2012-2022
慶應義塾大学医学部
システム医学講座

このウェブサイトは、2012年から2022年まで慶應義塾大学医学部で教授を務めた 洪 実（現、名誉教授）の研究室（システム医学講座）の研究リソースへのアクセスを提供しています。

当時のウェブサイトによると、「システム医学講座では、大量の情報（ビッグデータ）を統合し、大局的（グローバル）に物事を視るという観点から医学・医療を進めることをゴールにしています。ここでは、「システム思考」という考え方と、「システム手法」という研究手段を柱に、生命現象の「部分を見ると同時に全体像をとらえる」研究を推進しています。このような研究手法は、生物学研究においては「システム生物学」と呼ばれていますが、我々の講座は基礎研究だけでなく、病気の診断法や治療法の開発など臨床医学への応用にも積極的に取り組んでいるため、「システム医学講座 （Department of Systems Medicine）」と名付けました。システム医学講座では、細胞・遺伝子の大規模網羅的解析、コンピュータによる大容量情報処理・シミュレーションなどを技術的な軸として、幹細胞の老化・若返り・分化制御等を通じて再生医療研究に取り組んでいきます。」

Research Resources
研究リソースへのリンク

Nakatake Y, Ko SBH, Sharov AA, Wakabayashi S, Murakami M, Sakota M, Chikazawa N, Ookura C, Sato S, Ito N, Ishikawa-Hirayama M, Mak SS, Jakt LM, Ueno T, Hiratsuka K, Matsushita M, Goparaju SK, Akiyama T, Ishiguro KI, Oda M, Gouda N, Umezawa A, Akutsu H, Nishimura K, Matoba R, Ohara O, Ko MSH (2020). Generation and Profiling of 2,135 Human ESC Lines for the Systematic Analyses of Cell States Perturbed by Inducing Single Transcription Factors. Cell Rep. 2020 May 19;31(7):107655. [PMID: 32433964]

1. Database for Transcription Factor (TF)-manipulated human ES cell data (linked from the paper) http://www.systemsmedicine.jp/crest/plasmid/
2. Cell Lines of TF-manipulated human ES cells: Deposited and available from RIKEN Bioresource Center Cell Bank (search “Minoru Ko” at https://cell.brc.riken.jp/en/). Total 2142 cell lines.
3. Plasmid vectors for mammalian gene expression: Deposited and available from addgene (search “Minoru Ko” in https://www.addgene.org/). Total 43 plasmids.

Publications

Peer-Reviewed Publications (*corresponding author)

1. Noda M, Ko M, Ogura A, Liu D-G, Amano T, Takano T, and Ikawa Y. (1985). Sarcoma viruses carrying ras oncogenes induce differentiation-associated properties in a neuronal cell line. Nature 318: 73-78.

*2. Ko MSH and Takano T. (1989). A highly inducible system of gene expression by positive feedback production of glucocorticoid receptors. DNA 8: 127-133.

*3. Ko MSH, Takahashi N, Sugiyama N, and Takano T. (1989). An auto-inducible vector conferring high glucocorticoid-inducibility upon stable transformant cells. Gene 84: 383-389.

*4. Ko MSH, Ko SBH, Takahashi N, Nishiguchi K, and Abe K. (1990). Unbiased amplification of a highly complex mixture of DNA fragments by "lone linker"-tagged PCR. Nucleic Acids Research 18: 4293-4294.

*5. Ko MSH, Nakauchi H, and Takahashi N. (1990). The dose-dependence of glucocorticoid-inducible gene expression results from changes in the number of transcriptionally active templates. EMBO Journal 9: 2834-2882.

*6. Ko MSH. (1990). An "equalized cDNA library" by the reassociation of short double-stranded cDNAs. Nucleic Acids Research 18: 5705-5711.

*7. Ko MSH. (1991). A stochastic model for gene induction. J Theor Biol 153: 181-184.

*8. Ko MSH. (1992). Induction mechanism of a single gene molecule: Stochastic or Deterministic? BioEssays 14: 341-346.

*9. Takahashi N and Ko MSH. (1993). The short 3′-end region of complementary DNAs as PCR-based polymorphic markers for an expression map of the mouse genome. Genomics 16, 161-168.

10. Rowe LB, Nadeau JH, Turner R, Frankel WN, Letts VA, Eppig JT, Ko MSH, Thurston SJ and Birkenmeier EH. (1994). Maps from two interspecific backcross DNA panels are available as a community genetic mapping resource. Mamm. Genome 5: 253-274.

*11. Horton JH, Hagen MD and Ko MSH. (1994). Optimized conditions for cycle sequencing of PCR products. PCR Methods & Applications 3: 359-360.

*12. Wang X., Qian J. and Ko MSH. (1994). Simple and robust screening of pooled YAC libraries by the restriction enzyme digestion of PCR products. Genet. Anal. Techn. Appl. 11: 63-68.

13. Ko MSH*, Wang X, Horton JH, Hagen MD, Takahashi N, Maezaki Y and Nadeau JH (1994). Genetic mapping of 40 cDNA clones on the mouse genome by PCR. Mamm. Genome. 5: 349-355.

*14. Takahashi N and Ko MSH. (1994). Towards a whole cDNA catalog: an equalized cDNA library from mouse embryos. Genomics. 23: 202-210.

15. Harada H, Hashimoto K and Ko MSH. (1996). The gene for multiple familial trichoepithelioma maps to chromosome 9p21. J. Invest. Dermatology, 107: 41-43.

*16. Yotsumoto S, Fujiwara H, Horton JH, Mosby TA, Wang X, Cui Y and Ko MSH. (1996). Cloning and expression analyses of mouse dystroglycan gene: Specific expression in maternal decidua at the peri-implantation stage. Hum Mol Genet, 5: 1259-1267.

17. Harada H, Hashimoto K, Toi Y, Yotsumoto S and Ko MSH. (1997). Basal cell carcinoma occurring in multiple familial trichoepithelioma: detection of loss of heterozygosity in chromosome 9q. Arch Dermatol, 133: 666-667.

18. D’Esposito M, Matarazzo MR, Ciccodicola A, Strazzullo M, Mazzarella R, Quaderi NA, Fujiwara H, Ko MSH, Rowe LB, Ricco A, Archidiacono N, Rocchi M, Schlessinger D and D’Urso M. (1997). Differential expression pattern of XqPAR-linked genes SYBL1 and IL9R correlates with the structure and evolution of the region. Hum Mol Genet, 6: 1917-1923.

19. Srivastava AK, Pispa J, Hartung AJ, Du Y, Ezer S, Jenks T, Shimada T, Pekkanen M, Ko MSH, Thesleff I, Kere J and Schlessinger D. (1997). The Tabby phenotype is caused by mutation in a mouse homologue of the EDA gene, which reveals novel mouse and human exons and encodes a protein (ectodysplasin-A) with collagenous domains. Proc. Natl. Acad. Sci. USA, 94: 13069-13074.

20. Jaradat SA, Ko MSH and Grossman LI. (1998). Tissue specific expression and mapping of the COX7AH gene in mouse. Genomics, 49: 363-370.

*21. Yotsumoto S, Shimada T, Cui CY, Nakashima H, Fujiwara H and Ko MSH. (1998). Expression of Adrenomedullin, a Hypotensive Peptide, in the Trophoblast Giant Cells at the Embryo Implantation Site in Mouse. Dev Biol, 203: 264-275.

*22. Ko MSH, Threat TA, Wang X, Horton JH, Cui Y, Pryor E, Paris J, Wells-Smith J, Kitchen JR, Rowe LB, Eppig J, Satoh T, Brant L, Fujiwara H, Yotsumoto S and Nakashima H (1998). Genome-wide mapping of unselected transcripts from extraembryonic tissue of 7.5-day mouse embryos reveals enrichment in the t-complex and under-representation on the X chromosome. Hum Mol Genet, 7: 1967-78.

23. Schlessinger D and Ko MSH (1998). Developmental Genomics and Its Relation to Aging. Genomics. 52, 113-118.

24. Abe K, Ko MSH and MacGregor G.R. (1998). A systematic molecular genetic approach to study mammalian germline development. Int. J. Dev. Biol. 42, 1051-1066.

*25. Nakashima H, Grahovac MJ, Mazzarella R, Kitchen JR, Threat TA and Ko MSH. (1999). Two novel mouse genes – Nubp2, mapped to the t-complex on Chromosome 17, and Nubp1, mapped to Chromosome 16 – establish a new gene family of nucleotide binding proteins in eukaryotes. Genomics, 60: 152-160.

26. Leach R, Ko MSH, Krawetz S. (1999). Assignment of amyloid-precursor-like protein 2 gene (APLP2) to 11q24 by fluorescent in situ hybridization. Cytogenet Cell Genet, 87: 215-216.

*27. Yotsumoto S, Kanzaki T, Ko MSH. (2000). Beta subunit of the high affinity immunoglobulin E receptor, a candidate for atopic dermatitis, is not imprinted. Br J Dermatol, 142:370-371.

