(#Corresponding author, §Equal contribution)


Jomon genome sheds light on East Asian population history

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.

bioRxiv, doi: https://doi.org/10.1101/579177.


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.


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.


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.


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.


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.


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.


Ancestral polymorphisms and sex-biased migration shaped the demographic history of brown bears and polar bears

Nakagome S.#, Mano S., Hasegawa M.

PLOS ONE, 8(11):e78813.

Kernel approximate Bayesian computation in population genetic inferences

Nakagome S., Fukumizu K., Mano S.

Statistical Application in Genetics and Molecular Biology, 12(6): 667-678.

Finding the factors of reduced genetic diversity on X chromosomes of Macaca fascicularis: male-driven evolution, demography, and natural selection

Osada N., Nakagome S., Mano S., Kameoka Y., Takahashi I., Terao K.

Genetics, 195:1007-1025.

Selected as "Recommended paper" in Faculty of 1000.

Biogeography revealed by Mariner-like transposable element sequences via a Bayesian coalescent approach

Nakagome S., Nakajima Y., Mano S.

Journal of Molecular Evolution, 77(3):64-69.

Comment on “Nuclear Genomic Sequences Reveal that Polar Bears Are an Old and Distinct Bear Lineage”

Nakagome S.#, Mano S., Hasegawa M.

Science, 339:1522.


Autosomal and Y-chromosomal STR markers reveal a close relationship between Hokkaido Ainu and Ryukyu islanders

Koganebuchi K., Katsumura T., Nakagome S., Ishida H., Kawamura S., Oota H., and The Asian Archival DNA Repository Consortium

Anthropological Science, 120(3): 199-208.

Evolutionary insights into the “population-specificity” of genetic factors associated with inflammatory bowel diseases

Nakagome S. and Oota H.

Ulcerative Colitis from Genetics to Complications, Mustafa M. Shennak (Editor), InTech (Rijeka, Croatia), pp. 1-20.

Crohn’s disease risk alleles on the NOD2 locus have been maintained by natural selection on standing variation

Nakagome S., Mano S., Kozlowski L., Bujnicki J. M., Shibata H., Fukumaki Y., Kidd J. R., Kidd. K. K., Kawamura S., Oota H.

Molecular Biology and Evolution, 29(6): 1569-1585.

Selected as "Recommended paper" in Faculty of 1000.


Population-specific susceptibility to Crohn’s disease and ulcerative colitis; dominant and recessive relative risks in the Japanese population

Nakagome S., Takeyama Y., Mano S., Sakisaka S., Matsui T., Kawamura S., Oota H.

Annals of Human Genetics, 74(2): 126-136.


Unequal rates of Y chromosome gene divergence during speciation of the family Ursidae

Nakagome S., Pecon-Slattery J., Masuda R.

Molecular Biology and Evolution, 25(7): 1344-1356.