ZFIN ID: ZDB-PERS-960805-298
Kimelman, David
Email: kimelman@u.washington.edu
URL: http://depts.washington.edu/kimellab/
Affiliation: Kimelman Lab
Address: Department of Biochemistry University of Washington Box 357350 Seattle, WA 98195-7350 USA
Country: United States
Phone: (206) 543-5730
Fax: (206) 616-8676

We are interested in the intercellular signals and transcription factors that pattern the early vertebrate embryo. Working with fish and frogs, we are exploring the complex mechanisms that underlie early pattern formation. Using frogs we have identified several key proteins involved in pre-gastrula and gastrula-stage development, and are exploring how these proteins pattern the embryo. Working with Charles Kimmel and colleagues, we have identified the molecular basis of floating head and spadetail, and are working to determine how these genes regulate early development.

Saunders, L.M., Srivatsan, S.R., Duran, M., Dorrity, M.W., Ewing, B., Linbo, T.H., Shendure, J., Raible, D.W., Moens, C.B., Kimelman, D., Trapnell, C. (2023) Embryo-scale reverse genetics at single-cell resolution. Nature. 623(7988):782-791
Dorrity, M.W., Saunders, L.M., Duran, M., Srivatsan, S.R., Barkan, E., Jackson, D.L., Sattler, S.M., Ewing, B., Queitsch, C., Shendure, J., Raible, D.W., Kimelman, D., Trapnell, C. (2023) Proteostasis governs differential temperature sensitivity across embryonic cell types. Cell. 186:50155027.e125015-5027.e12
Ye, Z., Braden, C.R., Wills, A., Kimelman, D. (2021) Identification of in vivo Hox13-binding sites reveals an essential locus controlling zebrafish brachyury expression. Development (Cambridge, England). 148(11):
Kimelman, D. (2020) The people behind the papers - Zhi Ye and David Kimelman. Development (Cambridge, England). 147(22)
Ye, Z., Kimelman, D. (2020) hox13 genes are required for mesoderm formation and axis elongation during early zebrafish development. Development (Cambridge, England). 147(22):
Kimelman, D. (2018) Ground, Path, and Fruition: Teaching Zebrafish Development to Tibetan Buddhist Monks in India. Zebrafish. 15(6):648-651
Kimelman, D., Smith, N.L., Lai, J.K.H., Stainier, D.Y. (2017) Regulation of posterior body and epidermal morphogenesis in Zebrafish by localized Yap1 and Wwtr1. eLIFE. 6
Kimelman, D. (2016) A novel cold-sensitive mutant of ntla reveals temporal roles of Brachyury in zebrafish. Developmental Dynamics : an official publication of the American Association of Anatomists. 245(8):874-80
Yoshimatsu, T., D'Orazi, F.D., Gamlin, C.R., Suzuki, S.C., Suli, A., Kimelman, D., Raible, D.W., Wong, R.O. (2016) Presynaptic partner selection during retinal circuit reassembly varies with timing of neuronal regeneration in vivo. Nature communications. 7:10590
Manning, A.J., Kimelman, D. (2015) Tbx16 and Msgn1 are required to establish directional cell migration of zebrafish mesodermal progenitors. Developmental Biology. 406(2):172-85
Bouldin, C.M., Manning, A.J., Peng, Y.H., Farr, G.H., Hung, K.L., Dong, A., Kimelman, D. (2015) Wnt signaling and tbx16 form a bistable switch to commit bipotential progenitors to mesoderm. Development (Cambridge, England). 142:2499-507
Bouldin, C.M., Kimelman, D. (2014) Dual fucci: a new transgenic line for studying the cell cycle from embryos to adults. Zebrafish. 11:182-3
Suli, A., Guler, A.D., Raible, D.W., Kimelman, D. (2014) A targeted gene expression system using the tryptophan repressor in zebrafish shows no silencing in subsequent generations.. Development (Cambridge, England). 141(5):1167-74
