Publication

国立遺伝学研究所　マウス開発研究室 (National Institute of Genetics, Mouse Genomics Resource Lab)　(*corresponding author)

Dagher S, DeAngelo D, Sato RY, Norimoto H, Koide T*, Ishiyama S.* (*co-corresponding author)
Comparative analysis of tickling and conspecific play in tame mice and golden hamsters.
Behavioural Brain Research. 496:115849,2026. DOI: 10.1016/j.bbr.2025.115849

Tokito R, Oishi K, Sugiyama T, Fujisawa Y, Kuba F, Yoshida K, Yoshida K, Yoshida M, Tanaka Y, Amo T, Yamaguchi N, Akiyama T, Imai Y, Yoshimi K, Koide T, and Kurihara Y.
COXFA4L3 enhances mitochondrial complex IV function to boost ATP synthesis and drive sperm motility.
Mitochondrion. 2025 Sep 28:102082 (2025). DOI: 10.1016/j.mito.2025.102082

Fujiwara K, Toyoda A, Biswa BB, Kishida T, Tsuruta M, Nakamura Y, Kimura N, Kawamoto S, Sato Y, Katsuki T, Sakura 100 Genome Consortium, Koide T.*
A Near Complete Genome Assembly of the Oshima Cherry Cerasus speciosa.
Scientific Data. 12, Article number: 162, 2025. DOI: 10.1038/s41597-025-04388-z

Nakamura M, Nomoto K, Mogi K, Koide T*, Kikusui T.* (*co-corresponding author)
Visual and olfactory signals of conspecifics induce emotional contagion in mice.
Proceedings of the Royal Society B. 291: 20241815, 2024. DOI: 10.1098/rspb.2024.1815

Niimura Y*, Biswa BB, Kishida T, Toyoda A, Fujiwara K, Ito M, Touhara K, Inoue-Murayama M, Jenkins SH, Adenyo C, Kayang BB, Koide T.* (*co-corresponding author)
Synchronized expansion and contraction of olfactory, vomeronasal, and taste receptor gene families in hystricomorph rodents.
Molecular Biology and Evolution. 41, 4: msae071, 2024. https://doi.org/10.1093/molbev/msae071

Venkatachalam B, Biswa B.B, Nagayama H, Koide T.*
Association of tameness and sociability but no sign of domestication syndrome in mice selectively bred for active tameness.
Genes, Brain and Behavior. 23, 1: e12887, 2024. DOI:10.1111/gbb.12887

Takanami K, Kuroiwa M, Ishikawa R, Imai Y, Oishi A, Hashino M, Shimoda Y, Sakamoto H, Koide T.
Function of gastrin-releasing peptide receptors in ocular itch transmission in the mouse trigeminal sensory system.
Frontiers in Molecular Neuroscience. 16:1280024, 2023. https://doi.org/10.3389/fnmol.2023.1280024

Ono K, Sujino T, Miyamoto K, Harada Y, Kojo S, Yoshimatsu Y, Tanemoto S, Koda Y, Zheng J, Sayama K, Koide T, Teratani T, Mikami Y, Takabayashi K, Nakamoto N, Hosoe N, London M, Ogata H, Mucida D, Taniuchi I, Kanai T.
Downregulation of chemokine receptor 9 facilitates CD4+CD8αα+ intraepithelial lymphocyte development.
Nature Communications. 14, Article number: 5152, 2023. https://doi.org/10.1038/s41467-023-40950-2

Imai Y, Tanave A, Matsuyama M, and Koide T.*
Efficient genome editing in wild strains of mice using the i-GONAD method.
Scientific Reports. 12, Article number: 13821, 2022. https://doi.org/10.1038/s41598-022-17776-x

Matsumura R, Yoshimi K, Sawai Y, Yasumune N, Kajihara K, Maejima T, Koide T, Node K, Akashi M.
The role of cell-autonomous circadian oscillation of Cry transcription in circadian rhythm generation.
Cell Reports. 39, 110703, 2022. DOI:10.1016/j.celrep.2022.110703

Iwamoto R, Takahashi T, Yoshimi K, Imai Y, Koide T, Hara M, Ninomiya T, Nakamura H, Sayama K, Yukita A.
Chemokine ligand 28 (CCL28) negatively regulates trabecular bone mass by suppressing osteoblast and osteoclast activities.
Journal of Bone Mineral Metabolism. 39(4): 558-571, 2021. https://doi.org/10.1007/s00774-021-01210-9

