PUBLICATIONS

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2019
  • Paraiso, K,, I L Blitz, Coley M, Cheung, Sudoh N., Taira, M., and Cho K.W.Y. (2019).Endodermal maternal transcription factors establish super enhancers during zygotic genome activation. Cell Reports,27:2962-2977 PMID:  31167141
  • Paraiso, K,, Blitz, IL., Zhou, J., and Cho K.W.Y. (2019).Morpholinos do not elicit an innate immune response during early Xenopusembryogenesis. Developmental Cell,49:643-650. PMID: 31112700
  • Ning Ma, Nabora Reyes de Mochel, Paula Pham Tae Yoo, Ken Cho#, Michelle Digman#. (2019).  Label-free assessment of pre-implantation embryo quality by the Fluorescence Lifetime Imaging Microscopy (FLIM)-phasor approach. Scientific Reports, I press (# shared senior authors).  
  • Gilchrist, ML., Cho, KWY. Veenstra. GJC. (2019).  An introduction to genomics protocols for Xenopus. Xenopus Laboratory Manual, Cold Spring Habor Press. in press
  • Gilchrist, ML., Veenstra. GJC., Cho, KWY. (2019). An introduction to transcriptomics and proteomics. Xenopus Laboratory Manual, Cold Spring Habor Press. in press
2018
  •  Jin S Cho, Ira L. Blitz and Ken W.Y. Cho, (2018). DNase-seq to study chromatin accessibility in early Xenopus tropicalisembryos. Chapter 14, Xenopus Laboratory Manual,Cold Spring Habor Press, 4 pdb.prot098335. doi: 10.1101/pdb.prot098335.PMID:30131367.
  • Ning Ma, Nabora Reyes de Mochel, Paula Pham Tae Yoo, Ken Cho#, Michelle Digman#.(2019).  Label-free assessment of pre-implantation embryo quality by the Fluorescence Lifetime Imaging Microscopy (FLIM)-phasor approach. bioRxiv 286682; doi: https://doi.org/10.1101/286682(# shared senior authors).
2017
  • Charney, R.M., Forouzmand, E., Cho, J.S., Cheung, J., Paraiso, K.D., Yasuoka, Y., Takahashi, S., Taira, M., Blitz, I.L., Xie, X. and. Cho K.W.Y. (2017). Foxh1 occupies cis-regulatory modules prior to dynamic transcription factor interactions controlling the mesendoderm gene program. Dev Cell.40:1-13. PMID:28325473.
  • Charney RM, Paraiso KD, Blitz IL, Cho KWY. (2017). A gene regulatory program controlling early Xenopus mesendoderm formation: Network conservation and motifs. Semin Cell Dev Biol.66:12-24. PMID: 28341363
  • Holmes, W.R., Mochel, S., Wang, Q., Du, H., Cinquin, O., Cho, K.W*., Nie, Q*. *contributed equally, co-senior authors. (2017). Gene Expression Noise Enhances Robust Organization of the Early Mammalian Blastocyst. PLoS Comput Biol. 2017 Jan 23;13(1):e1005320.
2016
  • Forouzmand, E., Owens, N.D.L., Blitz, I.L., Paraiso, K.D., Khokha, M.K., Gilchrist, M.J., Xie X., Cho, K.W.Y. (2016).  Developmentally regulated long non-coding RNAs in Xenopus tropicalis. Dev Biol, S0012-1606(16)30120-8. doi: 10.1016/j.ydbio.2016.06.016. PMID: 27418388 
  • Blitz, I.L., Paraiso, K.D., Patrushev, I., Chiu, W.T.Y., Cho, K.W.Y*., Gilchrist,M.J.* (2016). A catalog of Xenopus tropicalis transcription factors and their regional expression in the early gastrula stage embryo. Dev Biol,. S0012-1606(16)30118-X. doi: 10.1016/j.ydbio.2016.07.002. PMID: 27475627. *contributed equally, co-senior authors. 
  • Blitz, I.L., Fish, M.B., and Cho, K.W.Y. (2016). Leapfrogging: Primordial Germ Cell Transplantation Permits Recovery of CRISPR/Cas9-Induced Mutations in Essential Genes. Development,  143(15):2868-75. PMID: 27385011
  • Owens, N.D.L. 1, Blitz, I.L. 1, Lane, M.A., Overton, J.D., Gilchrist, M.J#, Cho, K.W.Y#., Khokha, M.K.  (2016). Embryogenesis kinetics measured by high-resolution absolute quantitation of transcripts. Submitted. 1: co-first authros, # contributed equally. In press. Cell Reports. Jan 26;14(3):632-47. PMID: 26774488
2015
  • Chiang, M., Hallman, S., Cinquin, A., Reyes de Mochel, N., Paz, A., Kawauchi, S., Calof, A., Cho, KWY., Fowlkes, C.C., & Cinquin, O. (2015). Analysis of in vivo single cell behavior by high throughput, human-in-the-loop segmentation of three-dimensional images. BMC Bioinformatics. DOI 10.1186/s12859-015-0814-7
  • Wang, X., Hsi, H., Guerrero-Juarez, CF., Pham, K., Cho, K., Monuki, ES, Cho, KWY., Gay, DL., Plikus, (2015). Principles and mechanisms of regeneration in the mouse model for wound-induced hair follicle neogenesis. Regeneration. doi: 10.1002/reg2.38.
  • Reyes de Mochel, NS., Luong, M., Chiang, M., Javier, A.L., Luu, E., Cinquin, O., and Cho, KWY. (2015). BMP signaling regulates both cell proliferation and ICM lineage commitment in preimplantation-stage mouse embryos. Dev Biol. 397, 45-55.
