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Dr. Shigeki Nakagome

Assistant Professor (Psychiatry)

Shigeki Nakagome is Ussher Assistant Professor in Genomic Medicine at School of Medicine. Dr. Nakagome received his Ph.D. at The University of Tokyo in 2010 with the focus on the evolutionary model in which high risk variants associated with Crohn's disease at the NOD2 locus may have exclusively spread into European populations by natural selection. As a postdoctoral researcher, Dr. Nakagome first joined The Institute of Statistical Mathematics from 2011 to 2014 where he was awarded a competitive Research Fellowship of the Japan Society for the Promotion of Science (JSPS) for Young Scientists and developed a new statistical method that incorporates kernel methods into Approximate Bayesian Computation (kernel ABC). Dr. Nakagome obtained further postdoctoral training on experimental aspects of functional genomics at The University of Chicago from 2013 to 2016 as JSPS Overseas Research Fellow. During this training, Dr. Nakagome has acquired expertise in population and functional genomics to develop statistical approaches for understanding selective pressures on immunity genes and to connect genetic polymorphisms to their functional consequences in the immune system.
  BAYESIAN COMPUTATION   Bioinformatics   Evolution   Evolutionary Biology   Evolutionary genetics   GENE POLYMORPHISMS   GENE REGULATION   GENE-EXPRESSION   Genomes, Genomics   Genomic structure and function, molecular approaches to gene function   Genomics   Host-pathogen interaction   Human Evolution   Human Population Genetics   INFLAMMATORY BOWEL DISEASE   microbiome   MOLECULAR EVOLUTION   POPULATION GENETICS
Details Date
Analysis Provider in GenomeAsia 100K 2018-Present
Member of Asian DNA Repository Consortium 2013-Present
Review Editor for Frontier in Ecology and Evolution 2013-Present
Language Skill Reading Skill Writing Skill Speaking
English Fluent Fluent Fluent
Japanese Fluent Fluent Fluent
Details Date From Date To
Irish Society of Human Genetics 2018 Present
European Society of Human Genetics 2018 Present
Society for Molecular Biology and Evolution 2009 Present
The American Society of Human Genetics 2009 Present
Shigeki Nakagome, The origins of Jomon and its contribution to modern Japanese, World Archaeological Congress 9, Prague, Czech Republic, July 4-9, 2021, Invited Talk, ACCEPTED  URL
Saitou, M. and Resendez, S. and Pradhan, A.J. and Wu, F. and Lie, N.C. and Hall, N.J. and Zhu, Q. and Reinholdt, L. and Satta, Y. and Speidel, L. and Nakagome, S. and Hanchard, N.A. and Churchill, G. and Lee, C. and Atilla-Gokcumen, G.E. and Mu, X. and Gokcumen, O., Sex-specific phenotypic effects and evolutionary history of an ancient polymorphic deletion of the human growth hormone receptor, Science Advances, 7, (39), 2021, Notes: [cited By 1], Journal Article, PUBLISHED  DOI
Cooke, N.P. and Mattiangeli, V. and Cassidy, L.M. and Okazaki, K. and Stokes, C.A. and Onbe, S. and Hatakeyama, S. and Machida, K. and Kasai, K. and Tomioka, N. and Matsumoto, A. and Ito, M. and Kojima, Y. and Bradley, D.G. and Gakuhari, T. and Nakagome, S., Ancient genomics reveals tripartite origins of Japanese populations, Science Advances, 7, (38), 2021, Notes: [cited By 3], Journal Article, PUBLISHED  DOI
Hudson M.J., Nakagome S., Whitman J.B., The evolving Japanese: the dual structure hypothesis at 30, Evolutionary Human Sciences, 2, 2020, p1 - 13, Notes: [doi:10.1017/ehs.2020.6], Journal Article, PUBLISHED  DOI
Saravanarajan K, Douglas AR, Ismail MS, Omorogbe J, Semenov S, Muphy G, O'Riordan F, McNamara D, Nakagome S, Genomic profiling of intestinal T-cell receptor repertoires in inflammatory bowel disease. , Genes and Immunity, 2020, pEpub Ahead of Print Feb 2020 , Journal Article, PUBLISHED  DOI