*28. Ko MSH, Kitchen JR, Wang X., Threat TA, Wang X, Hasegawa A, Sun T, Grahovac MJ, Kargul GJ, Lim MK, Cui Y, Sano Y, Tanaka T, Liang Y, Mason S, Paonessa PD, Sauls AD, DePalma GE, Sharara R, Rowe LB, Eppig J, Morrell C, Doi H (2000). Large-scale cDNA analysis reveals phased gene expression patterns during preimplantation mouse development. Development, 127: 1737-1749.

29. Chou SR, Brownell A, Ko MSH, Kaplan J. (2000). Interferon gamma receptor gene: key role in determining accessibility of NK-triggering antigens to recognition by Self-reactive NK cells. Cell Immunol. 2000 Mar 15;200(2):88-97.

*30. Tanaka TS, Jaradat SA, Lim MK, Kargul GJ, Wang X, Grahovac MJ, Pantano S, Sano Y, Piao Y, Nagaraja R, Doi H, Wood 3 WH, Becker KG, and Ko MSH (2000). Genome-wide expression profiling of mid-gestation placenta and embryo using a 15000 mouse developmental cDNA microarray, Proc. Natl. Acad. Sci. USA, 97: 9127-9132.

*31. Kargul GJ, Nagaraja R, Shimada T, Grahovac M, Lim MK, Nakashima H, Waeltz P, Ma P, Chen E, Schlessinger D and Ko MSH (2000). Eleven densely clustered genes, seven of them novel, in 176 kb of mouse t-complex DNA. Genome Res, 10: 916-923.

*32. Nicholson RH, Pantano S, Eliason JF, Galy A, Weiler S, Kaplan J, Hughes MR, and Ko MSH (2000). Phemx, a novel mouse gene expressed during hematopoiesis, maps to the imprinted cluster on distal chromosome 7. Genomics, 68: 13-21.

33. Cocchia M, Huber R, Pantano S, Chen EY, Forabosco A, Ko MSH, and Schlessinger D (2000). PLAC1, an Xq26 gene with placenta-specific expression. Genomics, 68: 305-312.

*34. Ko MSH (2001). Embryogenomics: developmental biology meets genomics. Trends Biotechnol. 19: 511-518.

*35. Kargul GJ, Dudekula DB, Qian Y, Lim MK, Jaradat SA, Tanaka TS, Carter MG, and Ko MSH (2001). Verification and initial annotation of the NIA mouse 15K cDNA clone set. Nature Genetics, 28:17-18.

36. Cintron VJ, Ko MSH, Chi KD, Gross JP, Srinivas PR, Goustin AS, Grunberger G (2001). Genetic mapping and functional studies of a natural inhibitor of the insulin receptor tyrosine kinase: the mouse ortholog of human alpha2-HS glycoprotein. Int J Exp Diabetes Res, 1: 249-263.

*37. Piao Y, Ko NT, Lim MK, Ko MSH (2001). Construction of long-transcript enriched cDNA libraries from submicrogram amounts of total RNAs by a universal PCR amplification method. Genome Res. 11: 1553-1558.

38. Barrett T, Xie T, Piao Y, Dillon-Carter O, Kargul GJ, Lim MK, Chrest FJ, Wersto R, Rowley DL, Juhaszova M, Zhou L, Vawter MP, Becker KG, Cheadle C, Wood WH 3rd, McCann UD, Freed WJ, Ko MSH, Ricaurte GA, Donovan DM (2001). A Murine Dopamine Neuron-Specific cDNA Library and Microarray: Increased COXI Expression during Methamphetamine Neurotoxicity. Neurobiol Dis. 8: 822-833.

39. Hudson TJ, Church DM, Greenaway S, Nguyen H, Cook A, Steen RG, Van Etten WJ, Castle AB, Strivens MA, Trickett P, Heuston C, Davison C, Southwell A, Hardisty R, Varela-Carver A, Haynes AR, Rodriguez-Tome P, Doi H, Ko MSH, Pontius J, Schriml L, Wagner L, Maglott D, Brown SD, Lander ES, Schuler G, Denny P (2001). A radiation hybrid map of mouse genes. Nat Genet. 29: 201-205.

*40. Sano Y, Shimada T, Nakashima H, Nicholson RH, Eliason JF, Kocarek TA, Ko MSH (2001). Random Monoallelic Expression of Three Genes Clustered within 60 kb of Mouse t Complex Genomic DNA. Genome Res. 11: 1833-1841.

41. Leach R, Duniec-Dmuchowski Z, Tanaka T, Ko MSH, Krawetz SA. Assignment of OVCOV1 (alias CGI-15) to human chromosome 20 band q13.1–>q13.2 by fluorescent in situ hybridization. Cytogenet Cell Genet. 2001;94(3-4):252-3.

42. Cui CY, Durmowicz M, Tanaka TS, Hartung AJ, Tezuka T, Hashimoto K, Ko MSH, Srivastava AK, Schlessinger D. (2002). EDA targets revealed by skin gene expression profiles of wild-type, Tabby and Tabby EDA-A1 transgenic mice. Hum Mol Genet. 2002 Jul 15;11(15):1763-73.

43. Leach RE, Duniec-Dmuchowski ZM, Pesole G, Tanaka TS, Ko MSH, Armant RD, Krawetz SA. (2002). Identification, molecular characterization, and tissue expression of OVCOV1. Mamm Genome 13: 619-24.

*44. VanBuren V, Piao Y, Dudekula DB, Qian Y, Carter MG, Martin PR, Stagg CA, Bassey UC, Aiba K, Hamatani T, Kargul GJ, Luo AG, Kelso J, Hide W and Ko MSH. (2002). Assembly, verification, and initial annotation of the NIA mouse 7.4K cDNA clone set. Genome Res 12: 1999-2003.

*45. Tanaka TS, Kunath T, Kimber WL, Jaradat SA, Stagg CA, Usuda M, Yokota T, Niwa H, Rossant J, and Ko MSH. (2002). Gene expression profiling of embryo-derived stem cells reveals candidate genes associated with pluripotency and lineage specificity. Genome Res 12: 1921-8.

*46. Suemizu H, Aiba H, Yoshikawa T, Sharov AA, Shimozawa N, Tamaoki N, and Ko MSH. (2003). Expression profiling of placentomegaly associated with nuclear transplantation of mouse ES cells. Dev Biol 253: 36-53.

*47. Kimber WL, Puri N, Borgmeyer C, Ritter D, Sharov A, Seidman M, and Ko MSH. (2003). Efficacy of 2-methoxyethoxy (2’-MOE)-modified antisense oligonucleotides for the study of mouse preimplantation development. Reprod Biomed Online 6, 318-322.

*48. Carter MG, Hamatani T, Sharov AA, Carmack CE, Qian Y, Ko NT, Dudekula DB, Brzoska PM, Hwang SS, and Ko MSH. (2003). In situ-synthesized novel microarray optimized for mouse stem cell and early developmental expression profiling. Genome Res. 13: 1011-21.

49. Galaviz-Hernandez C, Stagg C, de Ridder G, Tanaka TS, Ko MSH, Schlessinger D, Nagaraja R. (2003). Plac8 and Plac9, novel placental-enriched genes identified through microarray analysis. Gene 309: 81-9.

50. Buttitta L, Tanaka TS, Chen AE, Ko MSH, and Fan C.M. (2003). Microarray analysis of somitogenesis reveals novel targets of different wnt signaling pathways in the somitic mesoderm. Dev Biol. 2003 Jun 1;258(1):91-104.

*51. Sharov AA, Piao Y, Matoba R, Dudekula DB, Qian Y, VanBuren V, Falco G, Martin PR, Stagg CA, Bassey UC, Wang Y, Carter MG, Hamatani T, Aiba K, Akutsu H, Sharova L, Tanaka TS, Kimber WL, Yoshikawa T, Jaradat SA, Pantano S, Nagaraja R, Boheler KR, Taub D, Hodes RJ, Longo DL, Schlessinger D, Keller J, Klotz E, Kelsoe G, Umezawa A, Vescovi AL, Rossant J, Kunath T, Hogan BL, Curci A, D’Urso M, Kelso J, Hide W, Ko MSH. (2003). Transcriptome Analysis of Mouse Stem Cells and Early Embryos. PLoS Biol. 1: 410-419.

*52. Carter MG, Piao Y, Dudekula DB, Qian Y, VanBuren V, Sharov AA, Tanaka TS, Martin PR, Bassey UC, Stagg CA, Aiba K, Hamatani T, Matoba R, argul GJ and Ko MSH (2003). The NIA cDNA Project in mouse stem cells and early embryos . C R Biol. 2003 Oct-Nov;326(10-11):931-40.

*53. Hamatani T, Carter MG, Sharov AA and Ko MSH. (2004). Dynamics of global gene expression changes during mouse preimplantation development. Dev. Cell: 6, 117-131. [Published online Dec. 18, 2003]

54. Abe K, Yuzuriha M, Sugimoto M, Ko MSH, Brathwaite M, Waeltz P, Nagaraja R (2004). Gene content of the 750-kb critical region for mouse embryonic ectoderm lethal tcl-w5. Mamm Genome15: 265-76.

