Chen Lab



  • Chen, J.K. (2023) Chemical developmental biology. In “Advanced Chemical Biology” (H. C. Hang, M. R. Pratt, and J. A. Prescher, Eds.) Wiley-VCH, Weinheim, Germany, pp. 647-668. [Wiley]
  • Darrah, K., Albright, S., Kumbhare, R., Tsang, M., Chen, J. K., and Deiters, A. (2023) Antisense oligonucleotide activation via enzymatic antibiotic resistance mechanism. ACS Chem. Biol., online ahead of print. [PubMed]


  • Feng, Z., Hom, M. E., Bearrood, T. E., Rosenthal, Z. C., Fernández, D., Ondrus, A. E., Gu, Y., McCormick, A. K., Tomaske, M. G., Marshall, C. R., Kline, T., Chen, C.-H., Mochly-Rosen, D., Kuo, C. J., and Chen, J. K. (2022) Targeting colorectal cancer with small-molecule inhibitors of ALDH1B1. Nat. Chem. Biol. 18: 1065-1075. [PubMed]
  • Pattanayak S., Sarode, B. R., Deiters, A., and Chen, J. K. (2022) Bicyclic caged morpholino oligonucleotides for optical gene silencing. ChemBioChem 23: e202200374. [PubMed]


  • Xu, J., Zheng, X., Feng, Z., Lu, Z., Zhang, Z., Huang W., Li, Y., Vuckovic, D, Li, Y., Dai, S., Chen, G., Wang, K., WAng, H., Chen, J.K., Mitch, W., and Cui, Y. (2021) Organic wastewater treatment by single-atom catalysis and electrolytically produced H2O2. Nat. Sustain. 4: 233-241.
  • Nano, P. R., Johnson, T. K., Kudo, T., Mooney, N. A., Ni, J., Demeter, J., Jackson, P. K., and Chen, J.K. (2021) Structure-activity mapping of ARHGAP36 reveals regulatory roles for its GAP homology and C-terminal domains. PLoS One 16:e0251684. [PubMed]
  • Darrah, K., Wesalo, J., Lukasak, B., Tsang, M., Chen, J. K., and Deiters, A. (2021) Small-molecule control of morpholino antisense oligonucleotide function through a Staudinger reduction. J. Am. Chem. Soc. 143:18665-18671. [PubMed]


  • Crapster, J. A.*, Rack, P. G., Hellmann, Z. J., Le, Austen D., Elias, J. E., Perrino, J. J., Behr, B., Li, Y., Lin, J., Zeng, H., and Chen, J. K.* (2020) HIPK4 is essential for murine spermiogenesis. eLife 9: e50209. [PubMed]
  • Hom, M. E., Ondrus, A. E., Sakata-Kato, T., Rack. P. G., and Chen, J. K. (2020) Bicyclic imidazolium inhibitors of Gli transcription factor activity. ChemMedChem 15: 1044-1049. [PubMed]
  • Mruk, K.*, Ciepla, P., Piza, P. A., Alnaqib, M. A., and Chen, J. K.* (2020) Targeted cell ablation in zebrafish using optogenetic transcriptional control. Development 147: dev183640. [PubMed]
  • Ciepla, P., Cho, U., and Chen, J. K. (2020) trLRET microscopy: ultrasensitive imaging of lanthanide luminophores. Methods Enzymol. 640: 225-248. [PubMed]
  • Cho, U.* and Chen, J.K.* (2020) Lanthanide-based optical probes of biological systems. Cell Chem. Biol. 27: 921-936. [PubMed]


  • Pattanayak, S., Vázquez-Maldonado, L. A., Deiters, A.*, and Chen, J. K.* (2019) Combinatorial control of gene function with wavelength-selective caged morpholinos. Methods Enzymol. 624:69-88. [PubMed]