Matsumoto Y, Nagayama H, Nakaoka H, Toyoda A, Goto T, Koide T.*
Combined Change of Behavioral Traits for Domestication and Gene‐Networks in Mice Selectively Bred for Active Tameness.
Genes, Brain, and Behavior. e12721, 2021. https://doi.org/10.1111/gbb.12721

Miki Y, Devi L, Imai Y, Minami N, Koide T, and Goel S.
Male fertility is not impacted by the deletion of the PDZ-binding kinase (Pbk) gene in mice.
Reproduction, Fertility and Development. 32(10): 893-902, 2020. doi.org/10.1071/RD19445

Tanave A, Koide T*.
A role for the rare endogenous retrovirus β4 in development of Japanese fancy mice.
Communications Biology. 3: 53, 2020. https://doi.org/10.1038/s42003-020-0781-z

Tanave A, Imai Y, Koide T.*
Nested retrotransposition in the East Asian mouse genome causes the classical nonagouti mutation.
Communications Biology. 2: 283, 2019. https://doi.org/10.1038/s42003-019-0539-7

Nagayama H, Matsumoto Y, Tanave A, Nihei M, Goto T, Koide T.*
Measuring active and passive tameness separately in mice.
J. Vis. Exp. 138: e58048, 2018. doi: 10.3791/58048

Horii Y, Nagasawa T, Sakakibara H, Takahashi A, Tanave A, Matsumoto Y, Nagayama H, Yoshimi K, Yasuda MT, Shimoi K, Koide T.*
Hierarchy in the home cage affects behaviour and gene expression in group-housed C57BL/6 male mice.
Scientific Reports 7: 6991, 2017. https://doi.org/10.1038/s41598-017-07233-5

Matsumoto Y, Goto T, Nishino J, Nakaoka H, Tanave A, Takano-Shimizu T, Mott RF, Koide T.*
Selective breeding and selection mapping using a novel wild-derived heterogeneous stock of mice revealed two closely-linked loci for tameness.
Scientific Reports 7: 4607, 2017. https://doi.org/10.1038/s41598-017-04869-1

Okabe S, Tsuneoka Y, Takahashi A, Oyama R, Watarai A, Maeda S, Honda Y, Nagasawa M, Mogi K, Nishimori K, Kuroda M, Koide T, Kikusui T.
Pup exposure facilitates retrieving behavior via the oxytocin neural system in female mice.
Psychoneuroendocrinology 79: 20-30, 2017. https://doi.org/10.1016/j.psyneuen.2017.01.036

Hirata H, Takahashi A, Shimoda Y, Koide T.*
Caspr3-deficient mice exhibit low motor learning during the early phase of the accelerated rotarod task.
PLoS ONE. 11(1):e0147887. 2016. doi: 10.1371/journal.pone.0147887.

Hirata H, Umemori J, Yoshioka H, Koide T, Watanabe K, Shimoda Y.
Cell adhesion molecule Caspr3 is expressed in the mouse basal ganglia during early postnatal stages.
Journal of Neuroscience Research. 94(1):74-89, 2016. doi: 10.1002/jnr.23670.

Takahashi A, Sugimoto H, Kato S, Shiroishi T, Koide T.*
Mapping of genetic factors that elicit intermale aggressive behavior on mouse chromosome 15: intruder effects and the complex genetic basis.
PLoS ONE. 10(9):e0137764. 2015. doi: 10.1371/journal.pone.0137764.

Takahashi A, Lee RX, Iwasato T, Itohara S, Arima H, Bettler B, Miczek KA, Koide T.
Glutamate input in the dorsal raphe nucleus as a determinant of escalated aggression in male mice.
The Journal of Neuroscience 22 April 2015, 35(16): 6452-6463, 2015. doi: 10.1523/JNEUROSCI.2450-14.2015

Takahashi A, Shiroishi T, Koide T.*
Genetic mapping of escalated aggression in wild-derived mouse strain MSM/Ms: association with serotonin-related genes.
Frontiers in Neuroscience Volume8, Article156, 2014. doi: 10.3389/fnins.2014.00156

Kato S, Ishii A, Nishi A, Kuriki S, Koide T.*
Segregation of a QTL cluster for home-cage activity using a new mapping method based on regression analysis of congenic mouse strains.
Heredity　113, 416-423, 2014. doi: 10.1038/hdy.2014.42.