55. Hamatani T, Daikoku T, Wang H, Matsumoto H, Carter MG, Ko MSH, Dey SK (2004). Global gene expression analysis identifies molecular pathways distinguishing blastocyst dormancy and activation. Proc Natl Acad Sci U S A. 2004 Jul 13;101(28):10326-31. Epub 2004 Jul 01.

*56. Hamatani T, Falco G, Carter MG, Akutsu H, Stagg CA, Sharov AA, Dudekula DB, VanBuren V, Ko MSH (2004). Age-associated alteration of gene expression patterns in mouse oocytes. Human Molecular Genetics; 13(19):2263-78. Epub 2004 Aug 18.

57. Gerhard DS, Wagner L, Feingold EA, Shenmen CM, Grouse LH, Schuler G, Klein SL, Old S, Rasooly R, Good P, Guyer M, Peck AM, Derge JG, Lipman D, Collins FS, Jang W, Sherry S, Feolo M, Misquitta L, Lee E, Rotmistrovsky K, Greenhut SF, Schaefer CF, Buetow K, Bonner TI, Haussler D, Kent J, Kiekhaus M, Furey T, Brent M, Prange C, Schreiber K, Shapiro N, Bhat NK, Hopkins RF, Hsie F, Driscoll T, Soares MB, Casavant TL, Scheetz TE, Brown-stein MJ, Usdin TB, Toshiyuki S, Carninci P, Piao Y, Dudekula DB, Ko MS, Kawakami K, Suzuki Y, Sugano S, Gruber CE, Smith MR, Simmons B, Moore T, Waterman R, Johnson SL, Ruan Y, Wei CL, Mathavan S, Gunaratne PH, Wu J, Garcia AM, Hulyk SW, Fuh E, Yuan Y, Sneed A, Kowis C, Hodgson A, Muzny DM, McPherson J, Gibbs RA, Fahey J, Helton E, Ketteman M, Madan A, Rodrigues S, Sanchez A, Whiting M, Madari A, Young AC, Wetherby KD, Granite SJ, Kwong PN, Brinkley CP, Pearson RL, Bouffard GG, Blakesly RW, Green ED, Dickson MC, Rodriguez AC, Grimwood J, Schmutz J, Myers RM, Butterfield YS, Griffith M, Griffith OL, Krzywinski MI, Liao N, Morrin R, Palmquist D, Petrescu AS, Skalska U, Smailus DE, Stott JM, Schnerch A, Schein JE, Jones SJ, Holt RA, Baross A, Marra MA, Clifton S, Makowski KA, Bosak S, Malek J; MGC Project Team. (2004). The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Genome Res. 2004 Oct;14(10B):2121-7.

*58. Ko MSH (2004). Embryogenomics of preimplantation mammalian development: Current Status. Reproduction, Fertility and Development 16: 79-85.

*59. Tanaka TS, Ko MSH. A global view of gene expression in the preimplantation mouse embryo: morula versus blastocyst. Eur J Obstet Gynecol Reprod Biol. 2004 Jul 1;115 Suppl 1:S85-91.

60. Herrera L, Ottolenghi C, Garcia-Ortiz JE, Pellegrini M, Manini F, Ko MS, Nagaraja R, Forabosco A, Schlessinger D. (2005). Mouse ovary developmental RNA and protein markers from gene expression profiling. Dev Biol. 2005 Mar 15;279(2):271-90.

61. Sakatani T, Kaneda A, Iacobuzio-Donahue CA, Carter MG, Witzel SD, Okano H, Ko MS, Ohlsson R, Longo DL, Feinberg AP. (2005). Loss of Imprinting of Igf2 Alters Intestinal Maturation and Tumorigenesis in Mice. Science. 2005 Feb 24.

*62. Sharov AA, Dudekula DB, Ko MSH (2005). A web-based tool for principal component and significance analysis of microarray data. Bioinformatics. 2005 May 15;21(10):2548-9. Epub 2005 Feb 25.

*63. Sharov AA, Dudekula DB, and Ko MSH (2005). Genome-wide assembly and analysis of alternative transcripts in mouse. Genome Res. 2005 May;15(5):748-54.

64. Akagi T, Usuda M, Matsuda T, Ko MSH, Niwa H, Asano M, Koide H, and Yokota T. (2005). Identification of Zfp-57 as a downstream molecule of STAT3 and Oct-3/4 in embryonic stem cells. Biochem Biophys Res Commun. 2005 May 27; 331(1): 23-30.

65. Tamura T, Thotakura P, Tanaka TS, Ko MSH, Ozato K (2005). Identification of target genes and a unique cis-element regulated by IRF-8 in developing macrophages. Blood. 2005 Jun 9; [Epub ahead of print]

*66. Carter MG, Sharov AA, VanBuren V, Dudekula DB, Carmack CE, Nelson C, Ko MSH (2005). Transcript copy number estimation using a mouse whole-genome oligonucleotide microarray. Genome Biol. 2005;6(7):R61. Epub 2005 Jun 30.

*67. Yoshikawa T, Piao Y, Zhong J, Matoba R, Carter MG, Wang Y, Goldberg I, Ko MSH (2006). High-throughput screen for genes predominantly expressed in the ICM of mouse blastocysts by whole mount in situ hybridization. Gene Expr Patterns.2006 Jan;6(2):213-24. Epub 2005 Dec 1.

*68. Aiba K, Sharov AA, Carter MG, Foroni C, Vescovi AL, Ko MSH (2005). Defining a developmental path to neural fate by global expression profiling of mouse embryonic stem cells and adult neural stem/progenitor cells. Stem Cells. 2005 Dec 15; [Epub ahead of print]

69. Park JM, Kohn MJ, Bruinsma MW, Vech C, Intine RV, Fuhrmann S, Grinberg A, Mukherjee I, Love PE, Ko MSH, Depamphilis ML, Maraia RJ (2006). The Multifunctional RNA-Binding Protein La Is Required for Mouse Development and for the Establishment of Embryonic Stem Cells. Mol Cell Biol. 2006 Feb;26(4):1445-51.

70. Das B, Cai L, Carter MG, Piao YL, Sharov AA, Ko MSH, Brown DD (2006). Gene expression changes at metamorphosis induced by thyroid hormone in Xenopus laevis tadpoles. Dev Biol. 2006 Feb 1; [Epub ahead of print]

*71. Ko MSH (2006). Expression profiling of the mouse early embryo: Reflections and perspectives. Dev Dyn. 2006 May 31; [PMID: 16739220]

72. Rogers NT, Halet G, Piao Y, Carroll J, Ko MSH and Swann K (2006). A Ca2+ signal during mouse egg activation affects preimplantation development, gene expression patterns, and blastocyst quality. Reproduction. 2006 Jul;132(1):45-57. [PMID: 16816332]

*73. Tanaka TS, Lopez de Silanes I, Sharova LV, Akutsu H, Yoshikawa T, Amano H, Yamanaka S, Gorospe M, Ko MSH (2006). Esg1, expressed exclusively in preimplantation embryos, germline, and embryonic stem cells, is a putative RNA-binding protein with broad RNA targets. Dev Growth Differ. 2006 Aug;48(6):381-90. [PMID: 16872451]

*74. Falco G, Stanghellini I, Ko MS (2006). Use of Chuk as an internal standard suitable for quantitative RT-PCR in mouse preimplantation embryos. Reprod Biomed Online. 2006 Sep;13(3):394-403. PMID: 16984773 [PubMed – indexed for MEDLINE]

*75. Aiba K, Carter MG, Matoba R, Ko MSH (2006). Genomic approaches to early embryogenesis and stem cell biology. Semin Reprod Med. 2006 Nov;24(5):330-9. PMID: 17123228

*76. Sharov AA, Dudekula DB, Ko MSH (2006). CisView: a browser and database of cis-regulatory modules predicted in the mouse genome. DNA Res. 2006 Jun 30;13(3):123-34. Epub 2006 Sep 15. PMID: 16980320

77. Nakatake Y, Fukui N, Iwamatsu Y, Masui S, Takahashi K, Yagi R, Yagi K, Miyazaki J, Matoba R, Ko MS, Niwa H (2006). Klf4 cooperates with Oct3/4 and Sox2 to activate the Lefty1 core promoter in embryonic stem cells. Mol Cell Biol. 2006 Oct;26(20):7772-82. Epub 2006 Sep 5. PMID: 16954384 [PubMed – indexed for MEDLINE]

78. Hamatani T, Ko MSH, Yamada M, Kuji N, Mizusawa Y, Shoji M, Hada T, Asada H, Maruyama T, Yoshimura Y (2006). Global gene expression profiling of preimplantation embryos. Hum Cell. 2006 Aug;19(3):98-117.