  • Cho, U., Riordan, D. P., Ciepla, P., Kocherlakota, K. S., Chen, J. K.*, and Harbury, P. B.* (2018) Ultrasensitive optical imaging with lanthanide lumiphores. Nat. Chem. Biol. 14: 15-21. [PubMed]
  • Breslow, D. K.*, Hoogendoorn, S., Kopp, A. R., Morgens, D. W., Vu, B. K., Han, K., Li, A., Hess, G. T., Bassik, M. C., Chen, J. K.*, and Nachury, M. V.* (2018) A CRISPR-based screen for Hedgehog signaling provides insights into ciliary function and ciliopathies. Nat. Genet. 50: 460-471. [PubMed]
  • Hwang, S., Mruk, K., Rahighi, S., Raub, A. G., Chen, C.-H., Dorn, L. E., Horikoshi, N., Wataksuki, S., Chen, J. K., and Mochly-Rosen, D. (2018) Correcting glucose-6-phosphate dehydrogenase (G6PD) deficiency with a small molecule activator. Nat. Commun. 9: 4045. [PubMed]
  • Gutzman, J. H., Graeden, E., Brachmann, I., Yamazoe, S., Chen, J. K., and Sive, H. (2018) Basal constriction during midbrain-hindbrain boundary morphogenesis is mediated by Wnt5b and focal adhesion kinase. Biol. Open 7:bio034520. [PubMed]


  • Ouyang, X., Panetta, N. J., Talbott, M. D., Payumo, A. Y., Halluin, C., Longaker M. T., and Chen, J. K. (2017) Hyaluronic acid synthesis is required for zebrafish tail fin regeneration. PLoS ONE 12: 16:e01718998. [PubMed]
  • Wong, W. T., Tian, X., Matrone, G., Tomoiaga, S. A., Au, K. F., Meng, S., Yamazoe, S., Chen, K., Burns, D. M., Chen, J. K., Blau, H. M., and Cooke, J. P. (2017) Discovery of novel determinants of endothelial lineage using chimeric heterokaryons. eLife 6:e23588. [PubMed]
  • Kowalik, L. and Chen, J. K. (2017) Illuminating developmental biology through photochemistry. Nat. Chem. Biol. 13: 587-598. [PubMed]
  • Steinman, J. B., Santarossa, C. C., Miller, R. M., Yu, L. S., Serpinskaya, A. S., Furukawa, H., Morimoto S., Tanaka, Y., Nishitani, M., Asano, M., Zalyte, R., Ondrus, A. E., Johnson, A. G., Fan Y., Nachury M. V., Fukase, Y., Aso, K., Foley, M. A., Gelfand, V. I., Chen, J. K., Carter, A. P. and Kapoor, T. M. (2017) Chemical structure-guided design of dynapyrazoles, cell-permeable dynein inhibitors with a unique mode of action. eLife 6: e25174. [PubMed]
  • Crapster. J. A., Hudgins, L., Chen, J. K., and Gomez-Ospina, N. (2017) A novel missense variant in the GLI3 zinc finger domain in a family with digital anomalies. Am. J. Med. Genet. A. 173: 3221-3225. [PubMed]


  • Lee, J., Rothenberg, M., Seeley, E. S., Zimdahl, B., Kawano, S., Lu, W. J., Shin, K., Sakata-Kato, T., Chen, J. K., Diehn, M., Clarke, M., and Beachy, P. A. (2016) Control of inflammation by stromal Hedgehog pathway activation restrains colitis. Proc. Natl. Acad. Sci. U. S. A. 113: E7545-E7553. [PubMed]
  • Schmitt, A. M., Garcia, J. T., Hung, T., Flynn, R. A., Shen, Y., Qu, K., Payumo, A. Y., Peres-da-Silva, A., Kenzelmann Broz, D., Baum, R., Guo, S., Chen, J. K., Attardi, L. D., and Chang, H. Y. (2016) An inducible long noncoding RNA amplifies DNA damage signaling. Nat. Genet. 48: 1370-1376. [PubMed]
  • Payumo, A. Y. , McQuade, L. E., Walker, W. J., Yamazoe, S., and Chen, J. K. (2016) Tbx16 regulates hox gene expression in mesodermal progenitor cells. Nat. Chem. Biol. 12: 694-701. [PubMed]
  • Chen, J.K. (2016) I ony have eye for ewe: the discovery of cyclopamine and development of Hedgehog pathway-targeting drugs. Nat. Prod. Rep. 33: 595-601. [PubMed]
  • See, S. K., Hoogendoorn, S., Chung, A. H., Ye, F., Steinman, J. B., Sakata-Kato, T., Miller, R. M., Cupido, T., Zalyte, R., Carter, A. P., Nachury, M. V., Kapoor, T. M., and Chen, J. K. (2016) Cytoplasmic dynein antagonists with improved potency and isoform selectivity. ACS Chem. Biol. 11: 53-60. [PubMed]


