PUBLICATIONS

Total Peer Reviewed Publication: 126 papers
Citations: 11213
h-index: 52
i10 index 90

Other publication. Visit My NCBI
http://www.ncbi.nlm.nih.gov/myncbi/browse/collection
2023
  • Pham, PD., Lu, H, Han, H., Zhou, JJ., Maden, A, Wang, W,, Murre, C., Cho, KWY. (2023). Transcriptional network governing extraembryonic endoderm cell fate choice. Dev Biol. 502:20-37.
  • Zhou JJ, Cho JS, Han H, Blitz IL., Wang W, Cho, KWY. (2023) Histone deacetylase 1 maintains lineage integrity through histone acetylome refinement during early embryogenesis, BioRxiv doi: https://doi.org/10.1101/2022.05.05.490762. eLife, 12:e79380.
  • Hussein, A., Blitz, IL., Cho, KWY. HiChIP to Study 3D Genome Organization in Xenopus tropicalis Embryos. In press.

2022
  • Zhou, JJ., Cho, K.W.Y. (2022). Epigenomic dynamics of early Xenopus embryos (review). Dev Growth Differ. 64508-516. doi: 10.1111/dgd.12813. Epub 2022 Oct 8. PMID: 36168140.
  • Zhou, JJ, Pham PD, Han, H,  Wang, W., Cho, KWY. (2022) Foxh1 engages in chromatin regulation revealed by protein interactome analyses, Development, Growth & Differentiation 64:297-305
  • Jansen C, Paraiso KD, Zhou JJ, Blitz IL, Fish MB, Charney RM, Cho JS, Yasuoka Y, Sudou N, Bright AR, Wlizla M, Veenstra GJC, Taira M, Zorn AM, Mortazavi A, Cho KWY. (2022) Uncovering the mesendoderm gene regulatory network through multi-omic data integration. Cell Reports 38(7):110364.
  •  Cho KWY, Blitz IL. (2022) Gene regulatory networks controlling Xenopus embryogenesis: Chapter 13 in Xenopus, from basic biology to disease models in the genomic era, Ed: Moody, S. and Faisod 
  • Han H, Nakaoka HJ, Hofmann L, Zhou JJ, Yu C, Zeng L, Nan J, Seo G, Vargas RE, Yang B, Qi R, Bardwell L, Fishman DA, Cho KWY, Huang L, Luo R, Warrior R, Wang W. (2022). The Hippo pathway kinases LATS1 and LATS2 attenuate cellular responses to heavy metals through phosphorylating MTF1. Nat Cell Biol. doi: 10.1038/s41556-021-00813-8.

2021
  • Cao Y, Tang L, Du K, Paraiso K, Sun Q, Liu Z, Ye X, Fang Y, Yuan F, Chen H, Chen Y, Wang X, Yu C, Blitz IL, Wang PH, Huang L, Cheng H, Lu X, Cho KW, Seldin M, Fang Z, Yang Q. (2021). Anterograde regulation of mitochondrial genes and FGF21 signaling by hepatic LSD1. JCI Insight. 6(17):147692
  • Cang Z, Wang Y, Cho KWY, Holmes W, Nie Q. (2020) Integrative data and hypothesis driven multiscale modeling via single-cell transcriptomics and spatial imaging. PLoS Comp Biol. https://doi.org/10.1371/journal.pcbi.1008571
  • Blitz IL, Cho KWY. (2021). Control of zygotic genome activation in Xenopus. Curr Top Dev Biol. 145:167-204
  • Cho JS, Blitz IL, Cho KWY. (2021). DNase-seq to Study Chromatin Accessibility in Early Xenopus tropicalis Embryos. Cold Spring Harb Protoc. (4). doi: 10.1101/pdb.prot098335. 

2020
  • Mukherjee S, Chaturvedi P, Rankin SA, Fish MB, Wlizla M, Paraiso KD, MacDonald M, Chen X, Weirauch MT, Blitz IL, Cho KW, Zorn AM.  (2020). Sox17 and β-catenin co-occupy Wnt-responsive enhancers to govern the endoderm gene regulatory network. Elife. 9:e58029. doi: 10.7554/eLife.58029.
  • Paraiso KD, Cho JS, Yong J, Cho KWY. Early Xenopus gene regulatory programs, chromatin states, and the role of maternal transcription factors. Curr Top Dev Bio 2020;139:35-60. doi: 10.1016/bs.ctdb.2020.02.009.
  • Afouda BA, Nakamura Y, Shaw S, Charney RM, Paraiso KD, Blitz IL, Cho KWY, Hoppler S. (2020). Foxh1/Nodal Defines Context-Specific Direct Maternal Wnt/β-Catenin Target Gene Regulation in Early Development iScience 23:101314.  doi: 10.1016/j.isci.2020.101314. 

​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, 9:13206.  (# shared senior authors).  
  • Gilchrist, ML., Cho, KWY. Veenstra. GJC. (2019).  An introduction to genomics protocols for Xenopus. Xenopus Laboratory Manual, Cold Spring Harbor Press. (5):pdb.top097915. 
  • Gilchrist, ML., Veenstra. GJC., Cho, KWY. (2019). An introduction to transcriptomics and proteomics. Xenopus Laboratory Manual, Cold Spring Harbor Press. 2020(2):pdb.top098350. 

2018
  •  Jin S Cho, Ira L. Blitz and Ken W.Y. Cho, (2018). DNase-seq to study chromatin accessibility in early Xenopus tropicalis embryos. Chapter 14, Xenopus Laboratory Manual,　Cold Spring Harbor Press, 4 pdb.prot098335. doi: 10.1101/pdb.prot098335.PMID:30131367.

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. Developmental 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.  8:3