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Dr. Shigeki Nakagome

Assistant Professor (Psychiatry)
ST JAMESS HOSPITAL
      
Profile Photo

Dr. Shigeki Nakagome

Assistant Professor (Psychiatry)
ST JAMESS HOSPITAL

 nakagoms@tcd.ie

 3531896 2241


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.
  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
Details Date
Associate Editor in Human Genome Variation 2024-Present
Analysis Provider in GenomeAsia 100K 2018-Present
Member of Asian DNA Repository Consortium 2013-Present
Review Editor for Frontier in Ecology and Evolution 2013-Present
Language Skill Reading Skill Writing Skill Speaking
English Fluent Fluent Fluent
Japanese Fluent Fluent Fluent
Details Date From Date To
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
Go Sato, Yuji Yamamoto, Kyuto Sonehara, Ryunosuke Saiki, Takafumi Ojima, Masahiro Kanai, Aoxing Liu, Ryuya Edahiro, Yuya Shirai, Shinichi Namba, Ho Namkoong, Takanori Hasaegawa, Yuriko N. Koyanagi, Yumiko Kasugai, Taiki Yamaji, Shiori Nakano, Giulio Genovese, Timo P. Sipilä, Awaisa Ghazal, Hiromu Tanaka, Shuhei Azekawa, Yoshifumi Uwamino, Kenichi Yamamoto, Ken Suzuki, Tsuyoshi Hata, Mamoru Uemura, Yoshito Takeda, Akinori Kanai, Shinichi Higashiue, Shuzo Kobayashi, Hisaaki Afuso, Kosho Matsuura, Yojiro Mitsumoto, Yasuhiko Fujita, FinnGen, the Japan COVID-19 Task Force, the Biobank Japan Project, Yoshiya Oda, Yutaka Suzuki, Takayuki Morisaki, Makoto Ishii, Yuko Kitagawa, Ryuji Koike, Akinori Kimura, Seiya Imoto, Satoru Miyano, Takanori Kanai, Jun Takayama, Motoki Iwasaki, Norie Sawada, Koichi Fukunaga, Keitaro Matsuo, Atsushi Kumanogoh, Yuichiro Doki, Hidetoshi Eguchi, Shigeki Nakagome, Gen Tamiya, Andrea Ganna, Aarno Palotie, Mark J. Daly, James F. Wilson, Masayuki Yamamoto, Koichi Matsuda, Seishi Ogawa, Toshimasa Yamauchi, Takashi Kadowaki, Yukinori Okada, Genetic regulation across germline and somatic variation on the Y chromosome contributes to type 2 diabetes, Nature Medicine, 32, (3), 2026, p894 - 905, p894-905 , Journal Article, PUBLISHED  DOI
Elena S. Gusareva, Amit Gourav Ghosh, V. N. Kharkov, Seik"Soon Khor, ". ". """"""", Nikita Moshkov, Namrata Kalsi, Aakrosh Ratan, Cassie E. Heinle, Niall P. Cooke, Cláudio M. Bravi, M. V. Smolnikova, Sergey Tereshchenko, ". ". """""""", I. Yu. Khitrinskaya, Andrey Marusin, Magomed O. Razhabov, ". ". """"""""", M. G. Swarovskaya, ". ". """""""""", Ksenia V. Vagaitseva, ". ". """"""", Aitalina Sukhomyasova, ". ". """"""""", Deepa Panicker, Poh Nee Ang, Choou Fook Lee, Yanqing Koh, See Ting Leong, Changsook Park, Sachin R. Lohar, Zhei Hwee Yap, Soo Guek Ng, Justine Dacanay, Daniela I. Drautz"Moses, Nurul Adilah Binte Ramli, Katsushi Tokunaga, Ian McGonigle, Inaho Danjoh, Andrés Moreno"Estrada, Atsushi Tajima, Hideyuki Tanabe, Yukio Nakamura, Shigeki Nakagome, Tatiana V. Tatarinova, Vadim Stepanov, Stephan C. Schuster, Hie Lim Kim, From North Asia to South America: Tracing the longest human migration through genomic sequencing, Science, 388, (6748), 2025, peadk5081 - eadk5081, peadk5081-eadk5081 , Journal Article, PUBLISHED  DOI
Madeleine Murray, Seiichi Nakamura, Melvin Fuentes, Rolando Canizales, Omar Talavera, Salvador Varela, Zoila Madrid, Carlos Carbajal, Masahiro Ogawa, Minoru Yoneda, Lara M. Cassidy, Takashi Gakuhari, Shigeki Nakagome, Ancient genomes reveal demographic trajectories during the Classic Maya period, Current Biology, 35, (11), 2025, p2709 - 2719.e5, p2709-2719.e5 , Journal Article, PUBLISHED  DOI