  • Payumo, A. Y., Walker, W. J., McQuade, L. E., Yamazoe, S., and Chen, J. K. (2015) Optochemical dissection of T-box gene-dependent medial floor plate development. ACS Chem. Biol. 10: 1466-1475. [PubMed]
  • Mruk K. and Chen, J. K. (2015) Thinking big with small molecules. J. Cell Biol. 209: 7-9. [PubMed]


  • Yamazoe, S., McQuade, L. E., and Chen, J. K. (2014) Nitroreductase-activated caged morpholino oligonucleotides for in vivo gene silencing. ACS Chem. Biol. 9: 1985-1990. [PubMed]
  • Yamazoe, S., Liu, Q., McQuade, L. E., Deiters, A.*, and Chen, J. K.* (2014) Sequential gene silencing using wavelength-selective caged morpholinos. Angew. Chem. Int. Ed. 53: 10114-10118. [PubMed]
  • Rack, P. G., Ni, J., Payumo, A. Y., Nguyen, V., Crapster, J. A., Novestadt, V., Kool, M., Jones, D. T. W., Mich, J. K., Firestone, A. J., Pfister S. M., Cho, Y.-J., and Chen, J. K. (2014) Arhgap36-dependent activation of Gli transcription factors. Proc. Natl. Acad. Sci. U. S. A. 111: 11061-11066. [PubMed]
  • Lee, J. J., Perera, R. M., Wang, H., Wu, D.-C., Liu, X. S., Han, S., Fitamant, J., Jones, P. D., Ghanta, K. S., Kawano, S., Nagle, J. M., Deshpande, V., Boucher, Y., Kato, T., Chen, J. K., Willmann, J. K., Bardeesy, N., and Beachy, P. A. (2014) Stromal response to Hedgehog signaling restrains pancreatic cancer progression. Proc. Natl. Acad. Sci. U. S. A. 111: E3091-E3100. [PubMed]
  • Mich, J. K., Payumo, A. Y., Rack, P. G., and Chen, J. K. (2014) In vivo imaging of Hedgehog pathway activation with a nuclear fluorescent reporter. PLoS ONE 9:e103661. [PubMed]
  • Sikirzhytski, V., Magidson, V., Steinman, J, He, J., LeBerre, M., Tikhonenko, I., Ault, J. G., McEwen, B. F., Chen, J. K., Sui, H., Piel, M., Kapoor, T. M., and Khodjakov, A. (2014) Direct kinetochore-spindle pole connections are not required for chromosome segregation. J. Cell Biol. 206: 231-243. [PubMed]
  • Bonger, K. M., Rakhit, R., Payumo, A. Y., Chen, J. K., and Wandless, T. J. (2014) A general method for regulating protein stability with light. ACS Chem. Biol. 9: 111-115. [PubMed]


  • Moore, J. C., Sheppard, S., Shestopalov, I. A., Yamazoe, S., Chen, J. K., and Lawson, N. (2013) Post-translational mechanisms contribute to Etv2 repression during vascular development. Dev. Biol. 384: 128-140. [PubMed]
  • Yi, J., Wu, X., Chung, A. H., Chen, J. K., Kapoor, T. M., and Hammer, J. A. (2013) Centrosome repositioning in T cells is biphasic and driven by microtubule end-on capture-shrinkage. J. Cell. Biol. 202: 779-792. [PubMed]
  • Liu, X., Kapoor, T. M., Chen, J. K., Huse, M. (2013) Diacylglycerol promotes centrosome polarization in T cells via reciprocal localization of dynein and myosin II. Proc. Natl. Acad. Sci. U. S. A. 110: 11976-11981. [PubMed]
  • Cho, Y. S., Jung, H. J., Soek S. H., Payumo, A. Y., Chen, J. K., and Kwon, H. J. (2013) Functional inhibition of UQCRB suppresses angiogenesis in zebrafish. Biochem. Biophys. Res. Comm. 433: 396-400. [PubMed]


