ZFIN ID: ZDB-LAB-050428-1
James Chen Lab
PI/Director: Chen, James K.
Contact Person: Chen, James K.
Email: jameschen@stanford.edu
URL: http://chen.stanford.edu
Address: Department of Chemical and Systems Biology Stanford University School of Medicine 269 Campus Drive, CCSR Room 3155C Stanford, CA 94305-5174 USA
Country: United States
Phone: 650-725-3582
Fax: 650-723-2253
Line Designation: st

Show all 4 genomic features


Feng, Brian Post-Doc Hyman, Joel Post-Doc O’Casio, Cory Post-Doc
Pattanayak, Sankha Post-Doc Firestone, Ari Graduate Student Mich, John Graduate Student
Ouyang, Shawn Graduate Student Rack, Paul Graduate Student Shestopalov, Ilya Research Staff
Jeung, Stuart L. Administrative Staff

Pattanayak, S., Sarode, B.R., Deiters, A., Chen, J.K. (2022) Bicyclic Caged Morpholino Oligonucleotides for Optical Gene Silencing. Chembiochem : a European journal of chemical biology. 23(21):e202200374
Kundu, J., Ghosh, A., Ghosh, U., Das, A., Nagar, D., Pattanayak, S., Ghose, A., Sinha, S. (2022) Synthesis of Phosphorodiamidate Morpholino Oligonucleotides Using Trityl and Fmoc Chemistry in an Automated Oligo Synthesizer. The Journal of organic chemistry. 87(15):9466-9478
Darrah, K., Wesalo, J., Lukasak, B., Tsang, M., Chen, J.K., Deiters, A. (2021) Small Molecule Control of Morpholino Antisense Oligonucleotide Function through Staudinger Reduction. Journal of the American Chemical Society. 143(44):18665-18671
Mruk, K., Ciepla, P., Piza, P.A., Alnaqib, M.A., Chen, J.K. (2020) Targeted cell ablation in zebrafish using optogenetic transcriptional control. Development (Cambridge, England). 147(12):
Pattanayak, S., Vázquez-Maldonado, L.A., Deiters, A., Chen, J.K. (2019) Combinatorial control of gene function with wavelength-selective caged morpholinos. Methods in enzymology. 624:69-88
Rost, M.S., Shestopalov, I., Liu, Y., Vo, A.H., Richter, C.E., Emly, S.M., Barrett, F.G., Stachura, D.L., Holinstat, M., Zon, L.I., Shavit, J.A. (2018) Nfe2 is dispensable for early but required for adult thrombocyte formation and function in zebrafish. Blood advances. 2:3418-3427
Gutzman, J.H., Graeden, E., Brachmann, I., Yamazoe, S., Chen, J.K., Sive, H. (2018) Basal constriction during midbrain-hindbrain boundary morphogenesis is mediated by Wnt5b and focal adhesion kinase. Biology Open. 7(11):
Hwang, S., Mruk, K., Rahighi, S., Raub, A.G., Chen, C.H., Dorn, L.E., Horikoshi, N., Wakatsuki, S., Chen, J.K., Mochly-Rosen, D. (2018) Correcting glucose-6-phosphate dehydrogenase deficiency with a small-molecule activator. Nature communications. 9:4045
Mandelbaum, J., Shestopalov, I.A., Henderson, R.E., Chau, N.G., Knoechel, B., Wick, M.J., Zon, L.I. (2018) Zebrafish blastomere screen identifies retinoic acid suppression of MYB in adenoid cystic carcinoma.. The Journal of experimental medicine. 215(10):2673-2685
Sinha, S., Khatra, H., Khan, P.P., Pattanayak, S., Bhadra, J., Rather, B., Chakrabarti, S., Saha, T. (2018) Hedgehog antagonist pyrimidine-indole hybrid molecule inhibits ciliogenesis through microtubule destabilization. Chembiochem : a European journal of chemical biology. 19(7):723-735
Cho, U., Riordan, D.P., Ciepla, P., Kocherlakota, K.S., Chen, J.K., Harbury, P.B. (2017) Ultrasensitive optical imaging with lanthanide lumiphores. Nature Chemical Biology. 14(1):15-21
Wong, W.T., Matrone, G., Tian, X., Tomoiaga, S.A., Au, K.F., Meng, S., Yamazoe, S., Sieveking, D., Chen, K., Burns, D.M., Chen, J.K., Blau, H.M., Cooke, J.P. (2017) Discovery of novel determinants of endothelial lineage using chimeric heterokaryons. eLIFE. 6
Ouyang, X., Panetta, N.J., Talbott, M.D., Payumo, A.Y., Halluin, C., Longaker, M.T., Chen, J.K. (2017) Hyaluronic acid synthesis is required for zebrafish tail fin regeneration. PLoS One. 12:e0171898
Bhadra, J., Pattanayak, S., Khan, P.P., Kundu, J., Sinha, S. (2016) Internal Oligoguanidinium-based Cellular Transporter Enhances Antisense Efficacy of Morpholinos in in vitro and Zebrafish model. Bioconjugate Chemistry. 27(10):2254-2259
Payumo, A.Y., McQuade, L.E., Walker, W.J., Yamazoe, S., Chen, J.K. (2016) Tbx16 regulates hox gene activation in mesodermal progenitor cells. Nature Chemical Biology. 12(9):694-701
Yamazoe, S., McQuade, L.E., Chen, J.K. (2014) Nitroreductase-Activatable Morpholino Oligonucleotides for in Vivo Gene Silencing. ACS Chemical Biology. 9(9):1985-90