Gakuhari, T. and Nakagome, S. and Rasmussen, S. and Allentoft, M.E. and Sato, T. and Korneliussen, T. and Chuinneagáin, B.N. and Matsumae, H. and Koganebuchi, K. and Schmidt, R. and Mizushima, S. and Kondo, O. and Shigehara, N. and Yoneda, M. and Kimura, R. and Ishida, H. and Masuyama, T. and Yamada, Y. and Tajima, A. and Shibata, H. and Toyoda, A. and Tsurumoto, T. and Wakebe, T. and Shitara, H. and Hanihara, T. and Willerslev, E. and Sikora, M. and Oota, H., Ancient Jomon genome sequence analysis sheds light on migration patterns of early East Asian populations, Communications Biology, 3, (1), 2020, Notes: [cited By 16], Journal Article, PUBLISHED  DOI
Nakagome S., Hudson R.R., Di Rienzo A., Inferring the model and onset of natural selection under varying population size from the site frequency spectrum and haplotype structure, Proceedings of the Royal Society B: Biological Sciences, 286, 2019, p20182541-, Journal Article, PUBLISHED  TARA - Full Text  DOI  URL
McColl H., Racimo F., Vinner L., Demeter F., Gakuhari T., Moreno-Mayar J., van Driem G., Gram Wilken U., Seguin-Orlando A., de la Fuente C., Wasef S., Shoocongdej R., Souksavatdy V., Sayavongkhamdy T., Saidin M., Allentoft M., Sato T., Korneliussen T., Prohaska A., Margarayan A., de Barros Damgaard P., Kaewsutthi S., Lertrit P., Nguyen T., Hung H., Minh Tran T., Nghia Truong H., Nguyen G., Shahidan S., Wiradnyana K., Matsumae H., Shigehara N., Yoneda M., Ishida H., Masuda Y., Yamada Y., Tajima A., Shibata H., Toyoda A., Hanihara T., Nakagome S., Deviese T., Bacon A., Duringer P., Ponche J., Shackelford L., Patole-Edoumba E., Nguyen T., Bellina-Pryce B., Galipaud J., Kinaston R., Buckley H., Pottier C., Rasmussen S., Higham T., Foley R.A., Mirazón Lahr M., Orlando L., Sikora M., Oota H., Higham C., Lambert D.M., Willerslev E., The prehistoric peopling of Southeast Asia, Science, 361, 2018, p88 - 92, Journal Article, PUBLISHED  DOI  URL
Cooke N.P., Nakagome S., Fine-tuning of Approximate Bayesian Computation for human population genomics, Current Opinion in Genetics & Development, 53, 2018, p60 - 69, Journal Article, PUBLISHED  DOI  URL
Lin M., Siford R.L., Martin A.R., Nakagome S., Möller M., Hoal E.G., Bustamante C.D., Gignoux C.R., Henn B.M., Rapid evolution of a skin-lightening allele in southern African KhoeSan, Proceedings of the National Academy of Sciences of the United States of America, 115, (52), 2018, p13324 - 13329, Journal Article, PUBLISHED  DOI  URL

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Evolutionary perspective on human disease - targets of natural selection and its by-products in, editor(s)Akihiro Fujimoto , Understanding human disease in the context of molecular evolution, Igaku-no Ayumi, Ishiyaku Shuppan, 2020, [Shigeki Nakagome], Book Chapter, ACCEPTED
Nakagome S., Systematic profiling of the T cell receptor repertoire in intestinal inflammation, ASHBi Seminar, Kyoto University Institute for the Advanced Study of Human Biology, 2020, Invited Talk, PUBLISHED
O'Connor C., McNamara D., Nakagome S., A statistical modelling reveals bi-directional chromatin scanning by RAG in the human TCR-alpha locus, bioRxiv, 2020, p14 , Journal Article, PUBLISHED
Nakagome S., Japanese Origins 2019: The Dual Structure Hypothesis at 30, Interdisciplinary TransEurasian Conference, Jena, Germany, January 9-10, 2019, Martine Robbeets, Invited Talk, PUBLISHED
Nakagome S., Population genetics inference on the mode, tempo, and origins of natural selection, 21st Annual Meeting of the Society of Evolutionary Studies, Japan, Hokkaido University, Sapporo, Japan, 2019, Invited Talk, PUBLISHED