*79. Matoba R, Niwa H, Masui S, Ohtsuka S, Carter MG, Sharov AA, Ko MS (2006). Dissecting oct3/4-regulated gene networks in embryonic stem cells by expression profiling. PLoS ONE. 2006 Dec 20;1:e26. PMID: 17183653 [PubMed – as supplied by publisher]

80. Masui S, Nakatake Y, Toyooka Y, Shimosato D, Yagi R, Takahashi K, Okochi H, Okuda A, Matoba R, Sharov AA, Ko MS, Niwa H (2007). Pluripotency governed by Sox2 via regulation of Oct3/4 expression in mouse embryonic stem cells. Nat Cell Biol. 2007 Jun;9(6):625-35. Epub 2007 May 21. PMID: 17515932 [PubMed – indexed for MEDLINE]

*81. Falco G, Lee SL, Stanghellini I, Bassey UC, Hamatani T, Ko MS (2007). Zscan4: a novel gene expressed exclusively in late 2-cell embryos and embryonic stem cells. Dev Biol.2007 Jul 15;307(2):539-50. Epub 2007 May 8. PMID: 17553482 [PubMed – indexed for MEDLINE]

*82. Sharova LV, Sharov AA, Piao Y, Shaik N, Sullivan T, Stewart CL, Hogan BL, Ko MS (2007). Global gene expression profiling reveals similarities and differences among mouse pluripotent stem cells of different origins and strains. Dev Biol. 2007 Jul 15;307(2):446-59. Epub 2007 May 10. PMID: 17560561 [PubMed – indexed for MEDLINE]

83. Ulloa-Montoya F, Kidder BL, Pauwelyn KA, Chase LG, Luttun A, Crabbe A, Geraerts M, Sharov AA, Piao Y, Ko MS, Hu WS, Verfaillie CM (2007). Comparative transcriptome analysis of embryonic and adult stem cells with extended and limited differentiation capacity. Genome Biol. 2007 Aug 6;8(8):R163 [Epub ahead of print] PMID: 17683608 [PubMed – as supplied by publisher]

84. Zahn JM, Poosala S, Owen AB, Ingram DK, Lustig A, Carter A, Weeraratna AT, Taub DD, Gorospe M, Mazan-Mamczarz K, Lakatta EG, Boheler KR, Xu X, Mattson MP, Falco G, Ko MS, Schlessinger D, Firman J, Kummerfeld SK, Wood WH 3rd, Zonderman AB, Kim SK, Becker KG. (2007). AGEMAP: a gene expression database for aging in mice. PLoS Genet. 2007 Nov 30;3(11):e201. Epub 2007 Oct 2. PMID: 18081424 [PubMed – in process]

85. Kaneda A, Wang CJ, Cheong R, Timp W, Onyango P, Wen B, Iacobuzio-Donahue CA, Ohlsson R, Andraos R, Pearson MA, Sharov AA, Longo DL, Ko MS, Levchenko A, Feinberg AP (2007). Enhanced sensitivity to IGF-II signaling links loss of imprinting of IGF2 to increased cell proliferation and tumor risk. Proc Natl Acad Sci U S A. 2007 Dec 26;104(52):20926-31. Epub 2007 Dec 17. PMID: 18087038 [PubMed – in process]

*86. Carter MG, Stagg CA, Falco G, Yoshikawa T, Bassey UC, Aiba K, Sharova LV, Shaik N, Ko MS (2007). An in situ hybridization-based screen for heterogeneously expressed genes in mouse ES cells. Gene Expr Patterns. 2007 Nov 4; [Epub ahead of print] PMID: 18178135 [PubMed – as supplied by publisher]

*87. Yan Z, Wang Z, Sharova L, Sharov AA, Ling C, Piao Y, Aiba K, Matoba R, Wang W, and Ko MS (2008). BAF250B-associated SWI/SNF chromatin-remodeling complex is required to maintain undifferentiated mouse embryonic stem cells. Stem Cells. 2008 May;26(5):1155-65. Epub 2008 Mar 6. [PMID: 18323406]

88. Vallée M, Aiba K, Piao Y, Palin MF, Ko MS, and Sirard MA (2008). Comparative analysis of oocyte transcript profiles reveals a high degree of conservation among species. Reproduction. 2008 Apr;135(4):439-48. [PMID: 18367505]

89. Masui S, Ohtsuka S, Yagi R, Takahashi K, Ko MS, and Niwa H (2008). Rex1/Zfp42 is dispensable for pluripotency in mouse ES cells. BMC Dev Biol. 2008 Apr 24;8:45. [PMID: 18433507]

*90. Sharov AA, Falco G, Piao Y, Poosala S, Becker KG, Zonderman AB, Longo DL, Schlessinger D, and Ko MSH (2008). Effects of aging and calorie restriction on the global gene expression profiles of mouse testis and ovary. BMC Biol. 2008 Jun 3;6:24. [PMID: 18522719]

*91. Sharov AA, Masui S, Sharova LV, Piao Y, Aiba K, Matoba R, Xin L, Niwa H, and Ko MS (2008). Identification of Pou5f1, Sox2, and Nanog downstream target genes with statistical confidence by applying a novel algorithm to time course microarray and genome-wide chromatin immunoprecipitation data. BMC Genomics. 2008 Jun 3;9:269. [PMID: 18522731]

92. Tsuji Y, Yoshimura N, Aoki H, Sharov AA, Ko MS, Motohashi T, and Kunisada T (2008). Maintenance of undifferentiated mouse embryonic stem cells in suspension by the serum- and feeder-free defined culture condition. Dev Dyn. 2008 Aug;237(8):2129-38. [PMID: 18624284]

*93. Yellaboina S, Dudekula DB, and Ko MSH (2008). Prediction of evolutionarily conserved interologs in Mus musculus. BMC Genomics. 2008 Oct 8;9:465. [PMID: 18842131]

94. Landry J, Sharov AA, Piao Y, Sharova LV, Xiao H, Southon E, Matta J, Tessarollo L, Zhang YE, Ko MS, Kuehn MR, Yamaguchi TP, and Wu C (2008). Essential role of chromatin remodeling protein Bptf in early mouse embryos and embryonic stem cells. PLoS Genet. 2008 Oct;4(10):e1000241. [PMID: 18974875]

*95. Sharova LV, Sharov AA, Nedorezov T, Piao Y, Shaik N, and Ko MS (2008). Database for mRNA Half-Life of 19 977 Genes Obtained by DNA Microarray Analysis of Pluripotent and Differentiating Mouse Embryonic Stem Cells. DNA Res. 2008 Nov 11. [PMID: 19001483]

*96. Aiba K, Nedorezov T, Piao Y, Nishiyama A, Matoba R, Sharova LV, Sharov AA, Yamanaka S, Niwa H, Ko MS (2009). Defining developmental potency and cell lineage trajectories by expression profiling of differentiating mouse embryonic stem cells. DNA Res. 2009 Feb;16(1):73-80. Epub 2008 Dec 26. PMID: 19112179 [PMCID: PMC2644347]

97. Kunisada M, Cui CY, Piao Y, Ko MS, Schlessinger D (2009). Requirement for Shh and Fox family genes at different stages in sweat gland development. Hum Mol Genet. 2009 May 15;18(10):1769-78. Epub 2009 Mar 6. PMID: 19270025 [PMCID: PMC2671986]

98. Sun C, Nakatake Y, Akagi T, Ura H, Matsuda T, Nishiyama A, Koide H, Ko MS, Niwa H, Yokota T (2009). Dax1 Binds to Oct3/4 and Inhibits Its Transcriptional Activity in Embryonic Stem Cells. Mol Cell Biol. 2009 Jun 15. [PMID: 19528230]

*99. Stanghellini I, Falco G, Lee SL, Monti M, Ko MS (2009). Trim43a, Trim43b, and Trim43c: Novel mouse genes expressed specifically in mouse preimplantation embryos. Gene Expr Patterns. 2009 Dec;9(8):595-602. Epub 2009 Aug 22. PMID: 19703589.

*100. Sharov AA, Ko MS (2009). Exhaustive search for over-represented DNA sequence motifs with CisFinder. DNA Res. 2009 Oct;16(5):261-73. Epub 2009 Sep 9. PMID: 19740934.

101. Vallejo G, Maschi D, Mestre-Citrinovitz AC, Aiba K, Maronna R, Yohai V, Ko MS, Beato M, Saragüeta P (2010). Changes in global gene expression during in vitro decidualization of rat endometrial stromal cells. J Cell Physiol. 2010 Jan;222(1):127-37. PMID: 19780023.