Arakawa T, Tanave A, Ikeuchi S, Takahashi A, Kakihara S, Kimura S, Sugimoto H, Asada N, Shiroishi T, Tomihara K, Tsuchiya T, Koide T.*
A male-specific QTL for social interaction behavior in mice mapped with automated pattern detection by a hidden Markov model incorporated into newly developed freeware.
Journal of Neuroscience Methods 234, 127-134, 2014. doi:10.1016/j.jneumeth.2014.04.012.

Takahashi A, Nagayasu K, Nishitani N, Kaneko S, Koide T.*
Control of intermale aggression by the medial prefrontal cortex activation in the mouse.
PLoS ONE 9(4): e94657, 2014. doi:10.1371/journal.pone.0094657.

Kanno K, Kokubo H, Takahashi A, Koide T, Ishiura S.
Enhanced prepulse inhibition and low sensitivity to a dopamine agonist in Hesr1-knockout mice.
Journal of Neuroscience Research 92: 287-297, 2014. doi: 10.1002/jnr.23291.

Goto T, Tanave A, Moriwaki K, Shiroishi T, Koide T.*
Selection for reluctance to avoid humans during the domestication of mice.
Genes, Brain, and Behavior 12: 760-770, 2013. doi: 10.1111/gbb.12088

Umemori J, Mori A, Ichiyanagi K, Uno T, Koide T.*
Identification of both copy number variation-type and constant-type core elements in a large segmental duplication region of the mouse genome.
BMC Genomics 14: 455, 2013. doi: 10.1186/1471-2164-14-455.

Koide T*, Goto T, Takano-Shimizu T.
Genomic mixing to elucidate the genetic system of complex traits.
Experimental Animals 61: 503-509, 2012. http://doi.org/10.1538/expanim.61.503.

Takahashi A, Schilit AN, Kim J, Debold JF, Koide T, Miczek KA.
Behavioral characterization of escalated aggression induced by GABA(B) receptor activation in the dorsal raphe nucleus.
Psychopharmacology 224: 155-156, 2012.

Sugimoto H, Okabe S, Kato M, Koshida N, Shiroishi T, Mogi K, Kikusui T, Koide T.*
A role for strain differences in waveforms of ultrasonic vocalizations during male–female interaction.
PLoS ONE 6: e22093, 2011. PubMed

Ishii A, Koide T, Takahashi A, Shiroishi T, Hettinger TP, Frank ME, Savoy LD, Formaker BK, Yertutanol S, Lionikas A and Blizard DA.
B6-MSM consomic mouse strains reveal multiple loci for genetic variation in sucrose octaacetate aversion.
Behavior Genetics 41: 716-723, 2011. PubMed

Koide T*, Ikeda K, Ogasawara M, Shiroishi T, Moriwaki K, and Takahashi A.
A new twist on behavioral genetics by incorporating wild-derived mouse strains.
Experimental Animals 60: 347-354, 2011. PubMed

Nishi A, Ishii A, Takahashi A, Shiroishi T, Koide T.*
QTL analysis of measures of mouse home-cage activity using B6/MSM consomic strains.
Mammalian Genome 21: 477-485, 2010. PubMed PDF (Open access)

Takahashi A, Tomihara K, Shiroishi T, Koide T.*
Genetic mapping of social interaction behavior in B6/MSM consomic mouse strains.
Behavior Genetics 40: 366-376, 2010. PubMed　PDF (Open access)

Tanaka N, Waki K, Kaneda H, Suzuki T, Yamada I, Furuse T, Kobayashi K, Motegi H, Toki H, Inoue M, Minowa O, Noda N, Takao K, Miyakawa T, Takahashi A, Koide T, Wakana S, Masuya H.
SDOP-DB: A comparative standardised-protocol database for mouse phenotypic analyses.
Bioinformatics 26(8): 1133-1134, 2010.

