Witchley JN, Mayer M, Wagner DE, Owen JH, Reddien PW. Muscle Cells Provide Instructions for Planarian Regeneration. Cell Reports 2013; 4:633–641. [PUBMED] [PDF]

2012

Wagner DE, Ho JJ, Reddien PW. Genetic Regulators of a Pluripotent Adult Stem Cell System in Planarians Identified by RNAi and Clonal Analysis. Cell Stem Cell 2012; 10:299-311. [PUBMED] [PDF] [Highlight in Nature Methods]

Sequential early markers (green > yellow > magenta) of the epidermal lineage in planarians. D.Wagner, 2012.

Sequential early markers (green > yellow > magenta) of the epidermal lineage in planarians. D.Wagner, 2012.

Clones of planarian stem cells (red) generate precise numbers of (blue) epidermal progenitors. D.Wagner, 2012.

Clones of planarian stem cells (red) generate precise numbers of (blue) epidermal progenitors. D.Wagner, 2012.

2011

[* co-first authors] Wagner DE*, Wang IE*, Reddien PW. Clonogenic neoblasts are pluripotent adult stem cells that underlie planarian regeneration. Science 2011; 332:811-6. [PUBMED] [PDF] [Science Perspective by Jonathan Slack] [Discover Magazine Blog] [Highlight in Nature Reviews Molecular Cell Biology]

2005

Wagner DE, Phillips CL, Ali WM, Nybakken GE, Crawford ED, Schwab AD, Smith WF, Fairman R. Towards the Development of Peptide Nanofilaments and Nanoropes as Smart Materials. PNAS 2005; 102:12656-61. [PUBMED]