*102. Nishiyama A, Xin L, Sharov AA, Thomas M, Mowrer G, Meyers E, Piao Y, Mehta S, Yee S, Nakatake Y, Stagg C, Sharova L, Correa-Cerro LS, Bassey U, Hoang H, Kim E, Tapnio R, Qian Y, Dudekula D, Zalzman M, Li M, Falco G, Yang HT, Lee SL, Monti M, Stanghellini I, Islam MN, Nagaraja R, Goldberg I, Wang W, Longo DL, Schlessinger D, Ko MS (2009). Uncovering early response of gene regulatory networks in ESCs by systematic induction of transcription factors. Cell Stem Cell. 2009 Oct 2;5(4):420-33. PMID: 19796622. [PMC2770715]

*103. Sharov AA, Ko MS (2009). Exhaustive search for over-represented DNA sequence motifs with CisFinder. DNA Res 2009; 16(5): 261-73. [PMC2762409]

*104. Sharova LV, Sharov AA, Nedorezov T, Piao Y, Shaik N, Ko MS (2009). Database for mRNA half-life of 19 977 genes obtained by DNA microarray analysis of pluripotent and differentiating mouse embryonic stem cells. DNA Res 2009; 16(1): 45-58. [PMC2644350]

*105. Stanghellini I, Falco G, Lee SL, Monti M, Ko MS (2009). Trim43a, Trim43b, and Trim43c: Novel mouse genes expressed specifically in mouse preimplantation embryos. Gene Expr Patterns 2009; 9(8): 595-602. [PMC2784184]

106. Sun C, Nakatake Y, Akagi T, Ura H, Matsuda T, Nishiyama A, Koide H, Ko MS, Niwa H, Yokota T (2009). Dax1 binds to Oct3/4 and inhibits its transcriptional activity in embryonic stem cells. Mol Cell Biol 2009; 29(16): 4574-83. [PMC2725734]

107. Canham MA, Sharov AA, Ko MS, Brickman JM (2010). Functional heterogeneity of embryonic stem cells revealed through translational amplification of an early endodermal transcript. PLoS Biol 2010; 8(5): e1000379. [PMC2876051]

108. Cui CY, Kunisada M, Piao Y, Childress V, Ko MS, Schlessinger D (2010). Dkk4 and Eda regulate distinctive developmental mechanisms for subtypes of mouse hair. PLoS One 2010; 5(4): e10009. [PMC2850388]

*109. Sharov AA, Piao Y, Ko MS (2010). Gene expression profiling of mouse embryos with microarrays. Methods Enzymol 2010; 477: 511-41. [PMC3166619]

110. Vong QP, Liu Z, Yoo JG, Chen R, Xie W, Sharov AA, Fan CM, Liu C, Ko MS, Zheng Y (2010). A role for borg5 during trophectoderm differentiation. Stem Cells 2010; 28(6): 1030-8. [PMC2957878]

*111. Zalzman M, Falco G, Sharova LV, Nishiyama A, Thomas M, Lee SL, Stagg CA, Hoang HG, Yang HT, Indig FE, Wersto RP, Ko MS (2010). Zscan4 regulates telomere elongation and genomic stability in ES cells. Nature 2010; 464(7290): 858-63. [PMC2851843]

*112. Correa-Cerro LS, Piao Y, Sharov AA, Nishiyama A, Cadet JS, Yu H, Sharova LV, Xin L, Hoang HG, Thomas M, Qian Y, Dudekula DB, Meyers E, Binder BY, Mowrer G, Bassey U, Longo DL, Schlessinger D, Ko MS (2011). Generation of mouse ES cell lines engineered for the forced induction of transcription factors. Sci Rep 2011; 1: 167. [PMC3240988]

*113. Kim Y, Sharov AA, McDole K, Cheng M, Hao H, Fan CM, Gaiano N, Ko MS, Zheng Y (2011). Mouse B-type lamins are required for proper organogenesis but not by embryonic stem cells. Science 2011; 334(6063): 1706-10. [PMC3306219]

*114. Sharov AA, Nishiyama A, Piao Y, Correa-Cerro LS, Amano T, Thomas M, Mehta S, Ko MS (2011). Responsiveness of genes to manipulation of transcription factors in ES cells is associated with histone modifications and tissue specificity. BMC Genomics 2011; 12: 102. [PMC3044670]

115. Cui CY, Childress V, Piao Y, Michel M, Johnson AA, Kunisada M, Ko MS, Kaestner KH, Marmorstein AD, Schlessinger D (2012). Forkhead transcription factor FoxA1 regulates sweat secretion through Bestrophin 2 anion channel and Na-K-Cl cotransporter 1. Proc Natl Acad Sci U S A 2012; 109(4): 1199-203. [PMC3268268]

116. Hammachi F, Morrison GM, Sharov AA, Livigni A, Narayan S, Papapetrou EP, O’Malley J, Kaji K, Ko MS, Ptashne M, Brickman JM (2012). Transcriptional activation by Oct4 is sufficient for the maintenance and induction of pluripotency. Cell Rep 2012; 1(2): 99-109.

*117. Hirata T, Amano T, Nakatake Y, Amano M, Piao Y, Hoang HG, Ko MS (2012). Zscan4 transiently reactivates early embryonic genes during the generation of induced pluripotent stem cells. Sci Rep 2012; 2: 208. [PMC3250575]

118. Ko SB, Azuma S, Yoshikawa T, Yamamoto A, Kyokane K, Ko MS, Ishiguro H (2012). Molecular mechanisms of pancreatic stone formation in chronic pancreatitis. Front Physiol 2012; 3: 415. [PMC3488765]

119. States JC, Singh AV, Knudsen TB, Rouchka EC, Ngalame NO, Arteel GE, Piao Y, Ko MS (2012). Prenatal arsenic exposure alters gene expression in the adult liver to a proinflammatory state contributing to accelerated atherosclerosis. PLoS One 2012; 7(6): e38713. [PMC3376138]

120. Xie H, Sun X, Piao Y, Jegga AG, Handwerger S, Ko MS, Dey SK (2012). Silencing or amplification of endocannabinoid signaling in blastocysts via CB1 compromises trophoblast cell migration. J Biol Chem 2012; 287(38): 32288-97. [PMC3442559]

*121. Yang HT, Ko MS (2012). Stochastic modeling for the expression of a gene regulated by competing transcription factors. PLoS One 2012; 7(3): e32376. [PMC3303788]

*122. Hung SS, Wong RC, Sharov AA, Nakatake Y, Yu H, Ko MS (2013). Repression of global protein synthesis by eif1a-like genes that are expressed specifically in the two-cell embryos and the transient zscan4-positive state of embryonic stem cells. DNA Res 2013; 20(4): 391-402. [PMC3738165]

123. Ko SB, Azuma S, Yokoyama Y, Yamamoto A, Kyokane K, Niida S, Ishiguro H, Ko MS (2013). Inflammation increases cells expressing ZSCAN4 and progenitor cell markers in the adult pancreas. Am J Physiol Gastrointest Liver Physiol 2013; 304(12): G1103-16. [PMC3680719]

124. Monti M, Zanoni M, Calligaro A, Ko MS, Mauri P, Redi CA (2013). Developmental arrest and mouse antral not-surrounded nucleolus oocytes. Biol Reprod 2013; 88(1): 2.

125. Morgani SM, Canham MA, Nichols J, Sharov AA, Migueles RP, Ko MS, Brickman JM (2013). Totipotent embryonic stem cells arise in ground-state culture conditions. Cell Rep 2013; 3(6): 1945-57. [PMC3701323]

*126. Nishiyama A, Sharov AA, Piao Y, Amano M, Amano T, Hoang HG, Binder BY, Tapnio R, Bassey U, Malinou JN, Correa-Cerro LS, Yu H, Xin L, Meyers E, Zalzman M, Nakatake Y, Stagg C, Sharova L, Qian Y, Dudekula D, Sheer S, Cadet JS, Hirata T, Yang HT, Goldberg I, Evans MK, Longo DL, Schlessinger D, Ko MS (2013). Systematic repression of transcription factors reveals limited patterns of gene expression changes in ES cells. Sci Rep 2013; 3: 1390. [PMC3589720]

*127. Amano T, Hirata T, Falco G, Monti M, Sharova LV, Amano M, Sheer S, Hoang HG, Piao Y, Stagg CA, Yamamizu K, Akiyama T, Ko MS (2013). Zscan4 restores the developmental potency of embryonic stem cells. Nat Commun 2013; 4: 1966. [PMC3682791]

128. Xu D, Shen W, Guo R, Xue Y, Peng W, Sima J, Yang J, Sharov A, Srikantan S, Yang J, Fox D, 3rd, Qian Y, Martindale JL, Piao Y, Machamer J, Joshi SR, Mohanty S, Shaw AC, Lloyd TE, Brown GW, Ko MS, Gorospe M, Zou S, Wang W (2013). Top3beta is an RNA topoisomerase that works with fragile X syndrome protein to promote synapse formation. Nat Neurosci 2013.