2014
  • Yang, G., Yuan, G., Cho, K.W.Y., and Chen, Y. (2014). An atypical canonical BMP signaling pathway regulates Msx1 expression during odontogenesis. J Biol Chem. 289, 31492-31502.
  • Chiu, WT., Le, R., Beisinger, J., Blitz, IL., Xie, X., Cho, KWY. (2014). Comprehensive genomic view of Foxh1 and Smad2/3 interaction in mesendoderm development. Development, 141, 4537-4547.
  • Nakayama, T., Blitz I.L., Fish, M.B., Sumanth, A., Cho, K.W.Y., Grainger R. (2014). Cas9-based genome editing in Xenopus tropicalis. Methods in Enzymplogy, 546, 355-375.
  • Yasuoka, Y., Suzuki, Y., Takahashi, S., Sudou, N., Haramoto, Y., Cho, KW., Asashima, M., Sugano, S., and Taira, M. (2014). Otx2 and TLE/Groucho occupancy marks tissue-specific cis-regulatory modules for head specification. Nature Communiations, 9:4322.
  • Blitz, IL., Luong, M., Chu, W. and Cho, K.W. (2014). Application of genomic approaches to developmental biology (book chapter for Principal of Developmental Genetics, 2nd edition. Edited by Sally Moody). 37-48.
  • Zheng, Z., Christley, S., Chiu, WT., Blitz, IL., Xie, X., Cho, KWY., Nie, Q. (2014) Inference of the Xenopus tropicalis embryonic regulatory network and spatial gene expression patterns. BMS Systems Biology. BMC Syst Biol. 8:3
2013
  • Blitz,IL., Biesinger, J., Xie, X., and Cho, KWY. (2013). Biallelic Genome Modification in F0 Xenopus tropicalis Embryos Using the CRISPR/Cas System. Genesis, 51:827-34.
2012
  • Doan, LT.,  Javier, A., Furr, NM., Nguyen, K., Cho, KW., and Monuki, ES. (2012). An ultrasensitive Bmp signaling reporter reveals that high Bmp signaling is not required for cortical hem fate. PLoS One. 7(9):e44009.
  • Javier, A., Doran, L., Luong, M., Sun, A., Monuki, E., Cho KWY. (2012). Bmp indicator mice reveal dynamic regulation of transcriptional response. PLoS One. 7(9):e42566.
  • Cho, KWY., Review on enhancers, Online Developmental Biology. (2012) DOI: 10.1002/wdev.53
​2011
  • Alexander C, Zuniga E, Blitz IL, Wada N, Le Pabic P, Javidan Y, Zhang T, Cho KW, Crump JG, Schilling TF. (2011). Combinatorial roles for BMPs and Endothelin 1 in patterning the dorsal-ventral axis of the craniofacial skeleton. Development. 138:5135-46. PMID: 22031543.
2009
  • Kim, H.J., Chun, B.G., Shin, H.S., Sun, A., Cho K.W.Y. and Jeon N.L. (2009). Microfluidic culture platform for investigating the proliferation and differentiation of stem cells. Methods in Bioengineering Series: Stem Cell Bioengineering (edited by Parekkadan, B and Yarmush M.L.) (Book chapter). 75-88. 
  • Karaulanov, E., Böttcher, R.T., Stannek, P., Wu, W., Rau, M., Ogata, S., Cho, K.W. and Niehrs, C. (2009). Unc5B interacts with FLRT3 and Rnd1 to modulate cell adhesion in Xenopus embryos. PLoS one.4:5742e.
  • Blitz, I.L., and Cho, K.W. (2009). Finding partners: How BMPs select their targets. Dev Dynamics 238:1321-1331.
  • Jarikji, Z., Horb, LZ., Shariff1, F., Mandato, C.A., Cho, KW, and Horb, M.E. (2009). The tetraspanin tm4sf3 is localized to the ventral pancreas and regulates fusion of the dorsal and ventral pancreatic buds. Development 136:1791-1800.
  • Hayata T, Blitz IL, Iwata N, Cho KW. (2009). Identification of embryonic pancreatic genes using Xenopus DNA microarrays. Dev Dyn. 238:1455-1466
2008
  • Maretto S, Müller PS, Aricescu AR, Cho KW, Bikoff EK, Robertson EJ. (2008). Ventral closure, headfold fusion and definitive endoderm migration defects in mouse embryos lacking the fibronectin leucine-rich transmembrane protein FLRT3. Dev Biol. 318:184-93.
2007
  • Ogata S, Cho KW. (2007). Dissection of organizer and animal pole explants from Xenopus laevis embryos and assembly of a cell adhesion assay.J Vis Exp. 3:187.
  • Ogata S, Kawauchi S, Calof A, Cho KW.  (2007). Plastic embedding and sectioning of Xenopus laevis embryos. J Vis Exp. 3:188.
  • Ogata S, Morokuma J, Hayata T, Kolle G, Niehrs C, Ueno N, Cho KW. (2007). TGF-beta signaling-mediated morphogenesis: modulation of cell adhesion via cadherin endocytosis. Genes Dev. 1817-31.
  • Park EC, Hayata T, Cho KW*, Han JK*. (2007). (note: Erratum in: Dev Dyn. 2007 Aug;236(8):2367, * co-senior authors). Xenopus cDNA microarray identification of genes with endodermal organ expression. Dev Dyn. 236:1633-49.
  • Suzawa K, Yukita A, Hayata T, Goto T, Danno H, Michiue T, Cho KW, Asashima M. (2007). Xenopus glucose transporter 1 (xGLUT1) is required for gastrulation movement in Xenopus laevis. Int J Dev Biol. 51:183-90.