Bouldin, C.M., Snelson, C.D., Farr, G.H. 3rd, and Kimelman, D. (2014) Restricted expression of cdc25a in the tailbud is essential for formation of the zebrafish posterior body. Genes & Development. 28(4):384-95
So, J., Martin, B.L., Kimelman, D., and Shin, D. (2013) Wnt/beta-catenin signaling cell-autonomously converts non-hepatic endodermal cells to a liver fate. Biology Open. 2(1):30-36
Veldman, M.B., Zhao, C., Gomez, G.A., Lindgren, A.G., Huang, H., Yang, H., Yao, S., Martin, B.L., Kimelman, D., and Lin, S. (2013) Transdifferentiation of fast skeletal muscle into functional endothelium in vivo by transcription factor etv2. PLoS Biology. 11(6):e1001590
McCarroll, M.N., Lewis, Z.R., Culbertson, M.D., Martin, B.L., Kimelman, D., and Nechiporuk, A.V. (2012) Graded levels of Pax2a and Pax8 regulate cell differentiation during sensory placode formation. Development (Cambridge, England). 139(15):2740-2750
Martin, B.L., and Kimelman, D. (2012) Canonical Wnt Signaling Dynamically Controls Multiple Stem Cell Fate Decisions during Vertebrate Body Formation. Developmental Cell. 22(1):223-232
Weiser, D.C., and Kimelman, D. (2012) Analysis of cell shape and polarity during zebrafish gastrulation. Methods in molecular biology (Clifton, N.J.). 839:53-68
Row, R.H., Maître, J.L., Martin, B.L., Stockinger, P., Heisenberg, C.P., and Kimelman, D. (2011) Completion of the epithelial to mesenchymal transition in zebrafish mesoderm requires Spadetail. Developmental Biology. 354(1):102-110
Martin, B.L., and Kimelman, D. (2010) Brachyury establishes the embryonic mesodermal progenitor niche. Genes & Development. 24(24):2778-2783
Landsverk, M.L., Weiser, D.C., Hannibal, M.C., and Kimelman, D. (2010) Alternative splicing of sept9a and sept9b in zebrafish produces multiple mRNA transcripts expressed throughout development. PLoS One. 5(5):e10712
Chung, W.S., Andersson, O., Row, R., Kimelman, D., and Stainier, D.Y. (2010) Suppression of Alk8-mediated Bmp signaling cell-autonomously induces pancreatic β-cells in zebrafish. Proceedings of the National Academy of Sciences of the United States of America. 107(3):1142-1147
Weiser, D.C., Row, R.H., and Kimelman, D. (2009) Rho-regulated Myosin phosphatase establishes the level of protrusive activity required for cell movements during zebrafish gastrulation. Development (Cambridge, England). 136(14):2375-2384
Wilkinson, R.N., Pouget, C., Gering, M., Russell, A.J., Davies, S.G., Kimelman, D., and Patient, R. (2009) Hedgehog and Bmp polarize hematopoietic stem cell emergence in the zebrafish dorsal aorta. Developmental Cell. 16(6):909-916
Row, R., and Kimelman, D. (2009) Bmp inhibition is necessary for post-gastrulation patterning and morphogenesis of the zebrafish tailbud. Developmental Biology. 329(1):55-63
Weiser, D.C., Julien, K.R., Lang, J.S., and Kimelman, D. (2008) Cell shape regulation by Gravin requires N-terminal membrane effector domains. Biochemical and Biophysical Research Communications. 375(4):512-516
Huang, H., Ruan, H., Aw, M.Y., Hussain, A., Guo, L., Gao, C., Qian, F., Leung, T., Song, H., Kimelman, D., Wen, Z., and Peng, J. (2008) Mypt1-mediated spatial positioning of Bmp2-producing cells is essential for liver organogenesis. Development (Cambridge, England). 135(19):3209-3218
Martin, B.L., and Kimelman, D. (2008) Regulation of canonical Wnt signaling by Brachyury is essential for posterior mesoderm formation. Developmental Cell. 15(1):121-133
