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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.

Publications and Further Research Outputs

Peer-Reviewed Publications

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

Alleyne D, Witonsky DB, Mapes B, Nakagome S, Sommars M, Hong E, Muckala KA, Di Rienzo A, Kupfer SS, Colonic transcriptional response to 1",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, 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

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

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 DOI TARA - Full Text

Lindo, J., Huerta-Sánchez, E., Nakagome, S., (...), 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

Shigeki Nakagome, Hiroki Oota, Population Genetics Analysis of the Origin of Modern Japanese, eLS , 2016 Journal Article, 2016

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 TARA - Full Text 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

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

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

Nakagome S, Mano S, Hasegawa M, Comment on "Nuclear genomic sequences reveal that polar bears are an old and distinct bear lineage"., Science (New York, N.Y.), 339, (6127), 2013, p1522 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, 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, 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

Kae Koganebuchi, Takafumi Katsumura, Shigeki Nakagome, Hajime Ishida, Shoji Kawamura, Hiroki Oota, THE Asian Archival DNA Repository Consortium, Autosomal and Y-chromosomal STR markers reveal a close relationship between Hokkaido Ainu and Ryukyu islanders, AS, 120, (3), 2012, p199--208 Journal Article, 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 Journal Article, 2012 TARA - Full Text DOI

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, 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, 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 TARA - Full Text DOI

Research Expertise


My general area of research interest is in understanding the biological roles of regulatory variants in human disease and evolution. Growing evidence shows that regulatory variants have facilitated local adaptations in humans and many of these variants may affect disease susceptibility. The main focus of my research is on gene by environment interactions (GEIs) that result in dysregulation of host immune response to commensal bacterial flora and contribute to the susceptibility to inflammatory bowel diseases (IBD). Because the gut microbiome plays key roles in the development of IBD, GEIs involving the microbiome are a likely contributor to IBD risk. Regulatory variants also have a well-recognized medical relevance in complex diseases and, in particular, the enrichment of the regulatory variants is strong in the case of IBD. Therefore, regulatory variation in response to the gut microbiome is likely to result in GEIs. My research leverages cutting-edge genomic and computational tools and approaches, integrating them into a novel way to analyze genomic data. The goals of my research are to understand how regulatory variants that interact with the gut microbiome contribute to the susceptibility to IBD and what evolutionary forces acted on such regulatory variants.


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



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


Society for Molecular Biology and Evolution 2009 – Present

The American Society of Human Genetics 2009 – Present