Publications — Nakagome

(#Corresponding author, §Equal contribution)

2024

Male-driven admixture facilitated subsistence shift in northern China

Nakagome S.#, Cooke N.P.

Anthropological Science

Ancient genomics reveals a genetic continuum with dual structure in the Classic Copan

Murray M., Nakamura S.#, Fuentes M., Ogawa M., Cassidy L.M., Gakuhari T.#, Nakagome S.#

bioRxiv, doi: https://doi.org/10.1101/2024.05.17.594672

Genomic imputation of ancient Asian populations contrasts local adaptation in pre-and post-agricultural Japan

Cooke N.P., Murray M., Cassidy L.M., Mattiangeli V., Okazaki K., Kasai K., Gakuhari T., Bradley D.G., Nakagome S.#

iScience, 27(6):110050

Medieval genomes from eastern Mongolia share a stable genetic profile over a millennium

Lee J., Sato T., Tajima A., Amgalantugs T., Tsogtbaatar B., Nakagome S., Miyake T., Shiraishi N., Jeong C., Gakuhari T.

Human Population Genetics and Genomics, 4(1):0004

2023

Genomic insights into a tripartite ancestry in the Southern Ryukyu Islands

Cooke N.P.#, Mattiangeli V., Cassidy L.M., Okazaki K., Kasai K., Bradley D.G., Gakuhari T., Nakagome S.#

Evolutionary Human Sciences, 5:e23

2021

Sex-specific phenotypic effects and evolutionary history of an ancient polymorphic deletion of the human growth hormone receptor

Saitou M., Resendez S., Pradhan A.J., Wu F., Lie N.C., Hall N.J., Zhu Q., Reinholdt L., Satta Y., Speidel L., Nakagome S., Hanchard N.A., Churchill G., Lee C., Atilla-Gokcumen G.E., Mu X., Gokcumen O.

Science Advances, 7:eabi4476

Ancient genomics reveals tripartite origins of Japanese populations

Cooke N.P.§, Mattiangeli V.§, Cassidy L.M., Okazaki K., Stokes C.A., Onbe S., Hatakeyama S., Machida K., Kasai K., Tomioka N., Matsumoto A., Ito M., Kojima Y., Bradley D.G.#, Gakuhari T.#, Nakagome S.#

Science Advances, 7:eabh2419

2020

Ancient Jomon genome sequence analysis sheds light on migration patterns of early East Asian populations

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.

Communication Biology, 3:437.

The evolving Japanese: the dual structure hypothesis at 30

Hudson M.J., Nakagome S., Whitman J.B.

Evolutionary Human Sciences, 2(e6):1-13.

A statistical modelling reveals bi-directional chromatin scanning by RAG in the human TCR-α locus

O'Connor C., McNamara D., Nakagome S.#

bioRxiv, doi: https://doi.org/10.1101/2020.02.21.959197

Genomic profiling of intestinal T-cell receptor repertoires in inflammatory bowel disease

Saravanarajan K., Douglas A.R., Ismail M. S., Omorogbe J., Semenov S., Muphy G., O’Riordan F., McNamara D., Nakagome S.#

Genes & Immunity, https://doi.org/10.1038/s41435-020-0092-x

2019

Inferring the model and onset of natural selection under varying population size from the site frequency spectrum and haplotype structure

Nakagome S.#, Hudson R.R., Di Rienzo A.

Proceedings of the Royal Society B: Biological Sciences, 286:20182541.

2018

Rapid evolution of a skin-lightening allele in southern African KhoeSan

Lin M., Siford R.L., Martin A.R., Nakagome S., Möller M., Hoal E.G., Bustamante C.D., Gignoux C.R., Henn B.M.

Proceedings of the National Academy of Sciences of the United States of America, 115(52):13324-13329.

Fine-tuning of Approximate Bayesian Computation for human population genomics

Cooke N.P., Nakagome S.#

Current Opinion in Genetics & Development, 53:60-69.

The prehistoric peopling of Southeast Asia

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.

Science, 361:88-92.

2017

Genetics of Schizophrenia: Ready to Translate?

Foley C., Corvin A., Nakagome S.

Current Psychiatry Reports, 19(6):61.

Selected as "Recommended paper" in Faculty of 1000.

An ancestral haplotype of the human PERIOD2 gene associates with reduced sensitivity to light-induced melatonin suppression

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.

PLOS ONE, 12(6):e0178373.

Confounding effects of microbiome on the susceptibility of TNFSF15 to Crohn’s disease in the Ryukyu Islands

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.

Human Genetics, 136(4):387-397.

Colonic transcriptional response to 1α,25(OH)2 vitamin D3 in African- and European-Americans

Alleyne D., Witonsky D.B., Mapes B., Nakagome S., Sommars M., Hong E., Muckala K.A., Di Rienzo A., Kupfer S.

The Journal of Steroid Biochemistry and Molecular Biology, 168:49-59.

2016

A time transect of exomes from a Native American population before and after European contact

Lindo J., Huerta-Sanchez E., Nakagome S., Rasmussen M., Petzelt B., Mitchell J., Cybulski J.S., Willerslev E., DeGiorgio M., Malhi R.S.

Nature Communications, 7:13175.

Mapping variation in cellular and transcriptional response to 1,25-dihydroxyvitamin D3 in peripheral blood mononuclear cells

Kariuki S.N., Maranville J.C., Baxter S.S., Jeong C., Nakagome S., Hrusch C.L., Witonsky D.B., Sperling A.I., Di Rienzo A.

PLOS ONE, 11(7):e0159779.

Patterns of transcriptional response to 1,25-dihydroxyvitamin D3 and bacterial lipopolysaccharide in primary human monocytes

Kariuki S.N., Blischak J.D., Nakagome S., Witonsky D.B., Di Rienzo A.

G3, 6(5):1345-1355.

Population Genetics Analysis of the Origin of Modern Japanese

Nakagome S.#, Oota H.

eLS, DOI: 10.1002/9780470015902.a0026516.

Estimating the ages of selection signals from different epochs in human history

Nakagome S.§, Alkorta-Aranburu G.§, Amato R., Howie B., Peter B.M., Hudson R.R., Di Rienzo A.

Molecular Biology and Evolution, 33(3):657-669.

Deep history of East Asian populations revealed through genetic analysis of the Ainu

Jeong C.§, Nakagome S.§#, Di Rienzo A.#

Genetics, 202(1):261-272.

2015

On the use of kernel approximate Bayesian computation to infer population history

Nakagome S.#

Genes and Genetic Systems, 90(3):153-162.

Model-based verification of hypotheses on the origin of modern Japanese revisited by Bayesian inference based on genome-wide SNP data

Nakagome S., Sato T., Ishida H., Hanihara T., Yamaguchi T., Kimura R., Mano S., Oota H., The Asian DNA Repository Consortium.

Molecular Biology and Evolution, 32(6):1533-1543.

Natural allelic variations of xenobiotic-metabolizing enzymes affect sexual dimorphism in Oryzias latipes

Katsumura T., Oda S., Nakagome S., Hanihara T., Kataoka H., Mitani H., Kawamura S., Oota H.

Proceedings of The Royal Society B, 281(1797):20142259.

2014

Genome-wide SNP analysis reveals population structure and demographic history of the Ryukyu Islanders in the southern part of the Japanese Archipelago

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.

Molecular Biology and Evolution, 31(11):2929–2940.

Dysbiosis of salivary microbiota in inflammatory bowel disease and its association with oral immunological biomarkers

Said H.S., 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.

DNA Research, 21(1):15-25.

Selected as "Recommended paper" in Faculty of 1000.