Dowse H, Umemori J, Koide T.
Ultradian Components in the Locomotor Activity Rhythms of the Genetically Normal Mouse, Mus musculus.
The Journal of Experimental Biology 213: 1788-1795, 2010. PubMed

Kubota T, Miyake K, Hirasawa T, Nagai K, Koide T.
Novel etiological and threrapeutic strategies for neurodiseases: Epigenetic understanding of gene-environment interactions.
J Pharmacol Sci 113: 3-8, 2010.

Umemori J, Nishi A, Lionikas A, Sakaguchi T, Kuriki S, Blizard DA and Koide T.*
QTL analyses of temporal and intensity components of home-cage activity in KJR and C57BL/6J strains.
BMC Genetics 10: 40, 2009. PubMed Open Access

Takahashi A, Nishi A, Ishii A, Shiroishi T, Koide T.*
Systematic analysis of emotionality in consomic mouse strains established from C57BL/6J and wild-derived MSM/Ms.
Genes, Brain and Behavior 7: 849-858, 2008. PubMed PDF

Takahashi A, Shiroishi T, Koide T.*
Multigenic factors associated with a hydrocephalus-like phenotype found in inter-subspecific consomic mouse strains.
Mammalian Genome 29: 333-338, 2008. PubMed

Shigeta Y, Kasai S, Han W, Hata H, Nishi A, Takamatsu Y, Hagino Y, Yamamoto H, Koide T, Shiroishi T, Kasai K, Tsunashima K, Kato N and Ikeda K.
Association of morphine-induced antinociception with variations in the 5' flanking and 3' untranslated regions of the μ opioid receptor gene in 10 inbred mouse strains.
Pharmacogenet. Genomics 18: 927-936, 2008.

Liu Y-H, Takahashi A, Kitano T, Koide T, Shiroishi T, Moriwaki K, and Saitou N.
Mosaic genealogy of the Mus musculus genome revealed by 21 nuclear genes from its three subspecies.
Genes and Genetic Systems 83(1): 77-88, 2008.

Blizard DA, Takahashi A, Galsworthy M, Martin B, Koide T.
Test standardization in behavioral neuroscience: a response to Stanford.
Journal of Psychopharmacology 21(2): 136-139, 2007.

Takahashi A, Kato K, Makino J, Shiroishi T, Koide T.*
Multivariate analysis of temporal descriptions of open-field behavior in wild derived mouse strains.
Behavior Genetics 36: 763-774, 2006.

Ogasawara M, Imanishi T, Moriwaki K, Gaudieri S, Tsuda H, Hashimoto H, Shiroishi T, Gojobori T, Koide T.
Length variation of CAG/CAA triplet repeats in 50 genes among 16 inbred mouse strains.
Gene 349: 107-119, 2005.

Esumi S, Kakazu N, Taguchi Y, Hirayama T, Sasaki A, Hirabayashi T, Koide T, Kitsukawa T, Hamada S, Yagi T.
Monoallelic yet combinatorial expression of variable exons of the protocadherin-a gene cluster in single neurons.
Nature Genetics 37: 171-176, 2005.

Taguchi Y, Koide T, Shiroishi T, Yagi T.
Molecular evolution of Cadherin-related neuronal receptor/protocadherin α (CNR/Pcdhα) gene cluster in Mus musculus subspecies.
Mol. Biol. Evol. 22: 1433-1443, 2005.

Koide T.*
Genetic analysis of spontaneous activity using wild derived mouse strains.
The Japanese Journal of Animal Psychology 54: 59-66, 2004.

Furuse T, Miura Y, Yagasaki K, Shiroishi T, Koide T.*
Identification of QTLs for differential capsaicin sensitivity between mouse strains KJR and C57BL/6.
Pain 105: 169-175, 2003.

国立遺伝学研究所哺乳動物遺伝研究室 (National Institute of Genetics, Mammalian Genetics Lab)

Isobe T, Yoshino M, Mizuno K, Fisher Lindahl K, Koide T, Gaudiery S, Gojobori T, Shiroishi T.
Molecular characterization of the Pb recombination hotspot in the mouse major histocompatibility complex class I region.
Genomics 80: 229-235: 2002.

Chan BWH, Chan K-S, Koide T, Yeung S-M, Leung MBW, Copp AJ, Loeken MR, Shiroishi T, Shum ASW.
Maternal Diabetes Increases the Risk of Caudal Regression Caused by Retinoic Acid.
Diabetes 51: 2811-2816, 2002.