Gakuhari T., Nakagome S., Rasumussen S., Allentoft M., Sato T., Korneliussen T., Ni Chuinneagain B., Matsumae H., Koganebuchi K., Schmidt R., Mizushima S., Kondo O., Shigehara N., Yoneda M., Kimura R., Ishida H., Masuyama Y., Yamada Y., Tajima A., Shibata H., Toyoda A., Tsurumoto T., Wakebe T., Shitara H., Hanihara T., Willerslev E., Sikora M., Oota H., Jomon genome sheds light on East Asian population history, 2019, Journal Article, SUBMITTED
Resendez S., Saitou M., Parisi L.R., Wu F., Nakagome S., Satta Y., Atilla-Gokcumen G.E., Mu X., Gokcumen O., Sex-specific phenotypic effects and evolutionary history of an ancient deletion polymorphism of the human growth hormone receptor, bioRxiv, 2019, p35 , Journal Article, PUBLISHED
Nakagome S., Identifying the Origin of Natural Selection in Modern Japanese, Future Perspective on Ancient Genomics in East Asia, Tokyo, Japan, October 21, 2018, Takashi Gakuhari, Invited Talk, PUBLISHED
Nakagome S., Applying population genetics to human complex disease, The 1739th Biological Symposium, National Institute of Genetics, Mishima, Japan, February 28, 2014, Invited Talk, PUBLISHED
Evolutionary consequence of the human Out-of-Africa in, editor(s)Hiroki Oota and Mariko Hasegawa , Human disease and evolution, Keiso-shobo, 2013, pp87 - 124, [Nakagome S. and Oota H.], Book Chapter, PUBLISHED


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Award Date
Japan Society for the Promotion of Science Overseas Research Fellowships 2014
Research Fellowships of the Japan Society for the Promotion of Science for Young Scientists (PD) 2012
Research Fellowships of the Japan Society for the Promotion of Science for Young Scientists (DC2) 2009
Postdoctoral Travel Award, Annual Meeting of the Society for Molecular Biology and Evolution, Kyoto, Japan 2011
Dean's Award in International Exchange Section, Graduate School of Frontier Sciences, The University of Tokyo (awarded as the organizing committee of international conference) 2009
Dean's Prize, College of Bioresource Sciences, Nihon University 2005
Scholarship at College of Bioresource Sciences, Nihon University 2001
Symbiosis between human host and gut microbiota is essential for our health, a disruption of which leads to autoimmune conditions, as is the case in inflammatory bowel disease (IBD). A critical challenge for the host under the intestinal environment is to mount an efficient and appropriate immune response to pathogens while maintaining tolerance to symbiotic bacteria. However, we still do not know the underlying molecular mechanisms whereby humans acquire tolerance to host trillions of microorganisms in their intestine. Our research team aims to understand the nature and function of host immune repertoires that provide the ability to discriminate pathogenic from symbiotic bacteria. Outcomes from our research will not only yield deeper insights into the host-microbiota crosstalk in IBD, but also pioneer personalized and targeted interventions to control this interaction for prevention and treatment of IBD. Taking advantage of our expertise in quantitative genetics and its application to high-throughput sequencing, we develop statistical and computational approaches to immunogenomics profiling on patients affected by IBD. Our research aims to describe (i) the patterns of inter-individual variation in the host immunity and bacterial activity, (ii) the processes of immune development that ends up with the breakdown of host tolerance to gut bacteria, and (iii) the impacts of past selective pressures during human evolution on an individual's ability to adapt to its own intestinal environments.