129. Livigni A, Peradziryi H, Sharov AA, Chia G, Hammachi F, Migueles RP, Sukparangsi W, Pernagallo S, Bradley M, Nichols J, Ko MS, Brickman JM (2013). A conserved Oct4/POUV-dependent network links adhesion and migration to progenitor maintenance. Curr Biol. 2013 Nov 18;23(22):2233-44. doi:10.1016/j.cub.2013.09.048. PMID:24210613

*130. Yamamizu K, Piao Y, Sharov AA, Zsiros V, Yu H, Nakazawa K, Schlessinger D, Ko MS (2013). Identification of transcription factors for lineage-specific ESC differentiation. Stem Cell Reports. 2013 Nov 27;1(6):545-59. doi: 10.1016/j.stemcr.2013.10.006. PMID:24371809

131. Sherman-Baust CA, Kuhn E, Valle BL, Shih IeM, Kurman RJ, Wang TL, Amano T, Ko MS, Miyoshi I, Araki Y, Lehrmann E, Zhang Y, Becker KG, Morin PJ (2014). A genetically engineered ovarian cancer mouse model based on fallopian tube transformation mimics human high-grade serous carcinoma development. J Pathol. 2014 Jul;233(3):228-37. doi: 10.1002/path.4353. PMID:24652535

*132. Piao Y, Hung SS, Lim SY, Wong RC, Ko MS (2014). Efficient generation of integration-free human induced pluripotent stem cells from keratinocytes by simple transfection of episomal vectors. Stem Cells Transl Med. 2014 Jul;3(7):787-91. doi: 10.5966/sctm.2013-0036. PMID:24904173

*133. Sharov AA, Nishiyama A, Qian Y, Dudekula DB, Longo DL, Schlessinger D, Ko MS (2014). Chromatin properties of regulatory DNA probed by manipulation of transcription factors. J Comput Biol. 2014 Aug;21(8):569-77. doi: 10.1089/cmb.2013.0126. PMID:24918633

*134. Yamamizu K, Schlessinger D, Ko MS (2014). SOX9 accelerates ESC differentiation to three germ layer lineages by repressing SOX2 expression through P21 (WAF1/CIP1). Development. 2014 Nov;141(22):4254-66. doi: 10.1242/dev.115436. PMID:25371362

*135. Sharov AA, Schlessinger D, Ko MS (2015). ExAtlas: An interactive online tool for meta-analysis of gene expression data. J Bioinform Comput Biol. 2015 Dec;13(6):1550019. doi: 10.1142/S0219720015500195. PMID:26223199

*136. Amano T, Jeffries E, Amano M, Ko AC, Yu H, Ko MS (2015). Correction of Down syndrome and Edwards syndrome aneuploidies in human cell cultures. DNA Res. 2015 Oct;22(5):331-42. doi: 10.1093/dnares/dsv016. PMID:26324424

*137. Akiyama T, Xin L, Oda M, Sharov AA, Amano M, Piao Y, Cadet JS, Dudekula DB, Qian Y, Wang W, Ko SB, Ko MS (2015). Transient bursts of Zscan4 expression are accompanied by the rapid derepression of heterochromatin in mouse embryonic stem cells. DNA Res. 2015 Oct;22(5):307-18. doi: 10.1093/dnares/dsv013. PMID:26324425

138. Motohashi T, Watanabe N, Nishioka M, Nakatake Y, Yulan P, Mochizuki H, Kawamura Y, Ko MS, Goshima N, Kunisada T (2016). Gene array analysis of neural crest cells identifies transcription factors necessary for direct conversion of embryonic fibroblasts into neural crest cells. Biol Open. 2016 Feb 12;5(3):311-22. doi: 10.1242/bio.015735. PMID:26873953

*139. Sharova LV, Sharov AA, Piao Y, Stagg CA, Amano T, Qian Y, Dudekula D, Schlessinger D, Ko MS (2016). Emergence of undifferentiated colonies from mouse embryonic stem cells undergoing differentiation by retinoic acid treatment. In Vitro Cell Dev Biol Anim. 2016 May;52(5):616-24. doi: 10.1007/s11626-016-0013-5. PMID:27130680

*140. Yamamizu K, Sharov AA, Piao Y, Amano M, Yu H, Nishiyama A, Dudekula DB, Schlessinger D, Ko MS (2016). Generation and gene expression profiling of 48 transcription-factor-inducible mouse embryonic stem cell lines. Sci Rep. 2016 May 6;6:25667. doi: 10.1038/srep25667. PMID:27150017

*141. Ko MS (2016). Zygotic Genome Activation Revisited: Looking Through the Expression and Function of Zscan4. Curr Top Dev Biol. 2016;120:103-24. doi: 10.1016/bs.ctdb.2016.04.004. PMID:27475850

*142. Ishiguro KI, Nakatake Y, Chikazawa-Nohtomi N, Kimura H, Akiyama T, Oda M, Ko SB, Ko MS (2016). Expression analysis of the endogenous Zscan4 locus and its coding proteins in mouse ES cells and preimplantation embryos. In Vitro Cell Dev Biol Anim. 2016 Oct 3. PMID:27699651

*143. Ishiguro KI, Monti M, Akiyama T, Kimura H, Chikazawa-Nohtomi N, Sakota M, Sato S, Redi CA, Ko SB, Ko MS (2016). Zscan4 is expressed specifically during late meiotic prophase in both spermatogenesis and oogenesis. In Vitro Cell Dev Biol Anim. 2016 Oct 3. PMID:27699653

144. Teratani-Ota Y, Yamamizu K, Piao Y, Sharova L, Amano M, Yu H, Schlessinger D, Ko MS, Sharov AA (2016). Induction of specific neuron types by overexpression of single transcription factors. In Vitro Cell Dev Biol Anim. 2016 Oct;52(9):961-973. PMID:27251161

*145. Akiyama T, Wakabayashi S, Soma A, Sato S, Nakatake Y, Oda M, Murakami M, Sakota M, Chikazawa-Nohtomi N, Ko SB, Ko MS (2016). Transient ectopic expression of the histone demethylase JMJD3 accelerates the differentiation of human pluripotent stem cells. Development. 2016 Oct 15;143(20):3674-3685. PMID:27802135

*146. Hirayama M, Ko SB, Kawakita T, Akiyama T, Goparaju SK, Soma A, Nakatake Y, Sakota M, Chikazawa-Nohtomi N, Shimmura S, Tsubota K, Ko MS (2017). Identification of transcription factors that promote the differentiation of human pluripotent stem cells into lacrimal gland epithelium-like cells. npj Aging and Mechanisms of Disease 2017; 3: 1. doi:10.1038/s41514-016-0001-8

*147. Goparaju SK, Kohda K, Ibata K, Soma A, Nakatake Y, Akiyama T, Wakabayashi S, Matsushita M, Sakota M, Kimura H, Yuzaki M, Ko SB, Ko MS (2017). Rapid differentiation of human pluripotent stem cells into functional neurons by mRNAs encoding transcription factors. Sci Rep. 2017 Feb 13;7:42367. doi: 10.1038/srep42367. PMID: 28205555

148. Matsumoto H, Kiryu H, Furusawa C, Ko MS, Ko SB, Gouda N, Hayashi T, Nikaido I (2017). SCODE: An efficient regulatory network inference algorithm from single-cell RNA-Seq during differentiation. Bioinformatics. 2017 Apr 4. doi: 10.1093/bioinformatics/btx194. PMID:28379368

149. Arai Y, Takahashi D, Asano K, Tanaka M, Oda M, Ko SBH, Ko MSH, Mandai S, Nomura N, Rai T, Uchida S, Sohara E (2017). Salt suppresses IFNγ inducible chemokines through the IFNγ-JAK1-STAT1 signaling pathway in proximal tubular cells. Sci Rep. 2017 Apr 20;7:46580. doi: 10.1038/srep46580. PMID:28425456

*150. Akiyama T, Wakabayashi S, Soma A, Sato S, Nakatake Y, Oda M, Murakami M, Sakota M, Chikazawa-Nohtomi N, Ko SBH, Ko MSH (2017). Epigenetic Manipulation Facilitates the Generation of Skeletal Muscle Cells from Pluripotent Stem Cells. Stem Cells Int. 2017; 2017:7215010. doi: 10.1155/2017/7215010. Epub 2017 Apr 9. Review. PMID:28491098

*151. Matsushita M, Nakatake Y, Arai I, Ibata K, Kohda K, Goparaju SK, Murakami M, Sakota M, Chikazawa-Nohtomi N, Ko SBH, Kanai T, Yuzaki M, Ko MSH (2017). Neural differentiation of human embryonic stem cells induced by the transgene-mediated overexpression of single transcription factors. Biochem Biophys Res Commun. 2017 Aug 19;490(2):296-301. Doi 10.1016/j.bbrc.2017.06.039. Epub 2017 Jun 10. PMID: 28610919

*152. Akiyama T, Sato S, Chikazawa-Nohtomi N, Soma A, Kimura H, Wakabayashi S, Ko SBH, Ko MSH (2018). Efficient differentiation of human pluripotent stem cells into skeletal muscle cells by combining RNA-based MYOD1-expression and POU5F1-silencing. Sci Rep. 2018 Jan 19;8(1):1189. doi: 10.1038/s41598-017-19114-y. PMID: 29352121

153. Ida H, Akiyama T, Ishiguro K, Goparaju SK, Nakatake Y, Chikazawa-Nohtomi N, Sato S, Kimura H, Yokoyama Y, Nagino M, Ko MSH, Ko SBH (2018). Establishment of a rapid and footprint-free protocol for differentiation of human embryonic stem cells into pancreatic endocrine cells with synthetic mRNAs encoding transcription factors. Stem Cell Res Ther. 2018 Oct 25;9(1):277. doi: 10.1186/s13287-018-1038-3.