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, Journal Article, PUBLISHED  DOI
Nakagome S., Cooke N.P., Male-driven admixture facilitated subsistence shift in northern China, Anthropological Science, 2024, Journal Article, PUBLISHED  DOI
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-, Journal Article, PUBLISHED  DOI
Kenichi Yamamoto, Shinichi Namba, Kyuto Sonehara, Ken Suzuki, Saori Sakaue, Niall P. Cooke, Shinichi Higashiue, Shuzo Kobayashi, Hisaaki Afuso, Kosho Matsuura, Yojiro Mitsumoto, Yasuhiko Fujita, Torao Tokuda, the Biobank Japan Project, Yuji Yamanashi, Yoichi Furukawa, Takayuki Morisaki, Yoshinori Murakami, Yoichiro Kamatani, Kaori Muto, Akiko Nagai, Yusuke Nakamura, Wataru Obara, Ken Yamaji, Kazuhisa Takahashi, Satoshi Asai, Yasuo Takahashi, Hiroki Yamaguchi, Yasunobu Nagata, Satoshi Wakita, Chikako Nito, Yu"ki Iwasaki, Shigeo Murayama, Kozo Yoshimori, Yoshio Miki, Daisuke Obata, Masahiko Higashiyama, Akihide Masumoto, Yoshinobu Koga, Yukihiro Koretsune, Koichi Matsuda, Takashi Gakuhari, Toshimasa Yamauchi, Takashi Kadowaki, Shigeki Nakagome, Yukinori Okada, Genetic legacy of ancient hunter-gatherer Jomon in Japanese populations, Nature Communications, 15, (1), 2024, p9780 - 9780, p9780-9780 , Journal Article, PUBLISHED  DOI
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-, Journal Article, PUBLISHED  DOI
Niall P Cooke, Valeria Mattiangeli, Lara M Cassidy, Kenji Okazaki, Kenji Kasai, Daniel G Bradley, Takashi Gakuhari, Shigeki Nakagome, Genomic insights into a tripartite ancestry in the Southern Ryukyu Islands, Evolutionary Human Sciences, 5, 2023, pe23-, Journal Article, PUBLISHED
Shigeki Nakagome, Faculty Opinions recommendation of Archaic humans have contributed to large-scale variation in modern human T cell receptor genes., Faculty Opinions " Post-Publication Peer Review of the Biomedical Literature, 2022, Dataset, PUBLISHED  DOI
  

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Shigeki Nakagome, Paleogenomic time-travel to Japan: Insights into demography, selection, and pathogen loads, International Symposium for Paleogenomics, Tokyo, Japan, 03/03/2024, 2024, Invited Talk, PUBLISHED
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, Journal Article, PUBLISHED
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], Book Chapter, PUBLISHED
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, Invited Talk, PUBLISHED
Shigeki Nakagome, Genomic insights into human past and health from a study of insular East Asia, TTMI Conference, Dublin, Ireland, 21/04/2023, 2023, Invited Talk, PUBLISHED
Shigeki Nakagome, Ancient Human and Pathogen Genomics in the Japanese archipelago, Paleogenomics and Paleopathology -Future perspective-, Kanazawa, Japan, 07/02/2023, 2023, Invited Talk, PUBLISHED
Shigeki Nakagome, Paleogenomics in the Japanese archipelago, Lecture Series of Anthropology, The University of Tokyo, Tokyo, Japan, 07/07/2023, 2023, Invited Talk, PUBLISHED
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, Invited Talk, PUBLISHED
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, Invited Talk, PUBLISHED
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, Invited Talk, PUBLISHED

  


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Award Date
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
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.