Webb, A.E., Driever, W., and Kimelman, D. (2008) psoriasis regulates epidermal development in zebrafish. Developmental Dynamics : an official publication of the American Association of Anatomists. 237(4):1153-1164
Martin, B.L., and Kimelman, D. (2007) Developmental Biology: Micro(RNA)-Managing Nodal. Current biology : CB. 17(22):R975--R977
Webb, A.E., Sanderford, J., Frank, D., Talbot, W.S., Driever, W., and Kimelman, D. (2007) Laminin alpha5 is essential for the formation of the zebrafish fins. Developmental Biology. 311(2):369-382
Weiser, D.C., Pyati, U.J., and Kimelman, D. (2007) Gravin regulates mesodermal cell behavior changes required for axis elongation during zebrafish gastrulation. Genes & Development. 21(12):1559-1571
Szeto, D.P., and Kimelman, D. (2006) The regulation of mesodermal progenitor cell commitment to somitogenesis subdivides the zebrafish body musculature into distinct domains. Genes & Development. 20(14):1923-1932
Pyati, U.J., Cooper, M.S., Davidson, A.J., Nechiporuk, A., and Kimelman, D. (2006) Sustained Bmp signaling is essential for cloaca development in zebrafish. Development (Cambridge, England). 133(11):2275-2284
Kimelman, D. (2006) Mesoderm induction: from caps to chips. Nature reviews. Genetics. 7(5):360-372
Hogan, B.M., Layton, J.E., Pyati, U.J., Nutt, S.L., Hayman, J.W., Varma, S., Heath, J.K., Kimelman, D., and Lieschke, G.J. (2006) Specification of the Primitive Myeloid Precursor Pool Requires Signaling through Alk8 in Zebrafish. Current biology : CB. 16(5):506-511
Kimelman, D. (2006) Squinting at the zebrafish axis. Developmental Cell. 10(1):6-7
Bjornson, C.R., Griffin, K.J., Farr, G.H. 3rd, Terashima, A., Himeda, C., Kikuchi, Y., and Kimelman, D. (2005) Eomesodermin is a localized maternal determinant required for endoderm induction in zebrafish. Developmental Cell. 9(4):523-533
Clements, W.K., and Kimelman, D. (2005) LZIC regulates neuronal survival during zebrafish development. Developmental Biology. 283(2):322-334
Pyati, U.J., Webb, A.E., and Kimelman, D. (2005) Transgenic zebrafish reveal stage-specific roles for Bmp signaling in ventral and posterior mesoderm development. Development (Cambridge, England). 132(10):2333-2343
Cooper, M.S., Szeto, D.P., Sommers-Herivel, G., Topczewski, J., Solnica-Krezel, L., Kang, H.C., Johnson, I., and Kimelman, D. (2005) Visualizing morphogenesis in transgenic zebrafish embryos using BODIPY TR methyl ester dye as a vital counterstain for GFP. Developmental Dynamics : an official publication of the American Association of Anatomists. 232(2):359-368
Webb, A.E., and Kimelman, D. (2005) Analysis of early epidermal development in zebrafish. Methods in molecular biology (Clifton, N.J.). 289:137-146
Szeto, D.P., and Kimelman, D. (2004) Combinatorial gene regulation by Bmp and Wnt in zebrafish posterior mesoderm formation. Development (Cambridge, England). 131(15):3751-3760
Mathieu, J., Griffin, K., Herbomel, P., Dickmeis, T., Strähle, U., Kimelman, D., Rosa, F.M., and Peyriéras, N. (2004) Nodal and Fgf pathways interact through a positive regulatory loop and synergize to maintain mesodermal cell populations. Development (Cambridge, England). 131(3):629-641
Griffin, K.J. and Kimelman, D. (2003) Interplay between FGF, one-eyed pinhead, and T-box transcription factors during zebrafish posterior development. Developmental Biology. 264(2):456-466
Chen, S., and Kimelman, D. (2003) Submission and Curation of Gene Expression Data. ZFIN Direct Data Submission.
