Dr. Shigeki Nakagome
Assistant Professor, Psychiatry
Biography
I am the Ussher Assistant Professor in Genomic Medicine at the School of Medicine, where I have led my independent research group since 2016. My work is deeply rooted in the dynamic field of population genomics, spanning the development of innovative computational methods, the exploration of evolutionary insights into human health and disease, and the unraveling of human history through ancient genomics. These diverse research endeavours have established me as a leader in leveraging ancient genomics to understand the genetic legacy of the human past and its impact on present-day health. My commitment to excellence in interdisciplinary research is reflected in my contributions to international collaborations and my ability to integrate diverse perspectives and methodologies. Looking ahead, I am eager to build upon this foundation, continuing to push the boundaries of our understanding of human evolution, genetics, and health through innovative research and collaboration.
Publications and Further Research Outputs
Peer-Reviewed Publications
Lee J., Sato T., Tajima A., Amgalantugs T., Tsogtbaatar B., Nakagome S., Miyake T., Shiraishi N., Jeong C., Gakuhari T., Medieval genomes from eastern Mongolia share a stable genetic profile over a millennium, Human Population Genetics and Genomics, 4, (1), 2024, p0004-
Nakagome S., Cooke N.P., Male-driven admixture facilitated subsistence shift in northern China, Anthropological Science, 2024
Cooke N.P., Murray M., Cassidy L.M., Mattiangeli V., Okazaki K., Kasai K., Gakuhari T., Bradley D.G., Nakagome S., Genomic imputation of ancient Asian populations contrasts local adaptation in pre- and post-agricultural Japan, iScience, 27, (110050), 2024
Cooke N.P., Mattiangeli V., Cassidy L.M., Okazaki K., Kasai K., Bradley D.G., Gakuhari T., Nakagome S., Genomic insights into a tripartite ancestry in the Southern Ryukyu Islands, Evolutionary Huma Sciences, 5, 2023, pe23-
Shigeki Nakagome, A tripartite ancestry model of modern Japanese genomic origins, World Archaeological Congress 9, Prague, Czech Republic, July 4-9, 2022
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
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
Hudson M.J., Nakagome S., Whitman J.B., The evolving Japanese: the dual structure hypothesis at 30, Evolutionary Human Sciences, 2, 2020, p1 - 13
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
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
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-
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
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
CookeN., Bradley D.G., Nakagome S., A simulation study on the origin of natural selection in an admixed population, Irish Society of Human Genetics 2018, Dublin, Ireland, September 21st, 2018
Cooke N.P., Nakagome S., Fine-tuning of Approximate Bayesian Computation for human population genomics, Current Opinion in Genetics & Development, 53, 2018, p60 - 69
Nakagome S., Chinen H., Iraha A., Hokama A., Takeyama Y., Sakisaka S., Matsui T., Kidd J.R., Kidd K.K., Said H.S., Suda W., Morita H., Hattori M., Hanihara T., Kimura R., Ishida H., Fujita J., Kinjo F., Mano S., Oota H. , Testing a host-microbiome interaction in the susceptibility of TNFSF15 to Crohn's disease in the Ryukyu Islands, Immunogenomics of disease: accelerating to patient benefit, Cambridge, UK, February 6th-8th, 2017
Nakagome S., Hudson R.R., Di Rienzo A., Estimating the onsets of selection on new mutations and standing variation in human populations, European Mathematical Genetics Meeting 2017, Tartu, Estonia, April 4-7, 2017
Foley C, Corvin A, Nakagome S, Genetics of Schizophrenia: Ready to Translate?, Current Psychiatry Reports, 19, (9), 2017, p61-
Akiyama T., Katsumura T., Nakagome S., Lee S., Joh K., Soejima H., Fujimoto K., Kimura R., Ishida H., Hanihara T., Yasukouchi A., Satta Y., Higuchi S., Oota H., An ancestral haplotype of the human PERIOD2 gene associates with reduced sensitivity to light-induced melatonin suppression, PLOS ONE, 12, (6), 2017, e0178373
Alleyne D, Witonsky DB, Mapes B, Nakagome S, Sommars M, Hong E, Muckala KA, Di Rienzo A, Kupfer SS, Colonic transcriptional response to 1alpha,25(OH)2 vitamin D3 in African- and European-Americans., The Journal of Steroid Biochemistry and Molecular Biology, 168, 2017, p49 - 59