Yamazoe, S., Liu, Q., McQuade, L.E., Deiters, A., Chen, J.K. (2014) Sequential Gene Silencing Using Wavelength-Selective Caged Morpholino Oligonucleotides. Angewandte Chemie (International ed. in English). 53(38):10114-8
Rack, P.G., Ni, J., Payumo, A.Y., Nguyen, V., Crapster, J.A., Hovestadt, V., Kool, M., Jones, D.T., Mich, J.K., Firestone, A.J., Pfister, S.M., Cho, Y.J., Chen, J.K. (2014) Arhgap36-dependent activation of Gli transcription factors. Proceedings of the National Academy of Sciences of the United States of America. 111:11061-6
Mich, J.K., Payumo, A.Y., Rack, P.G., Chen, J.K. (2014) In vivo imaging of hedgehog pathway activation with a nuclear fluorescent reporter. PLoS One. 9:e103661
Bonger, K.M., Rakhit, R., Payumo, A.Y., Chen, J.K., and Wandless, T.J. (2014) General Method for Regulating Protein Stability with Light. ACS Chemical Biology. 9(1):111-5
Moore, J.C., Sheppard, S., Shestopalov, I.A., Chen, J.K., and Lawson, N. (2013) Post-transcriptional mechanisms contribute to Etv2 repression during vascular development. Developmental Biology. 384(1):128-40
Cho, Y.S., Jung, H.J., Seok, S.H., Payumo, A.Y., Chen, J.K., and Kwon, H.J. (2013) Functional inhibition of UQCRB suppresses angiogenesis in zebrafish. Biochemical and Biophysical Research Communications. 433(4):396-400
Yamazoe, S., Shestopalov, I.A., Provost, E., Leach, S.D., and Chen, J.K. (2012) Cyclic Caged Morpholinos: Conformationally Gated Probes of Embryonic Gene Function. Angewandte Chemie (International ed. in English). 51(28):6908-6911
Shestopalov, I.A., Pitt, C.L., and Chen, J.K. (2012) Spatiotemporal resolution of the Ntla transcriptome in axial mesoderm development. Nature Chemical Biology. 8(3):270-276
England, S., Batista, M.F., Mich, J.K., Chen, J.K., and Lewis, K.E. (2011) Roles of Hedgehog pathway components and retinoic acid signalling in specifying zebrafish ventral spinal cord neurons. Development (Cambridge, England). 138(23):5121-5134
Mich, J.K., and Chen, J.K. (2011) Hedgehog and retinoic acid signaling cooperate to promote motoneurogenesis in zebrafish. Development (Cambridge, England). 138(23):5113-5119
Hillman, R.T., Feng, B.Y., Ni, J., Woo, W.M., Milenkovic, L., Hayden Gephart, M.G., Teruel, M.N., Oro, A.E., Chen, J.K., and Scott, M.P. (2011) Neuropilins are positive regulators of Hedgehog signal transduction. Genes & Development. 25(22):2333-46
Clanton, J.A., Shestopalov, I., Chen, J., and Gamse, J.T. (2011) Lineage labeling of zebrafish cells with laser uncagable fluorescein dextran. Journal of visualized experiments : JoVE.
Shestopalov, I. (2011) Development and application of light-controlled gene silencing methods in zebrafish embryos. Ph.D. Thesis.
Shestopalov, I.A., and Chen, J.K. (2011) Spatiotemporal control of embryonic gene expression using caged morpholinos. Methods in cell biology. 104:151-172
Shestopalov, I.A., and Chen, J.K. (2010) Oligonucleotide-Based Tools for Studying Zebrafish Development. Zebrafish. 7(1):31-40
Mich, J.K. (2010) Roles for hedgehog signaling in zebrafish development. Ph.D. Thesis.
Ouyang, X., Shestopalov, I.A., Sinha, S., Zheng, G., Pitt, C.L., Li, W.H., Olson, A.J., and Chen, J.K. (2009) Versatile Synthesis and Rational Design of Caged Morpholinos. Journal of the American Chemical Society. 131(37):13255-13269
Yang, H., Xiang, J., Wang, N., Zhao, Y., Hyman, J., Jiang, J., Chen, J.K., Yang, Z., and Lin, S. (2009) Converse conformational control of smoothened activity by structurally related small molecules. The Journal of biological chemistry. 284(31):20876-20884
Mich, J.K., Blaser, H., Thomas, N.A., Firestone, A.J., Yelon, D., Raz, E., and Chen, J.K. (2009) Germ cell migration in zebrafish is cyclopamine-sensitive but Smoothened-independent. Developmental Biology. 328(2):342-354
Chen, J.K., and Hurlstone, A.F. (2008) Targeted and Conditional Gene Expression Workshop, 8th International Conference on Zebrafish Development and Genetics. Zebrafish. 5(3):193-195
Esengil, H., and Chen, J.K. (2008) Gene regulation technologies in zebrafish. Molecular Biosystems. 4(4):300-308
Shestopalov, I.A., Sinha, S., and Chen, J.K. (2007) Light-controlled gene silencing in zebrafish embryos. Nature Chemical Biology. 3(10):650-651
Esengil, H., Chang, V., Mich, J.K., and Chen, J.K. (2007) Small-molecule regulation of zebrafish gene expression. Nature Chemical Biology. 3(3):154-155