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Dr. Shigeki Nakagome
Assistant Professor, Psychiatry

Biography

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.

Publications and Further Research Outputs

Peer-Reviewed Publications

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, 2021 URL

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, 2020 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 Journal Article, 2020 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, 2019 DOI TARA - Full Text 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, 2018 DOI URL

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 Poster, 2018 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, 2018 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, 2018 DOI URL

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 Journal Article, 2017

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 Poster, 2017

Foley C, Corvin A, Nakagome S, Genetics of Schizophrenia: Ready to Translate?, Current Psychiatry Reports, 19, (9), 2017, p61- Journal Article, 2017 URL DOI

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 Journal Article, 2017 DOI URL

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 Oral Presentation, 2017 URL

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 Journal Article, 2017

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 Journal Article, 2016 DOI

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 Journal Article, 2016 TARA - Full Text DOI

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 Journal Article, 2016 DOI TARA - Full Text

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 Journal Article, 2016 DOI TARA - Full Text

Nakagome S., Oota H., Population Genetics Analysis of the Origin of Modern Japanese, eLS , 2016 Journal Article, 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 Journal Article, 2016 DOI

Nakagome S, On the use of kernel approximate Bayesian computation to infer population history., Genes & genetic systems, 90, (3), 2015, p153-62 Journal Article, 2015 DOI

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 Journal Article, 2015 DOI

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 Journal Article, 2014 DOI

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 Oral Presentation, 2014 URL

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 Journal Article, 2014 TARA - Full Text DOI

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 Journal Article, 2014 DOI

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 Journal Article, 2013 DOI TARA - Full Text

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 Journal Article, 2013 DOI

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 Journal Article, 2013 DOI

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 Journal Article, 2013 DOI TARA - Full Text

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 Journal Article, 2013 DOI

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 Poster, 2013 URL

Nakagome S., Fukumizu K., Mano S., Kernel Bayesian computation, Population Genetics Group Meeting 45, Nottingham, UK, January 4-7, 2012 Oral Presentation, 2012 URL

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 Journal Article, 2012 DOI TARA - Full Text

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 Journal Article, 2012

Nakagome S., Fukumizu K., Mano S., Kernel Bayesian computation, XXVIth International Biometric Conference, Kobe, Japan, August 26-31, 2012 Oral Presentation, 2012 URL

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] Book Chapter, 2012 TARA - Full Text DOI

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 Poster, 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 Oral Presentation, 2011 URL

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 Poster, 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 Journal Article, 2010 DOI

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 Poster, 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 Journal Article, 2008 DOI TARA - Full Text

Non-Peer-Reviewed Publications

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, 2020 DOI

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, 2020

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, 2020

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, 2019 URL

Nakagome S., Japanese Origins 2019: The Dual Structure Hypothesis at 30, Interdisciplinary TransEurasian Conference, Jena, Germany, January 9-10, 2019, Martine Robbeets Invited Talk, 2019 URL

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, 2019 DOI

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, 2019

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, 2018 URL

Nakagome S., Applying population genetics to human complex disease, The 1739th Biological Symposium, National Institute of Genetics, Mishima, Japan, February 28, 2014 Invited Talk, 2014 URL

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 Invited Talk, 2013

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, 2013 URL

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 Invited Talk, 2011

Research Expertise

Description

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.

Keywords

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

Recognition

Representations

Analysis Provider in GenomeAsia 100K 2018-Present

Review Editor for Frontier in Ecology and Evolution 2013-Present

Member of Asian DNA Repository Consortium 2013-Present

Awards and Honours

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

Memberships

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