• Yoshida J, Watanabe H, Yamauchi K, Nishikubo T, Isotani A, Ohtsuka S, Niwa H, Akutsu H, Umezawa A, Suemori H, Takashima Y, Kondoh G, Takeda J, Horie K*. Inhibition of N-myristoyltransferase Promotes Naive Pluripotency in Mouse and Human Pluripotent Stem Cells. bioRxiv doi: https://doi.org/10.1101/2021.06.22.449326.
• Kashiwagi K, Yoshida J, Kimura H, Shinjo K, Kondo Y, Horie K*. Mutation of the SWI/SNF complex component Smarce1 decreases nucleosome stability in ES cells and impairs differentiation. J Cell Sci 137(6):jcs260467, 2024. (PubMed)
• Onodera Y, Kobayashi J, Mitani S, Hosoda C, Banno K, Horie K, Okano T, Shimizu T, Shima M, Tatsumi K. Terminus-Selective Covalent Immobilization of Heparin on a Thermoresponsive Surface Using Click Chemistry for Efficient Binding of Basic Fibroblast Growth Factor. Macromol Biosci 24: e2300307, 2024. (PubMed)
• Higashitani Y and Horie K*. Long-read sequence analysis of MMEJ-mediated CRISPR genome editing reveals complex on-target vector insertions that may escape standard PCR-based quality control. Scientific Rep 13: 11652, 2023. (PubMed)
• Miyata M, Yoshida J, Takagishi I, Horie K*. Comparison of CRISPR/Cas9-mediated Megabase-scale Genome Deletion Methods in Mouse Embryonic Stem Cells. DNA Res 30: dsac045, 2023.  (PubMed)
• Lin Y†,　Banno K†* (†equal contribution)(*Corresponding author), Gil CH†, Myslinski J, Hato T, Shelley WC, Gao H, Xuei X, Liu Y, Basile DP, Yoshimoto M, Prasain N, Tarnawsky SP, Adams RH, Naruse K, Yoshida J, Murphy MP, Horie K, Yoder MC*. Origin, prospective identification, and function of circulating endothelial colony-forming cells in mice and humans. JCI Insight 8: e164781, 2023.  (PubMed)
• Shimonishi N, Ogiwara K, Yoshida J,  Horie K, Nakajima Y, Furukawa S, Takeyama M, Nogami K. Impaired factor V-related anticoagulant mechanisms and deep vein thrombosis associated with A2086D and W1920R mutations. Blood Adv Feb 13, 2023, Online ahead of print.  (PubMed)
• Yoshimura T, Horiuchi K, Shimonishi N, Ogiwara K, Horie K, Shima M, Nogami K. Modified expi293 cell culture system using piggyBac transposon enables efficient production of human FVIII. Int J Hematol Published online: 14 October 2022. doi.org/10.1007/s12185-022-03468-9
• Miyagawa F, Tagaya Y, Ozato K, Horie K, Asada H. Inflammatory Monocyte-derived Dendritic Cells Mediate Autoimmunity in Murine Model of Systemic Lupus erythematosus. J Transl Autoimmun 3: 100060, 2020.  (PubMed)
• Ijiri T, Kondoh G, Horie K, Takeda J, Matsuda Y. The Mroh4 (maestro heat-like repeat family member 4) gene affects spermatogenesis and sperm morphogenesis in mice. Bulletin of the Transdisciplinary Science Research Institute, Setsunan University. vol 5 (1): p41-56 2020.