  • 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. Angew. Chem. Int. Ed. 51: 6908-6911. [PubMed]
  • Firestone, A. J., Weinger, J. S., Maldonado, M., Barlan, K., Langston, L. D., O’Donnell, M. D., Gelfand, V. I., Kapoor, T. M.*, and Chen, J. K.* (2012) Small-molecule inhibitors of the AAA+ ATPase motor cytoplasmic dynein. Nature 484: 125-129. [PubMed]
  • Kuo, A. J., Song, J., Cheung, P., Ishibe-Murakami, S., Yamazoe, S., Chen, J. K., Patel, D. J., and Gozani, O. (2012) ORC1 BAH domain links H4K20me2 to DNA replication licensing and Meier-Gorlin syndrome. Nature 484: 115-119. [PubMed]
  • Shestopalov, I. A., Pitt, C. L. W., and Chen, J. K. (2012) Spatiotemporal resolution of the Ntla transcriptome in axial mesoderm development. Nat. Chem. Biol. 8: 270-276. [PubMed]


  • 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 138: 5121-5134. [PubMed]
  • Mich, J.K.* and Chen, J.K.* (2011) Hedgehog and retinoic acid signalling cooperate to promote motoneurogenesis in zebrafish. Development 138: 5113-5119. [PubMed]
  • 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 Dev. 25: 2333-2346. [PubMed]
  • Heine, V. M., Griveau, A., Chapin, C., Ballard, P. L., Chen, J. K., and Rowitch, D. H. (2011) Small-molecule Smoothened agonist prevents glucocorticoid-induced neonatal cerebellar injury. Science Transl. Med. 3: 105ra104. [PubMed]
  • Park, K.-S., Martelotto, L. G., Peifer, M., Sos, M. L., Karnezis, A. N., Mahjoub, M. R., Bernard, K., Conklin, J., Szczepny, A., Yuan, J., Guo, R., Opsina, B., Falzon, J., Bennett, S., Brown, T. J., Markovic, A., Devereux, W. L., Ocasio, C. A., Chen, J. K., Stearns, T., Thomas, R. K., Dorsch, M., Buonamici, S., Watkins, D. N., Peacock, C. D., and Sage, J. (2011) A crucial requirement for Hedgehog signalling in small cell lung cancer. Nature Med. 17: 1504-1508. [PubMed]
  • Sakata, T. and Chen, J. K. (2011) Chemical ‘Jekyll and Hyde’s: Small-molecule inhibitors of developmental signaling pathways. Chem. Soc. Rev. 40: 4318-4331. [PubMed]
  • Clanton, J.A., Shestopalov, I., Chen, J. K., and Gamse, J. T. (2011) Lineage labeling of zebrafish cells with laser uncageable fluorescein dextran. J. Vis. Exp. doi: 10.3791/2672. [PubMed]
  • Firestone A. J., and. Chen J. K.. (2021) Small-molecular inhibitors of the Hedgehog pathway. In “Hedgehog signaling activation in human cancer and its clinical implications” (J. Xie, Ed.) Springer, New York, NY, pp. 163-186. [Springer]


  • Shestopalov, I. A. and Chen, J. K. (2010) Oligonucleotide-based tools for studying zebrafish development. Zebrafish 7:31-40. [PubMed]
  • Firestone, A. J. and Chen, J. K. (2010) Controlling destiny through chemistry: Small-molecule regulators of cell fate. ACS Chem. Biol. 15: 15-34. [PubMed]
  • Ouyang, X. and Chen, J. K. (2010) Synthetic strategies for studying embryonic development. Chem. Biol. 17: 590-606. [PubMed]