Nakagome S, Chinen H, Iraha A, Hokama A, Takeyama Y, Sakisaka S, Matsui T, Kidd JR, Kidd KK, Said HS, Suda W, Morita H, Hattori M, Hanihara T, Kimura R, Ishida H, Fujita J, Kinjo F, Mano S, Oota H, Confounding effects of microbiome on the susceptibility of TNFSF15 to Crohn's disease in the Ryukyu Islands., Human Genetics, 2017
Kariuki SN, Blischak JD, Nakagome S, Witonsky DB, Di Rienzo A, Patterns of Transcriptional Response to 1,25-Dihydroxyvitamin D3 and Bacterial Lipopolysaccharide in Primary Human Monocytes., G3 (Bethesda, Md.), 6, (5), 2016, p1345-55
Kariuki SN, Maranville JC, Baxter SS, Jeong C, Nakagome S, Hrusch CL, Witonsky DB, Sperling AI, Di Rienzo A, Mapping Variation in Cellular and Transcriptional Response to 1,25-Dihydroxyvitamin D3 in Peripheral Blood Mononuclear Cells., PloS one, 11, (7), 2016, pe0159779
Nakagome S, Alkorta-Aranburu G, Amato R, Howie B, Peter BM, Hudson RR, Di Rienzo A, Estimating the Ages of Selection Signals from Different Epochs in Human History., Molecular biology and evolution, 33, (3), 2016, p657-69
Lindo, J., Huerta-Sánchez, E., Nakagome, S., Rasmussen M., Petzelt B., Mitchell J., Cybulski J.S., Willerslev E., Degiorgio, M., Malhi, R.S., A time transect of exomes from a Native American population before and after European contact, Nature Communications, 7, 2016, p13175
Nakagome S., Oota H., Population Genetics Analysis of the Origin of Modern Japanese, eLS , 2016
Jeong C, Nakagome S, Di Rienzo A, Deep History of East Asian Populations Revealed Through Genetic Analysis of the Ainu., Genetics, 202, (1), 2016, p261-72
Nakagome S, Sato T, Ishida H, Hanihara T, Yamaguchi T, Kimura R, Mano S, Oota H, Model-based verification of hypotheses on the origin of modern Japanese revisited by Bayesian inference based on genome-wide SNP data., Molecular biology and evolution, 32, (6), 2015, p1533-43
Nakagome S, On the use of kernel approximate Bayesian computation to infer population history., Genes & genetic systems, 90, (3), 2015, p153-62
Katsumura T, Oda S, Nakagome S, Hanihara T, Kataoka H, Mitani H, Kawamura S, Oota H, Natural allelic variations of xenobiotic-metabolizing enzymes affect sexual dimorphism in Oryzias latipes., Proceedings. Biological sciences / The Royal Society, 281, (1797), 2014
Nakagome S. and Mano S., Application of kernel approximate Bayesian computation to demographic inferences, Annual Meeting of the Society for Molecular Biology and Evolution 2014, San Juan, Puerto Rico, June 9-12, 2014
Sato T, Nakagome S, Watanabe C, Yamaguchi K, Kawaguchi A, Koganebuchi K, Haneji K, Yamaguchi T, Hanihara T, Yamamoto K, Ishida H, Mano S, Kimura R, Oota H, Genome-wide SNP analysis reveals population structure and demographic history of the ryukyu islanders in the southern part of the Japanese archipelago., Molecular biology and evolution, 31, (11), 2014, p2929-40
Said HS, Suda W, Nakagome S, Chinen H, Oshima K, Kim S, Kimura R, Iraha A, Ishida H, Fujita J, Mano S, Morita H, Dohi T, Oota H, Hattori M, Dysbiosis of salivary microbiota in inflammatory bowel disease and its association with oral immunological biomarkers., DNA research : an international journal for rapid publication of reports on genes and genomes, 21, (1), 2014, p15-25
Nakagome S, Fukumizu K, Mano S, Kernel approximate Bayesian computation in population genetic inferences., Statistical applications in genetics and molecular biology, 12, (6), 2013, p667-78
Nakagome S, Mano S, Hasegawa M, Comment on "Nuclear genomic sequences reveal that polar bears are an old and distinct bear lineage"., Science, 339, (6127), 2013, p1522
Osada N, Nakagome S, Mano S, Kameoka Y, Takahashi I, Terao K, Finding the factors of reduced genetic diversity on X chromosomes of Macaca fascicularis: male-driven evolution, demography, and natural selection., Genetics, 195, (3), 2013, p1027-35
Nakagome S, Mano S, Hasegawa M, Ancestral polymorphisms and sex-biased migration shaped the demographic history of brown bears and polar bears., PloS one, 8, (11), 2013, pe78813
Nakagome S, Nakajima Y, Mano S, Biogeography revealed by mariner-like transposable element sequences via a Bayesian coalescent approach., Journal of molecular evolution, 77, (3), 2013, p64-9