• Yamanishi A, Matsuba A, Kondo R, Akamatsu R, Tanaka S, Tokunaga M, Horie K, Kokubu C, Ishida Y, Takeda J. Collection of homozygous mutant mouse embryonic stem cells arising from autodiploidization during haploid gene trap mutagenesis. Nucleic Acids Res 46: e63, 2018. (PubMed)
• Moriguchi S, Kita S, Fukaya M, Osanai M, Inagaki R, Sasaki Y, Izumi H, Horie K, Takeda J, Saito T, Sakagami H, Saido TC, Iwamoto T, Fukunaga K. Reduced expression of Na⁺/Ca²⁺ exchangers is associated with cognitive deficits seen in Alzheimer's disease model mice. Neuropharmacology 131: 291-303, 2018. (PubMed)
• Moriguchi S, Kita S, Yabuki Y, Inagaki R, Izumi H, Sasaki Y, Tagashira H, Horie K, Takeda J, Iwamoto T, Fukunaga K. Reduced CaM Kinase II and CaM Kinase IV Activities Underlie Cognitive Deficits in NCKX2 Heterozygous Mice. Mol Neurobiol 55: 3889-3900, 2018. (PubMed)
• Yoshida J, Akagi K, Misawa R, Kokubu C, Takeda J, Horie K. Chromatin states shape insertion profiles of the piggyBac, Tol2 and Sleeping Beauty transposons and murine leukemia virus. Scientific Rep 7: 43613, 2017. (PubMed)
• Tokunaga M, Kokubu C, Maeda Y, Sese J, Horie K, Sugimoto N, Kinoshita T, Yusa K, Takeda J. Simulation and estimation of gene number in a biological pathway using almost complete saturation mutagenesis screening of haploid mouse cells. BMC Genomics 15: 1016, 2014. (PubMed)
• Igawa K, Kokubu C, Yusa K, Horie K, Yoshimura Y, Yamauchi K, Suemori H, Yokozeki H, Toyoda M, Kiyokawa N, Okita H, Miyagawa Y, Akutsu H, Umezawa A, Katayama I, Takeda J. Removal of reprogramming transgenes improves the tissue reconstitution potential of keratinocytes generated from human induced pluripotent stem cells. Stem Cells Transl Med 3: 992-1001, 2014. (PubMed)
• Hikiji H, Endo D, Horie K, Harayama T, Akahoshi N, Igarashi H, Kihara Y, Yanagida K, Takeda J, Koji T, Shimizu T, Ishii S. TDAG8 activation inhibits osteoclastic bone resorption. FASEB J 28: 871-879, 2014. (PubMed)
• Yamanishi A, Yusa K, Horie K, Tokunaga M, Kusano K, Kokubu C, Takeda J. Enhancement of microhomology-mediated genomic rearrangements by transient loss of mouse Bloom syndrome helicase. Genome Res 23: 1462-1473, 2013. (PubMed)
• Nakajima K, Terao M, Takaishi M, Kataoka S, Goto-Inoue N, Setou M, Horie K, Sakamoto F, Ito M, Azukizawa H, Kitaba S, Murota H, Itami S, Katayama I, Takeda J, Sano S. Barrier Abnormality Due to Ceramide Deficiency Leads to Psoriasiform Inflammation in a Mouse Model. J Invest Dermatol 133: 2555-2565, 2013. (PubMed)
• Umemura Y, Yoshida J, Wada M, Tsuchiya Y, Minami Y, Watanabe H, Kondoh G, Takeda J, Inokawa H, Horie K*, Yagita K* (*Corresponding author). An in vitro ES cell-based clock recapitulation assay model identifies CK2a as an endogenous clock regulator. PLoS One 8: e67241, 2013. (PubMed)
• Tamai T, Yamaguchi O, Hikoso S, Takeda T, Taneike M, Oka T, Oyabu J, Murakawa T, Nakayama H, Uno Y, Horie K, Nishida K, Sonenberg N, Shah AM, Takeda J, Komuro I, Otsu K. Rheb (Ras homologue enriched in brain)-dependent mammalian target of rapamycin complex 1 (mTORC1) activation becomes indispensable for cardiac hypertrophic growth after early postnatal period. J Biol Chem 288: 10176-10187, 2013. (PubMed)