  • Ouyang, X., Shestopalov, I. A., Sinha, S., Zheng, G., Pitt, C. L. W., Li, W.-H., Olson, A. J., and Chen, J. K. (2009) Versatile synthesis and rational design of caged morpholinos. J. Am. Chem. Soc. 131: 13255-13269. [PubMed]
  • Hyman, J. M., Firestone, A. J., Heine, V. M., Zhao, Y., Ocasio, C. A., Han, K., Sun, M., Rack, P. G., Sinha, S., Wu, J. J., Solow-Cordero, D. E., Jiang, J., Rowitch, D. H., and Chen, J. K. (2009) Small-molecule inhibitors reveal multiple strategies for Hedgehog pathway blockade. Proc. Natl. Acad. Sci. U. S. A. 106:14132-14137. [PubMed]
  • 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. J. Biol. Chem. 284: 20876-20884. [PubMed]
  • 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. Dev. Biol. 328: 342-354. [PubMed]
  • Cupido, T., Rack, P. G., Firestone, A. J., Hyman, J. M., Han, K., Sinha, S., Ocasio, C. A, and Chen, J. K. (2009) The imidazopyridine derivative JK184 reveals dual roles for microtubules in Hedgehog signaling. Angew. Chemie Intl. Ed. Engl. 48: 2321-2324. [PubMed]
  • Stanton, B. Z., Peng, L. F., Maloof, N., Nakai, K., Wang, X., Herlihy, K. M., Duffner, J. L., Taveras, K. M., Hyman, J. M., Lee, S. W., Koehler, A. N., Chen, J. K., Fox, J. L., Mandinova, A., and Schreiber, S. L. (2009) A small molecule that binds Hedgehog and blocks its signaling in human cells. Nat. Chem. Biol. 5: 154-156. [PubMed]


  • Low, W.-C., Wang, C., Pan, Y., Huang, X.-Y., Chen, J. K., and Wang, B. (2008) The decoupling of Smoothened from G-alpha-i proteins has little effect on Gli3 protein processing and Hedgehog-regulated chick neural tube patterning. Dev. Biol. 321: 188-196. [PubMed]
  • Shestopalov, I. A. and Chen, J. K. (2008) Chemical technologies for probing embryonic development. Chem. Soc. Rev. 37: 1294-1307. [PubMed]
  • Esengil, H. and Chen, J. K. (2008) Gene regulation technologies for zebrafish. Mol. BioSystems 4: 300-308. [PubMed]


  • Shestopalov, I., Sinha, S., and Chen, J. K. (2007) Light-controlled gene silencing in zebrafish embryos. 
Nat. Chem. Biol. 3: 650-651. [PubMed]
  • Esengil, H., Chang, V., Mich, J. K., and Chen, J. K. (2007) Small-molecule regulation of zebrafish gene expression. Nat. Chem. Biol. 3: 154-155. [PubMed]


  • Meloni, A. R., Fralish, G. B., Kelly, P., Salahpour, A., Chen, J. K., Wechsler-Reya, R. J., Lefkowitz, R. J. and Caron, M. G. (2006) Smoothened signal transduction is promoted by G-protein coupled receptor kinase 2. Mol. Cell. Biol. 26: 7550-7560. [PubMed]
  • Sinha, S. and Chen, J.K. (2006) Purmorphamine activates the Hedgehog pathway by targeting Smoothened. Nat. Chem. Biol. 2: 29-30. [PubMed]


  • Chen, W., Ren, X., Nelson, C. D, Barak, L. S., Chen, J. K., Beachy, P. A., de Sauvage, F., and Lefkowitz, R. J. (2004) Activity-dependent internalization of Smoothened mediated by beta-Arrestin 2 and GRK2. Science 306: 2257-2260. [PubMed]
  • Chen, J. K., Taipale, J., Young, K. E., Maiti, T., and Beachy, P. A. (2002) Small molecule modulation of Smoothened activity. Proc. Natl. Acad. Sci. U. S. A. 99: 14071-14076. [PubMed]
  • Chen, J. K., Taipale, J., Cooper, M. K., and Beachy, P. A. (2002) Inhibition of Hedgehog signaling by direct binding of cyclopamine to Smoothened. Genes Dev. 16: 2743-2748. [PubMed]
  • Berman, D. M., Karhadkar, S. S., Hallahan, A. R. Pritchard, J. I., Eberhart, C. G., Watkins, D. N., Chen, J. K., Cooper, M. K., Taipale, J., Olson, J. M., and Beachy, P. A. (2002) Medulloblastoma growth inhibition by Hedgehog pathway blockade. Science 297: 1559-1561. [PubMed]
  • Taipale, J., Chen, J. K., Cooper, M. K., Wang, B., Mann, R. K., Milenkovic, L., Scott, M. P., and Beachy, P. A. (2000) The effects of oncogenic mutations in Smoothened and Patched can be reversed by cyclopamine. Nature 406: 1005-1009. [PubMed]