Concha, M.L., Russell, C., Regan, J.C., Tawk, M., Sidi, S., Gilmour, D.T., Kapsimali, M., Sumoy, L., Goldstone, K., Amaya, E., Kimelman, D., Nicolson, T., Gründer, S., Gomperts, M., Clarke, J.D.W., and Wilson, S.W. (2003) Local tissue interactions across the dorsal midline of the forebrain establish CNS laterality. Neuron. 39(3):423-438
Szeto, D.P., Griffin, K.J.P., and Kimelman, D. (2002) hrT is required for cardiovascular development in zebrafish. Development (Cambridge, England). 129(21):5903-5101
Griffin, K.J.P. and Kimelman, D. (2002) One-Eyed Pinhead and Spadetail are essential for heart and somite formation. Nature cell biology. 4(10):821-825
Lee, H. and Kimelman, D. (2002) A dominant-negative form of p63 is required for epidermal proliferation in zebrafish. Developmental Cell. 2(5):607-616
Kimelman, D. and Schier, A.F. (2002) Mesoderm induction and patterning. Results and problems in cell differentiation. 40:15-27
Imai, Y., Gates, M.A., Melby, A.E., Kimelman, D., Schier, A.F., and Talbot, W.S (2001) The homeobox genes vox and vent are redundant repressors of dorsal fates in zebrafish. Development (Cambridge, England). 128(12):2407-2420
Faucourt, M., Houliston, E., Besnardeau, L., Kimelman, D., and Lepage, T. (2001) The pitx2 homeobox protein is required early for endoderm formation and nodal signaling. Developmental Biology. 229(2):287-306
Mione, M., Shanmugalingam, S., Kimelman, D., and Griffin, K. (2001) Overlapping expression of zebrafish T-brain-1 and eomesodermin during forebrain development. Mechanisms of Development. 100(1):93-97
Chen, S.R. and Kimelman, D. (2000) The role of the yolk syncytial layer in germ layer patterning in zebrafish. Development (Cambridge, England). 127(21):4681-4689
Melby, A.E., Beach, C., Mullins, M., and Kimelman, D. (2000) Patterning the early zebrafish by the opposing actions of bozozok and vox/vent. Developmental Biology. 224(2):275-285
Griffin, K.J., Stoller, J., Gibson, M., Chen, S., Yelon, D., Stainier, D.Y., and Kimelman, D. (2000) A conserved role for H15-related T-Box transcription factors in zebrafish and Drosophila heart formation. Developmental Biology. 218(2):235-247
Sumoy, L., Kiefer, J., and Kimelman, D. (1999) Conservation of intracellular Wnt signaling components in dorsal-ventral axis formation in zebrafish. Development genes and evolution. 209:48-58
Griffin, K.J.P., Amacher, S.L., Kimmel, C.B., and Kimelman, D. (1998) Molecular identification of spadetail: regulation of zebrafish trunk and tail mesoderm formation by T-box genes. Development (Cambridge, England). 125:3379-3388
Melby, A.E., Kimelman, D., and Kimmel, C.B. (1997) Spatial regulation of floating head expression in the developing notochord. Developmental Dynamics : an official publication of the American Association of Anatomists. 209(2):156-165
Sumoy, L., Keasey, J.B., Dittman, T.D., and Kimelman, D. (1997) A role for notochord in axial vascular development revealed by analysis of phenotype and the expression of VEGR-2 in zebrafish flh and ntl mutant embryos. Mechanisms of Development. 63(1):15-27
Talbot, W.S., Trevarrow, B., Halpern, M.E., Melby, A.E., Farr, G., Postlethwait, J.H., Jowett, T., Kimmel, C.B., and Kimelman, D. (1995) A homeobox gene essential for zebrafish notochord development. Nature. 378:150-157