• Morimoto N, Kita S, Shimazawa M, Namimatsu H, Tsuruma K, Hayakawa K, Mishima K, Egashira N, Iyoda T, Horie I, Gotoh Y, Iwasaki K, Fujiwara M, Matsuda T, Baba A, Komuro I, Horie K, Takeda J, Iwamoto T, Hara H. Preferential involvement of Na⁺/Ca²⁺ exchanger type-1 in the brain damage caused by transient focal cerebral ischemia in mice. Biochem Biophys Res Commun 429:186-190, 2012. (PubMed)
• Yamamoto M, Okuyama M, Ma JS, Kimura T, Kamiyama N, Saiga H, Ohshima J, Sasai M, Kayama H, Okamoto T, Huang DC, Soldati-Favre D, Horie K, Takeda J, Takeda K. A cluster of interferon-γ-inducible p65 GTPases plays a critical role in host defense against Toxoplasma gondii. Immunity 37: 302-313, 2012. (PubMed)
• Horie K, Kokubu C, Yoshida J, Akagi K, Isotani A, Oshitani A, Yusa K, Ikeda R, Huang Y, Bradley A, Takeda J. A homozygous mutant embryonic stem cell bank applicable for phenotype-driven genetic screening. Nat Methods 8: 1071-1077, 2011. (PubMed)
• LaRocque JR, Stark JM, Oh J, Bojilova E, Yusa K, Horie K, Takeda J, Jasin M. Interhomolog recombination and loss of heterozygosity in wild-type and Bloom syndrome helicase (BLM)-deficient mammalian cells. Proc Natl Acad Sci USA 108: 11971-11976, 2011. (PubMed)
• Okada I, Hamanoue H, Terada K, Tohma T, Megarbane A, Chouery E, Abou-Ghoch J, Jalkh N, Cogulu O, Ozkinay F, Horie K, Takeda J, Furuichi T, Ikegawa S, Nishiyama K, Miyatake S, Nishimura A, Mizuguchi T, Niikawa N, Hirahara F, Kaname T, Yoshiura K, Tsurusaki Y, Doi H, Miyake N, Furukawa T, Matsumoto N, Saitsu H. SMOC1 is essential for ocular and limb development in humans and mice. Am J Hum Genet 88: 30-41, 2011. (PubMed)
• Horie K, Gaitanaris G, Gragerov A. Selection of targeted mutants from a library of randomly mutagenized ES cells. Methods Mol Biol 693: 283-294, 2011. (PubMed)
• Kakefuda K, Oyagi A, Ishisaka M, Tsuruma K, Shimazawa M, Yokota K, Shirai Y, Horie K, Saito N, Takeda J, Hara H. Diacylglycerol kinase β knockout mice exhibit lithium-sensitive behavioral abnormalities. PLoS One 5: e13447, 2010. (PubMed)
• Horie K, Kokubu C, Takeda J. Functional genomics in the mouse using the sleeping beauty transposon system. Methods Enzymol 477: 71-89. 2010. (PubMed)
• Shirai Y, Kouzuki T, Kakefuda K, Moriguchi S, Oyagi A, Horie K, Morita SY, Shimazawa M, Fukunaga K, Takeda J, Saito N, Hara H. Essential role of neuron-enriched diacylglycerol kinase (DGK), DGKbeta in neurite spine formation, contributing to cognitive function. PLoS One 5: e11602, 2010. (PubMed)
• Yagita K, Horie K, Koinuma S, Nakamura W, Yamanaka I, Urasaki A, Shigeyoshi Y, Kawakami K, Shimada S, Takeda J, Uchiyama Y. Development of the circadian oscillator during differentiation of mouse embryonic stem cells in vitro. Proc Natl Acad Sci USA 107: 3846-3851, 2010. (PubMed)
• Kokubu C, Horie K, Abe K, Ikeda R, Mizuno S, Uno Y, Ogiwara S, Ohtsuka M, Isotani A, Okabe M, Imai K, Takeda J. A transposon-based chromosomal engineering method to survey a large cis-regulatory landscape in mice. Nat Genet 41: 946-952, 2009.
• Kitada K, Keng VW, Takeda J, Horie K. Generating mutant rats using the Sleeping Beauty transposon system. Methods 49: 236-242, 2009.