Nakagome S., Chinen H., Iraha A., Hokama A., Takeyama Y., Sakisaka S., Matsui T., Kidd J.R., Kidd K.K., Said H.S., Suda W., Morita H., Hattori M., Hanihara T., Kimura R., Ishida H., Fujita J., Kinjo F., Mano S., Oota H., Evolutionary insights into genetic and environmental factors for Crohn's disease in Ryuku and Northern Kyushu, American Society of Human Genetics 2013 Annual Meeting, Boston, USA, October 22-26, 2013
Nakagome S., Fukumizu K., Mano S., Kernel Bayesian computation, XXVIth International Biometric Conference, Kobe, Japan, August 26-31, 2012
Evolutionary Insights into the "Population-Specificity" of the Genetic Factors Associated with Inflammatory Bowel Diseases in, editor(s)Mustafa M. Shennak , Ulcerative Colitis from Genetics to Complications, 2012, [Shigeki Nakagome, Hiroki Oot]
Nakagome S., Fukumizu K., Mano S., Kernel Bayesian computation, Population Genetics Group Meeting 45, Nottingham, UK, January 4-7, 2012
Nakagome S, Mano S, Kozlowski L, Bujnicki JM, Shibata H, Fukumaki Y, Kidd JR, Kidd KK, Kawamura S, Oota H, Crohn's disease risk alleles on the NOD2 locus have been maintained by natural selection on standing variation., Molecular biology and evolution, 29, (6), 2012, p1569-85
Koganebuchi K., Katsumura T., Nakagome S., Ishida H., Kawamura S., Oota H., The Asian Archival DNA Repository Consortium, Autosomal and Y-chromosomal STR markers reveal a close relationship between Hokkaido Ainu and Ryukyu islanders, Anthropological Science, 120, (3), 2012, p199--208
Nakagome S., Mano S., Kozlowski L., Bujnicki J. M., Shibata H., Fukumaki Y., Kidd J. R., Kidd. K. K., Kawamura S., Oota H., Population specific susceptibility to Crohn's disease and signals of natural selection on standing variation, American Society of Human Genetics 2011 Annual Meeting, Montreal, Canada, October 11-15, 2011
Nakagome S., Mano S., Kozlowski L., Bujnicki J. M., Shibata H., Fukumaki Y., Kidd J. R., Kidd. K. K., Kawamura S., Oota H., Population specific distribution of Crohn's disease risk alleles on the NOD2 locus and natural selection on standing variation, Annual Meeting of the Society for Molecular Biology and Evolution 2011, Kyoto, Japan, July 26-30, 2011
Nakagome S., Mano S., Kidd J. R., Kidd K. K., Kawamura S., and Oota H., An evolutionary analysis of the NOD2 gene associated with Crohn's disease, Annual Meeting of the Society for Molecular Biology and Evolution 2010, Lyon, France, July 4-8, 2010
Nakagome S, Takeyama Y, Mano S, Sakisaka S, Matsui T, Kawamura S, Oota H, Population-specific susceptibility to Crohn's disease and ulcerative colitis; dominant and recessive relative risks in the Japanese population., Annals of human genetics, 74, (2), 2010, p126-36
Nakagome S., Takeyama Y., Mano S., Sakisaka S., Matsui T., Kawamura S., and Oota H., A population specific susceptibility and genotype risk to Crohn's disease and ulcerative colitis, American Society of Human Genetics 2009 Annual Meeting, Honolulu, USA, October 20-24, 2009
Nakagome S, Pecon-Slattery J, Masuda R, Unequal rates of Y chromosome gene divergence during speciation of the family Ursidae., Molecular biology and evolution, 25, (7), 2008, p1344-56
Non-Peer-Reviewed Publications
Murray M., Nakamura S., Fuentes M., Ogawa M., Cassidy L.M., Gakuhari T., Nakagome S., Ancient genomics reveals a genetic continuum with dual structure in the Classic Copan, bioRxiv, 2024
Shigeki Nakagome, Paleogenomic time-travel to Japan: Insights into demography, selection, and pathogen loads, International Symposium for Paleogenomics, Tokyo, Japan, 03/03/2024, 2024
Shigeki Nakagome, Ancient Human and Pathogen Genomics in the Japanese archipelago, Paleogenomics and Paleopathology -Future perspective-, Kanazawa, Japan, 07/02/2023, 2023
Shigeki Nakagome, Applicability of ancient genomics to decoding the legacy of human past in insular East Asia, Research Seminar at Kanazawa University School of Medicine, Kanazawa, Japan, 25/07/2023, 2023
Shigeki Nakagome, Genomic insights into human past and health from a study of insular East Asia, TTMI Conference, Dublin, Ireland, 21/04/2023, 2023
Shigeki Nakagome, Paleogenomics in the Japanese archipelago, Lecture Series of Anthropology, The University of Tokyo, Tokyo, Japan, 07/07/2023, 2023
Shigeki Nakagome, Exploring the past to understand our health today: an ancient genomics study in insular East Asia, TTMI Seminar Series, Dublin, Ireland, 14/03/2023, 2023
Shigeki Nakagome, Tracing genetic origins and legacy of Japanese populations: Insights from ancient genomics in insular East Asia, Seminar at UCL, London, UK, 26/04/2023, 2023