*154. Hiratsuka K, Monkawa T, Akiyama T, Nakatake Y, Oda M, Goparaju SK, Kimura H, Chikazawa-Nohtomi N, Sato S, Ishiguro K, Yamaguchi S, Suzuki S, Morizane R, Ko SBH, Itoh H, Ko MSH (2019). Induction of human pluripotent stem cells into kidney tissues by synthetic mRNAs encoding transcription factors. Sci Rep. 2019 Jan 29;9(1):913. doi: 10.1038/s41598-018-37485-8. PMID: 30696889 Free PMC Article

155. Nishihara K, Shiga T, Nakamura E, Akiyama T, Sasaki T, Suzuki S, Ko MSH, Tada N, Okano H, Akamatsu W (2019). Induced Pluripotent Stem Cells Reprogrammed with Three Inhibitors Show Accelerated Differentiation Potentials with High Levels of 2-Cell Stage Marker Expression. Stem Cell Reports. 2019 Feb 12;12(2):305-318. doi: 10.1016/j.stemcr.2018.12.018. Epub 2019 Jan 31. PMID: 30713040 Free PMC Article

156. Ishiguro KI, Matsuura K, Tani N, Takeda N, Usuki S, Yamane M, Sugimoto M, Fujimura S, Hosokawa M, Chuma S, Ko MSH, Araki K, Niwa H (2020). MEIOSIN Directs the Switch from Mitosis to Meiosis in Mammalian Germ Cells. Dev Cell. 2020 Feb 24;52(4):429-445.e10. doi: 10.1016/j.devcel.2020.01.010. Epub 2020 Feb 6. PMID: 32032549

*157. Nakatake Y, Ko SBH, Sharov AA, Wakabayashi S, Murakami M, Sakota M, Chikazawa N, Ookura C, Sato S, Ito N, Ishikawa-Hirayama M, Mak SS, Jakt LM, Ueno T, Hiratsuka K, Matsushita M, Goparaju SK, Akiyama T, Ishiguro KI, Oda M, Gouda N, Umezawa A, Akutsu H, Nishimura K, Matoba R, Ohara O, Ko MSH (2020). Generation and Profiling of 2,135 Human ESC Lines for the Systematic Analyses of Cell States Perturbed by Inducing Single Transcription Factors. Cell Rep. 2020 May 19;31(7):107655. doi: 10.1016/j.celrep.2020.107655. PMID: 32433964

158. Tanosaki S, Tohyama S, Fujita J, Someya S, Hishiki T, Matsuura T, Nakanishi H, Ohto-Nakanishi T, Akiyama T, Morita Y, Kishino Y, Okada M, Tani H, Soma Y, Nakajima K, Kanazawa H, Sugimoto M, Ko MSH, Suematsu M, Fukuda K (2020). Fatty Acid Synthesis Is Indispensable for Survival of Human Pluripotent Stem Cells. iScience. 2020 Sep 6;23(9):101535. doi: 10.1016/j.isci.2020.101535.

159. Akiyama T, Sato S, Ko SBH, Sano O, Sato S, Saito M, Nagai H, Ko MSH, Iwata H (2020). Synthetic mRNA-based differentiation method enables early detection of Parkinson’s phenotypes in neurons derived from Gaucher disease-induced pluripotent stem cells. Stem Cells Transl Med. 2021 Apr;10(4):572-581. doi: 10.1002/sctm.20-0302. Epub 2020 Dec 20. PMID: 33342090

160. Makino K, Shimizu-Hirota R, Goda N, Hashimoto M, Kawada I, Kashiwagi K, Hirota Y, Itoh H, Jinzaki M, Iwao Y, Ko M, Ko S, Takaishi H (2021). Unbiased, comprehensive analysis of Japanese health checkup data reveals a protective effect of light to moderate alcohol consumption on lung function. Sci Rep. 2021 Aug 5;11(1):15954. doi: 10.1038/s41598-021-95515-4. PMID: 34354190

161. Tanosaki S, Akiyama T, Kanaami S, Fujita J, Ko MSH, Fukuda K, Tohyama S (2022). Purification of cardiomyocytes and neurons derived from human pluripotent stem cells by inhibition of de novo fatty acid synthesis. STAR Protoc. 2022 Apr 28;3(2):101360. doi: 10.1016/j.xpro.2022.101360. eCollection 2022 Jun 17. PMID: 35516845

*162. Amano T, Yu H, Amano M, Leyder E, Badiola M, Ray P, Kim J, Ko AC, Achour A, Weng NP, Kochba E, Levin Y, Ko MSH (2023). Controllable self-replicating RNA vaccine delivered intradermally elicits predominantly cellular immunity. iScience. 2023 Mar 5;26(4):106335. doi10.1016/j.isci.2023.106335. eCollection 2023 Apr 21. PMID: 36968065

163. Kobori C, Takagi R, Yokomizo R, Yoshihara S, Mori M, Takahashi H, Javaregowda PK, Akiyama T, Ko MSH, Kishi K, Umezawa A (2023). Functional and long-lived melanocytes from human pluripotent stem cells with transient ectopic expression of JMJD3. Stem Cell Res Ther. 2023 Sep 8;14(1):242. doi: 10.1186/s13287-023-03479-1. PMID: 37679843.

164. Choy C, Chen J, Li J, Gallagher DT, Lu J, Wu D, Zou A, Hemani H, Baptiste BA, Wichmann E, Yang Q, Ciffelo J, Yin R, McKelvy J, Melvin D, Wallace T, Dunn C, Nguyen C, Chia CW, Fan J, Ruffolo J, Zukley L, Shi G, Amano T, An Y, Meirelles O, Wu WW, Chou CK, Shen RF, Willis RA, Ko MSH, Liu YT, De S, Pierce BG, Ferrucci L, Egan J, Mariuzza R, Weng NP (2023). SARS-CoV-2 infection establishes a stable and age-independent CD8+ T cell response against a dominant nucleocapsid epitope using restricted T cell receptors. Nat Commun. 2023 Oct 23;14(1):6725. doi: 10.1038/s41467-023-42430-z. PMID: 37872153.

165. Arora S, Yang J, Akiyama T, James DQ, Morrissey A, Blanda T, Badjatia N, Lai WKM, Ko MSH, Pugh BF, Mahony S (2023). Joint sequence & chromatin neural networks characterize the differential abilities of Forkhead transcription factors to engage inaccessible chromatin. bioRxiv. 2023 Oct 31:2023.10.06.561228. doi: 10.1101/2023.10.06.561228. Preprint. PMID: 37873361.

166. Koseki T, Teramachi M, Koga M, Ko MSH, Amano T, Yu H, Amano M, Leyder E, Badiola M, Ray P, Kim J, Ko AC, Achour A, Weng NP, Imai T, Yoshida H, Taniuchi S, Shintani A, Fujigaki H, Kondo M, Doi Y (2023). A Phase I/II Clinical Trial of Intradermal, Controllable Self-Replicating Ribonucleic Acid Vaccine EXG-5003 against SARS-CoV-2. Vaccines (Basel). 2023 Nov 27;11(12):1767. doi: 10.3390/vaccines11121767. PMID: 38140172 Free PMC article.

*167. Akiyama T, Ishiguro KI, Chikazawa N, Ko SBH, Yukawa M, Ko MSH (2024). ZSCAN4-binding motif-TGCACAC is conserved and enriched in CA/TG microsatellites in both mouse and human genomes. DNA Res. 2024 Feb 1;31(1):dsad029. doi: 10.1093/dnares/dsad029. PMID: 38153767 Free PMC article.

*168. Myers KC, Davies SM, Lutzko C, Wahle R, Grier DD, Aubert G, Norris K, Baird DM, Koga M, Ko AC, Amano T, Amano M, Yu H, Ko MSH (2025). Clinical Use of ZSCAN4 for Telomere Elongation in Hematopoietic Stem Cells. NEJM Evid. 2025 Mar;4(3):EVIDoa2400252. doi: 10.1056/EVIDoa2400252. Epub 2025 Feb 25. PMID: 39998303 Clinical Trial.

169. Morita A, Ishii M, Asakura T, Yotsukura M, Hegab AE, Kusumoto T, Namkoong H, Ogawa T, Nakatake Y, Oda M, Saito F, Kamata H, Hamamoto J, Okamori S, Ebisudani T, Yasuda H, Sugimoto S, Kuze Y, Seki M, Suzuki Y, Hasegawa N, Asamura H, Watanabe H, Ko M, Sato T, Ieda M, Fukunaga K (2025). Direct reprogramming of mouse fibroblasts into self-renewable alveolar epithelial-like cells. NPJ Regen Med. 2025 Jun 23;10(1):30. doi: 10.1038/s41536-025-00411-4. PMID: 40550799 Free PMC article. Preprint.

Reviews and Book Chapters (*corresponding author)

*1. Ko M SH (1995). Equalized cDNA libraries. In: Larrick, J.W., and Siebert, P.D. (Eds). Reverse Transcriptase PCR. London, Ellis Horwood, 1995, pp. 245-264.

2. Chen G., Jaradat SA, Banerjee N, Tanaka TS, Ko MSH, and Zhang MQ (2002). Evaluation and Comparison of Clustering Algorithms in Analyzing ES Cell Gene Expression Data. Statistica Sinica 12: 241-262, 2002.