• Saito ES, Keng VW, Takeda J, Horie K. Translation from nonautonomous type IAP retrotransposon is a critical determinant of transposition activity: implication for retrotransposon-mediated genome evolution. Genome Res 18: 859-868, 2008.
• Zeng H†, Horie K†(†equal contribution), Madisen L, Pavlova MN, Gragerova G, Rohde AD, Schimpf BA, Liang Y, Ojala E, Kramer F, Roth P, Slobodskaya O, Dolka I, Southon EA, Tessarollo L, Bornfeldt KE, Gragerov A, Pavlakis GN, Gaitanaris GA. An inducible and reversible mouse genetic rescue system. PLoS Genet 4: e1000069, 2008.
• Takeda J, Keng WV, Horie K. Germline mutagenesis mediated by Sleeping Beauty transposon system in mice. Genome Biol 18: 859-868, 2008.
• Gragerov A†, Horie K†(†equal contribution), Pavlova M, Madisen L, Zeng H, Gragerova G, Rhode A, Dolka I, Roth P, Ebbert A, Moe S, Navas C, Finn E, Bergmann J, Vassilatis DK, Pavlakis GN, Gaitanaris G. Large-scale, saturating insertional mutagenesis of the mouse genome. Proc Natl Acad Sci USA 104: 14406-14411, 2007.
• Horie K, Saito ES, Keng VW, Ikeda R, Ishihara H, Takeda J. Retrotransposons influence the mouse transcriptome: implication for the divergence of genetic traits. Genetics 176: 815-827, 2007.
• Kitada K, Ishishita S, Tosaka K, Takahashi R, Ueda M, Keng VW, Horie K, Takeda J. Transposon-tagged mutagenesis in the rat. Nat Methods 4: 131-133, 2007.
• Ikeda R, Kokubu C, Yusa K, Keng VW, Horie K, Takeda J. Sleeping Beauty transposase has an affinity for heterochromatin conformation. Mol Cell Biol 27: 1665-1676, 2007.
• Mao C, Tili EG, Dose M, Haks MC, Bear SE, Maroulakou I, Horie K, Gaitanaris GA, Fidanza V, Ludwig T, Wiest DL, Gounari F, Tsichlis PN. Unequal contribution of Akt isoforms in the double-negative to double-positive thymocyte transition. J Immunol 178: 5443-5453, 2007.
• Yae K, Keng VW, Koike M, Yusa K, Kouno M, Uno Y, Kondoh G, Gotow T, Uchiyama Y, Horie K and Takeda J. Sleeping Beauty transposon-based phenotypic analysis of mice: lack of arpc3 results in defective trophoblast outgrowth. Mol Cell Biol 26: 6185-6196, 2006.
• Hayakawa T, Yusa K, Kouno M, Takeda J, and Horie K. Bloom’s syndrome gene-deficient phenotype in mouse primary cells induced by a modified tetracycline-controlled trans-silencer. Gene 369: 80-89, 2006.
• Keng VW, Yae K, Hayakawa T, Mizuno S, Uno Y, Yusa K, Kokubu C, Kinoshita T, Akagi K, Jankins NA, Copeland NG, Horie K, Takeda J. Region-specific saturation germline mutagenesis in mice using the Sleeping Beauty transposon system. Nat Methods 2: 763-769, 2005.
• Liu G, Geurts AM, Yae K, Srinivasan AR, Fahrenkrug AC, Largaespada DA, Takeda J, Horie K, Olson WK, and Hackett PB. Target-Site Preferences of Sleeping Beauty Transposons. J Mol Biol346: 161-173, 2004. 
• Yusa K, Horie K, Kondoh G, Kouno M, Maeda Y, Kinoshita T and Takeda J. Genome-wide phenotype analysis in ES cells by regulated disruption of Bloom’s syndrome gene. Nature 429: 896-899, 2004.
• Yusa K, Takeda J and Horie K: Enhancement of Sleeping Beauty transposition by CpG methylation: a possible role of heterochromatin formation. Mol Cell Biol 24: 4004-4018, 2004.