Furuse T, Takano-Shimizu T, Moriwaki K, Shiroishi T, Koide T.*
QTL analyses of spontaneous locomotor activity using mouse strains from Mishima battery.
Mammalian Genome 13: 411-415, 2002.

Furuse T, Blizard DA, Moriwaki K, Miura Y, Yagasaki K, Shiroishi T, Koide T.*
Genetic diversity underlying capsaicin intake in the Mishima battery of mouse strains.
Brain Research Bulletin 57: 49-55, 2002.

Watanabe T, Yoshimura A, Mishima Y, Endo Y, Shiroishi T, Koide T, Sasaki H, Asakura H, Kominami R.
Differential chromatin packaging of genomic imprinted regions between expressed and non-expressed alleles.
Human Molecular Genetics 9: 3029-3035, 2000.

Koide T*, Moriwaki K, Ikeda K, Niki H and Shiroishi T.
Multi-phenotype behavioral characterization of inbred strains derived from wild stocks of Mus musculus.
Mammalian Genome 11: 664-670, 2000.

Shum ASW, Poon LLM, Tang WWT, Koide T, Chan BWH, Leung Y-CG, Shiroishi T and Coop AJ.
Retinoic acid induces down regulation of Wnt-3a, apoptosis and diversion of tail bud cells to a neural fate in the mouse embryo.
Mechanisms of Development 84: 17-30, 1999.

Sato H, Koide T, Sagai T, Ishiguro S, Tamai M, Saitou N, Shiroishi T.
The genomic organization of type I keratin genes in mice.
Genomics 56: 303-309, 1999.

Koide T*, Moriwaki K, Uchida K, Mita A, Sagai T, Yonekawa H, Katoh H, Miyashita N, Tsuchiya K, Nielsen TJ and Shiroishi T.
A new inbred strain JF1 established from Japanese fancy mouse carrying the classic piebald allele.
Mammalian Genome 9: 15-19, 1998.

Sato H, Koide T, Masuya H, Wakana S, Sagai T, Ishiguro S, Tamai M and Shiroishi T.
A new mutation Rim3 resembling Reden is mapped close to retinoic acid receptor alpha (Rara) gene on mouse Chromosome 11.
Mammalian Genome 9: 20-25, 1998.

Sagai T, Koide T, Endo M, Tanoue K, Kikkawa H, Yonekawa H, Ishiguro S, Tamai S, Matsuda Y, Wakana S and Shiroishi T.
rim2 (recombination induced mutation 2) is a new allele of pearl and a mouse model of human Hermansky-Pudlak Syndrome (HPS): genetic and physical mapping.
Mammalian Genome 9: 2-7, 1998.

Obata Y, Kaneko-Ishino T, Koide T, Takai Y, Ueda T, Domeki I, Shiroishi T, Ishino F and Kono T.
Disruption of primary imprinting during oocyte growth leads to the modified expression of imprinted genes during embryogenesis.
Development 125: 1553-1560, 1998.

ケンブリッジ大学, Wellcome/CRC Institute, Prof Azim Surani's lab

Ainscough J F-X, Koide T, Tada M, Barton S, and Surani MA.
Imprinting of Igf2 and H19 from a 130kb YAC transgene.
Development 124: 3621-3632, 1997.

Koide T, Ainscough J,Wijgerde M and Surani MA.
Comparative analysis of Igf-2/H19 imprinted domain: identification of a highly conserved intergenic DNase I hypersensitive region.
Genomics 24: 1-8, 1994.

国立遺伝学研究所　日本学術振興会特別研究

Mizuno K, Koide T, Sagai T, Moriwaki K and Shiroishi T.
Molecular analysis of a recombinational hotspot adjacent to Lmp2 gene in the mouse MHC: fine location and chromatin structure.
Mammalian Genome 7: 490-496, 1996

Shiroishi T, Koide T, Yoshino M, Sagai T and Moriwaki K.
Hotspots of homologous recombination in mouse meiosis.
Adv. Biophys. 31: 63-76, 1994.

Koide T, Yoshino M, Niwa M, Ishiura M, Shiroishi T and Moriwaki K.
The amplified long genomic sequence (ALGS) located in the centromeric regions of mouse chromosomes.
Genomics 13: 1186-1191, 1992.