*3. Kimber WL, Piao Y, Tanaka TS, Yoshikawa T, Hamatani T, Carter MG, and Ko MSH (2003). Systematic Analysis of Mouse Preimplantation Development. In: Watson, A. (Ed). Mammalian Embryo Genomics: Biological Resource Management in Agriculture. Paris, OECD (Organization for Economic Co-Operation and Development), 2003, pp. 37-46.

4. Ottolenghi, C., Uda, M., Hamatani, T., Crisponi, L., Garcia, Jose-Elias., Ko, M.S.H., Pilia, G., Sforza, C., Schlessinger, D., and Forabosco, A (2004). Aging of Oocyte, Ovary and Human Reproduction.Ann. New York Acad. Sci. 1034: 117-131, 2004.

*5. Tanaka TS, Carter MG, Aiba K, Jaradat SA, and Ko MSH (2004). Genomic approaches to stem cell biology. In: Odorico, J.S., Pederson, R.A., and Zhang, S.U. (Eds): Human Pluripotent Stem Cells.New York, BIOS Scientific Publishers Ltd, 2004, pp. 339-361.

*6. VanBuren V, and Ko MSH (2004). Principles and Application of Embryogenomics. In: Meyers, R.A. (Ed.): Encyclopedia of Molecular Cell Biology and Molecular Medicine, 2^nd Edition. Weinheim, WILEY-VCH, 2004, pp. 529-555.

*7. VanBuren V, and Ko MSH (2004). Regulation of genome activity and genetic networks in mammals. In: Ruvinsky, A., and Graves, J.M. (Eds): Mammalian Genomics. Cambridge, CABI Publishing, 2004, pp. 201-220.

*8. Ko MSH (2005). Molecular biology of preimplantation embryos: primer for philosophical discussions. Reprod. Biomed. Online 10 Suppl 1: 80-87, 2005.

9. McMahan J, Cohen J, Ko MSH, Johnson M, Robertson J, Murphy T, Brinsden P, Hussein F, Savulescu J, McLaren A, McLean S, Harris J, Schulman J, Edwards R, Pedersen R, Stock G, Grudzinskas G, and Boivin J (2005). Discussion (day 2 session 2): Modern genetics and the human embryo in vitro. Reprod. Biomed. Online10 Suppl 1: 107-110, 2005.

*10. Ko MSH and McLaren A (2006). Epigenetics of germ cells, stem cells, and early embryos. Meeting Report. Dev. Cell 10, 161-166.

*11. Ko, M.S.H. (2006). Meet our Editor. Reprod Biomed Online. 12: 143.

*12. Sharov AA and Ko MSH (2007). Previews: Human ES cell profiling broadens the reach of bivalent domains. Cell Stem Cell 1, 237-238. [PMID: 18371354]

*13. Ko MSH (2008). Stem Cell Biology, Chapter 66, pages 66-1 – 66-3, Harrison’s Principles of Internal Medicine, 17^th Edition. (Eds. Fauci AS, Braunwald E, Kasper DL, Hauser SL, Longo DL, Jameson JL, Loscalzo J). McGraw-Hill, NY.

*14. Ko MSH (2011). Stem Cell Biology. In: Fauci, A.S., Braunwald, E., Kasper, D.L., Hauser, S.L., Longo, D.L., Jameson, J.L., and Loscalzo, J. (Eds.): Harrison’s Principles of Internal Medicine, 18th Edition. New York, McGraw-Hill.

*15. Ko MSH (2015). Stem Cell Biology. In: Fauci, A.S., Braunwald, E., Kasper, D.L., Hauser, S.L., Longo, D.L., Jameson, J.L., and Loscalzo, J. (Eds.): Harrison’s Principles of Internal Medicine, 19th Edition. New York, McGraw-Hill.

日本語総説など（抜粋）

1. 洪 実（1985）。遺伝子の発現調節と細胞の分化。「遺伝子工学入門－組み換えDNA実験は何を明らかにしたかー 高野 利也編著」南山堂。第７章 ７－８（pp. 249-256）

2. 洪 実（1993）。 均一化cDNAライブラリーとその応用。蛋白質核酸酵素 Vol.38, No. 3. （pp. 420-428）

3. 洪 実（1994）。 均一化cDNAライブラリーの作製法。「実験医学別冊バイオマニュアルシリーズ２、遺伝子ライブラリーの作製法。野島博編集」。羊土社。（pp. 135-144）

4. 洪 実（2001）。マウスの発生ゲノム学。「ポストシークエンスのゲノム科学４。ゲノムから個体へ　生命システムの理解に向けて 榊 佳之 (著, 編集), 小原 雄治 (編集)」中山書店。（pp. 135-146）

5. 中武 悠樹, 西山 晃, 洪 実（2012）。転写調節因子を自在に誘導できるES細胞バンクの作製とその応用。「再生医療を実現化する幹細胞のメディカルサイエンスstemnessと分化の制御、新規因子の発見から三次元組織形成など臨床につながる最新成果まで」実験医学 (0288-5514)30巻10号 Page1639-1645 (2012.06)

6. 洪 実（2013）。発生のシステム生物学と再生医療。発達腎研究会誌 (0919-7532) 21巻1号、 Page2-6　(2013.04)

7. 洪 繁、洪 実 (2013)。膵臓の組織修復と組織幹細胞。「実験医学増刊　臓器円環による恒常性の維持・変容・破綻」実験医学　2013.3、羊土社。

8. 天野 朋和, 洪 実（2014）。Zscan4によるテロメア維持と4倍体補完能の回復。「iPS細胞/ES細胞の生物学」遺伝: 生物の科学 (0387-0022)68巻1号 Page50-57(2014.01)。

9. 平田 哲也, 天野 朋和, 大須賀 穣, 洪 実（2014）。着床前期胚特異的遺伝子Zscan4と多能性幹細胞。産科と婦人科 (0386-9792)81巻3号 Page309-316(2014.03)。

10. 秋山 智彦, 洪 繁, 洪 実（2014）。着床前期胚、生殖細胞、幹細胞にかかわるZSCAN4。「生殖細胞-全能性を獲得し、世代を紡ぐサイクル」実験医学 (0288-5514)32巻6号 Page870-876(2014.04)。

11. 洪 実（2014）。幹細胞を維持する遺伝子ZSCAN4の発見。「血管!発見!物語」Vascular Medicine (1880-2478)10巻1号 Page77-81(2014.04)。

12. 洪 実（2014）。産婦人科臨床医のためのシステム生物学入門。「オミックスデータからみた婦人科疾患と遺伝情報の解釈-システム生物学の理解を通した婦人科腫瘍学の新展開」産科と婦人科 (0386-9792)81巻6号 Page689-693(2014.06)。

13. 山水 康平, 中武 悠樹, 洪 繁, 洪 実（2015）。分化誘導と分化転換転写因子を用いた多能性幹細胞から任意細胞への分化誘導法の開発。「再生医療2015幹細胞と疾患iPS細胞の研究最前線」実験医学 (0288-5514)33巻2号 Page239-246(2015.02)。

14. 秋山 智彦, 中武 悠樹, 山水 康平, 相馬 淳美, 洪 繁, 洪 実（2015）。転写因子操作による多能性幹細胞からの自在な細胞分化誘導技術の確立を目指して。「再生医療-新たな医療を求めて- 臨床応用を目指した基礎研究　再生医療を進めるための技術開発」日本臨床 (0047-1852)73巻、増刊5 、再生医療 Page330-336(2015.06) 。

15. 秋山智彦、小田真由美、石黒啓一郎、洪 繁、洪 実（2015）。Zscan4による特異的なヘテロクロマチン制御を介したマウスES細胞のゲノム安定化。「染色体研究Update」細胞工学　Vol.34, No.11, Page1052-1056　秀潤社　2015年10月22日発行。

16. 山水康平、洪 実（2013）。転写因子ネットワーク解析を応用した多能性幹細胞の分化誘導法。「再生医療と疾患解明の鍵となる組織幹細胞」実験医学　増刊。Vol. ６４，No.１７.　Page2949－2955。

17. 洪 繁、石井雅通、土井健太郎、洪 実（2016）。電子カルテ情報のビックデータ解析のための情報基盤：SS-MIX2全文検索エンジン・ビューアiDOC。「医療ビックデータをいかに解析するか」医学のあゆみ　Vol.259 No.7 2016 11/12　Page778-782。

18. 秋山 智彦、中武 悠樹、洪 繁、小原 収、的場 亮、阿久津 英憲、西村 邦裕、洪 実　（2021）。500以上の転写因子を個別に発現誘導できるヒトES細胞の樹立と解析。生物の科学　遺伝　2021。

19. 洪 繁, 秋山 智彦, GOPARAJU Sravan, 平山 雅敏, 洪 実（2017）。Quick-Tissueテクノロジー: ヒト転写因子合成mRNAを用いたヒト多能性幹細胞の新しい細胞分化誘導法とその将来展望。Bio Industry 34(8) 18‐28 2017。