• Kouno M, Kondoh G, Horie K, Komazawa N, Ishii N, Takeda J, Hashimoto T. Ahnak/Desmoyokin is dispensable for proliferation, differentiation, and maintenance of integrity in mouse epidermis. J Invest Dermatol 123: 700-707, 2004.
• Silic-Benussi M, Cavallari I, Zorzan T, Rossi E, Hiraragi H, Rosato A, Horie K, Saggioro D, Lairmore MD, Willems L, Chieco-Bianchi L, D’Agostino DM and Ciminale V. Suppression of tumor growth and cell proliferation by p13II, a mitochondrial protein of human T-cell leukemia virus type 1. Proc Natl Acad Sci USA 101: 6629-6634, 2004.
• Horie K, Yusa K, Yae K, Odajima J, Fischer SE, Keng VW, Hayakawa T, Mizuno S, Kondoh G, Ijiri T, Matsuda Y, Plasterk RH and Takeda J: Characterization of Sleeping Beauty transposition and its application to genetic screening in mice. Mol Cell Biol 23: 9189-207, 2003.
• Takagi S, Tojo H, Tomita S, Sano S, Itami S, Hara M, Inoue S, Horie K, Kondoh G, Hosokawa K, Gonzalez FJ and Takeda J: Alteration of the 4-sphingenine scaffolds of ceramides in keratinocyte-specific Arnt-deficient mice affects skin barrier function. J Clin Invest 112: 1372-82, 2003.
• Koike H, Horie K, Fukuyama H, Kondoh G, Nagata S and Takeda J. Efficient biallelic mutagenesis with Cre/loxP-mediated inter-chromosomal recombination. EMBO Rep 3: 433-437, 2002.
• von Gegerfelt AS, Liska V, Li PL, McClure HM, Horie K, Nappi F, Montefiori DC, Pavlakis GN, Marthas ML, Ruprecht RM and Felber BK: Rev-independent SIV strains are non-pathogenic in neonate macaques. J Virol 76: 96-104, 2002.
• Horie K, Kuroiwa A, Ikawa M, Okabe M, Kondo G, Matsuda Y and Takeda J: Efficient chromosomal transposition of a Tc1/mariner-like transposon Sleeping Beauty in mice. Proc Natl Acad Sci USA 98: 9191-9196, 2001.
• Nomura M, Takihara Y, Motaleb Md, Horie K, Higashinakagawa T and Shimada K: Sequence-specific DNA binding activity in the RAE28 protein, a mouse homologue of the drosophila polyhoameotic protein. Biochem Mol Biolo Int 46: 905-912, 1998.
• Stauber RH, Horie K, Carney P, Hudson EA, Tarasova NI, Gaitanaris GA and Pavlakis GN: Development and applications of enhanced green fluorescent protein mutants. Biotechniques 24: 462-471, 1998.
• Togashi S, Lim S-K, Kawano H, Ito S, Ishihara T, Okada Y, Nakano S, Kinoshita T, Horie K, Episkopou V, Gottesman ME, Costantini F, Shimada K and Maeda S: Serum amyloid P component enhances induction of murine amyloidosis. Lab Invest 77: 525-531, 1997.
• Horie K, Maeda S, Nishiguchi S, Gottesman ME, and Shimada K: A replacement vector used to introduce subtle mutations into mouse genes. Gene 166: 197-204, 1995.
• Horie K and Shimada K: Gene targeting by a vector with hairpin-shaped oligonucleotide caps. Biochem Mol Biol Int 32: 1041-1048, 1994.
• Nishiguchi S, Joh T, Horie K, Zou Z, Yasunaga T and Shimada K: A survey of genes expressed in undifferentiated mouse embryonal carcinoma F9 cells: characterization of low-abundance mRNAs. J Biochem 116: 128-139, 1994.
• Horie K, Nishiguchi S, Maeda S and Shimada K: Structures of replacement vectors for efficient gene targeting. J Biochem 115: 477-485, 1994.