Untangling the history of Japanese populations through paleogenomics in, editor(s)Yukinori Okada , Statistical Genomics in the era of post-GWAS, Yodosha, 2023, [Shigeki Nakagome]
Shigeki Nakagome, A paleogenomic time travel to pre- and proto-historic Japan, TCD Asian Studies Lecture Series, Dublin, Ireland, 21/10/2022, 2022
Shigeki Nakagome, A paleogenomic time-travel through agricultural transformation at the edge of Asia, RIKEN IMS Seminar, Japan, 29/08/2022, 2022
Shigeki Nakagome, Exploring the origins of modern Japanese through paleogenomics, The 33rd Takato Molecular Cell Biology Symposium, Japan, 26/08/2022, 2022
Shigeki Nakagome, Paleogenomic analysis on human demography and adaptation in insular East Asia, ASHBi Seminar, Kyoto University Institute for the Advanced Study of Human Biology, 01/08/2022, 2022
Shigeki Nakagome, The tripartite genomic origins of modern Japanese, Research seminar at Department of Statistical Genetics, Osaka University Graduate School of Medicine, Osaka, Japan, 26/07/2022, 2022
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]
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
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
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
Nakagome S., Japanese Origins 2019: The Dual Structure Hypothesis at 30, Interdisciplinary TransEurasian Conference, Jena, Germany, January 9-10, 2019, Martine Robbeets
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
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
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
Nakagome S., Applying population genetics to human complex disease, The 1739th Biological Symposium, National Institute of Genetics, Mishima, Japan, February 28, 2014
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.]
Nakagome S., Evolutionary study of Crohn's disease gene, Invited seminar at National Institute of Biomedical Genomics, West-Bengal, India, March 5, 2013, Partha P. Majumder
Nakagome S., Mano S., Kozlowski L., Bujnicki J. M., Kidd J. R., Kidd. K. K., Kawamura S., Oota H., An evolutionary study of human complex diseases, Workshop on Evolutionary Analyses and Applications, Xi'an and Lhasa, China, June 9, 2011
Research Expertise
Description
My research centres on exploring the evolutionary factors that contribute to health disparities among human populations. I am particularly interested in how exposures to various environmental pressures in the past, including infectious diseases, have shaped genetic diversity and influenced disease susceptibility across different regions of the world. By integrating ancient genomes with modern genetic data, my work aims to reveal patterns of local adaptations and their lasting impacts on health today. A key aspect of my research is the study of populations outside Europe, which have historically received less attention. By analysing ancient DNA from diverse regions, including those beyond Western Eurasia, we aim to reveal how different environments and historical challenges have influenced human evolution. This approach not only deepens our understanding of global human history but also provides valuable insights into how past adaptations continue to affect health outcomes today.Recognition
Representations
Associate Editor in Human Genome Variation
Analysis Provider in GenomeAsia 100K
Review Editor for Frontier in Ecology and Evolution
Member of Asian DNA Repository Consortium
Awards and Honours
Japan Society for the Promotion of Science Overseas Research Fellowships
Research Fellowships of the Japan Society for the Promotion of Science for Young Scientists (PD)
Research Fellowships of the Japan Society for the Promotion of Science for Young Scientists (DC2)
Postdoctoral Travel Award, Annual Meeting of the Society for Molecular Biology and Evolution, Kyoto, Japan
Dean's Award in International Exchange Section, Graduate School of Frontier Sciences, The University of Tokyo (awarded as the organizing committee of international conference)
Dean's Prize, College of Bioresource Sciences, Nihon University
Scholarship at College of Bioresource Sciences, Nihon University
Memberships
Irish Society of Human Genetics
European Society of Human Genetics
Society for Molecular Biology and Evolution
The American Society of Human Genetics