more details: see Researchmap
* is a corresponding author. † equally contributions.
Matsumae H*†, Savage PE*†, Ranacher P†, Blasi DE*, Currie TE, Sato T, Tajima A, Brown S, Stoneking M,Shimizu KK, Oota H*, Bickel B. "Exploring deep-time relationships between cultural and genetic evolution in Northeast Asia". 2019. BioRxiv 513929. -> Now published from Science Advances.
Sato T, Adachi N, Kimura R, Hosomichi K, Yoneda M, Oota H, Tajima A, Toyoda T, Kanzawa-Kiriyama H, Matsumae H, Koganebuchi K, Shimizu KK, Shinoda K, Hanihara T, Weber A, Kato H, Ishida H, "Whole-Genome Sequencing of a 900-Year-Old Human Skeleton Supports Two Past Migration Events from the Russian Far East to Northern Japan ", Genome biology and evolution 13(9) Sept. 1 2021
Matsumae H*†, Ranacher P*†, Savage PE*†, Blasi DE*, Currie TE, Sato T, Tajima A, Brown S, Stoneking M,Shimizu KK, Oota H*, Bickel B*. "Exploring correlations in genetic and cultural variation across language families in Northeast Asia", Sci. Adv. 2021, August 18:Vol. 7, no. 34, eabd9223, DOI: 10.1126/sciadv.abd9223
Our paper is highlighted by Focus in Science Advances! Simon Greenhill "Do languages and genes share cultural evolutionary history?", Oct 6, 2021 https://www.science.org/doi/10.1126/sciadv.abm2472
Press-release in English: https://www.media.uzh.ch/en/Press-Releases/2021/Grammar.html
Press-release in Japanese: https://www.tokai.ac.jp/news/detail/post_341.html
News from American Association for the Advancement of Science (AAAS) (by Shannon Kelleher): https://www.aaas.org/news/correlation-discovered-between-genetic-history-grammar-northeast-asia
Media report :
Gakuhari T, Nakagome S, Rasmussen S, Allentoft ME, Sato T, Korneliussen T, Chuinneagáin BN, Matsumae H, Koganebuchi K, Schmidt R, Mizushima S, Kondo O, Shigehara N, Yoneda M, Kimura R, Ishida H, Masuyama T, Yamada Y, Tajima A, Shibata H, Toyoda A, Tsurumoto T, Wakebe T, Shitara H, Hanihara T, Willerslev E, Sikora M, Oota H. "Ancient Jomon genome sequence analysis sheds light on migration patterns of early East Asian populations.", Commun Biol. 2020 Aug 25;3(1):437. doi: 10.1038/s42003-020-01162-2. PMID: 32843717.
McColl H, Racimo F, Vinner L, Demeter F, Gakuhari T, Moreno-Mayar JV, van Driem G, Gram Wilken U, Seguin-Orlando A, de la Fuente Castro C, Wasef S, Shoocongdej R, Souksavatdy V, Sayavongkhamdy T, Saidin MM, Allentoft ME, Sato T, Malaspinas AS, Aghakhanian FA, Korneliussen T, Prohaska A, Margaryan A, de Barros Damgaard P, Kaewsutthi S, Lertrit P, Nguyen TMH, Hung HC, Minh Tran T, Nghia Truong H, Nguyen GH, Shahidan S, Wiradnyana K, Matsumae H, Shigehara N, Yoneda M, Ishida H, Masuyama T, Yamada Y, Tajima A, Shibata H, Toyoda A, Hanihara T, Nakagome S, Deviese T, Bacon AM, Duringer P, Ponche JL, Shackelford L, Patole-Edoumba E, Nguyen AT, Bellina-Pryce B, Galipaud JC, Kinaston R, Buckley H, Pottier C, Rasmussen S, Higham T, Foley RA, Lahr MM, Orlando L, Sikora M, Phipps ME, Oota H, Higham C, Lambert DM, Willerslev E. "The prehistoric peopling of Southeast Asia", Science, 2018, Jul 6;361(6397):88-92. doi: 10.1126/science.aat3628. PMID: 29976827.
Menardo F., Praz C.R., Wyder S., Ben-David R., Bourras S., Matsumae H., McNally K.E., Parlange F., Riba A., Roffler S., Schaefer L.K., Shimizu K.K., Valenti L., Zbinden H., Wicker T., Keller B." Hybridization of powdery mildew strains gives rise to pathogens on novel agricultural crop species." 2016, Nat Genet. doi:10.1038/ng.3485 PMID:26752267.
Matsumae H *, Ishiwata R, Minamoto T, Ishida N, Ogishima S, and Tanaka H. "Detection of periodic patterns in microarray data reveals novel oscillating transcripts of biological rhythms in Ciona intestinalis" 2015, Artificial Life and Robotics, doi:10. 1007/ s10015-015-0237-6. Link to the paper.
A source code of COSOPT in our paper is available from Github.
Savage P.E. , Matsumae H, Oota H, Stoneking M, Currie T, Tajima A, Gillan M and Brown S. "How ‘Circumpolar’ is Ainu Music? Musical and Genetic Perspectives on the History of the Japanese Archipelago", Ethnomusicology Forum, 2015. DOI: 10.1080/17411912.2015.1084236 link
Takezawa Y, Kato K, Oota H, Caulfiel T, Fujimoto A, Honda S (Henry S), Kamatani N, Kawamura S, Kawashima K, Kimura R, Matsumae H, Saito A, Savage P.E., Seguchi N, Shimizu K, Terao S, Yamaguchi-Kabata Y, Yasukouchi A, Yoneda M and Tokunaga K. “Human genetic research, race, ethnicity and the labeling of populations: Recommendations based on an interdisciplinary workshop in Japan”, BMC Medical Ethics, 15:33, 2014.
Matsuoka Y, Matsumae H, Kato M, Eisfeld AJ, Neumann G, Hase T, Ghosh S, Shoemaker J.E, Lopes T.J.S, Watanabe T, Watanabe S, Fukuyama S, Kitano H and Kawaoka Y. “A comprehensive map of the influenza A virus replication cycle”, BMC Systems Biology, 7:97, 2013. PMID: 24088197.
Matsumae H, Hamada M, Fujie M, Niimura Y, Tanaka H, Kawashima T. “A methodical microarray design enables surveying of expression of a broader range of genes in Ciona intestinalis”, Gene, 519(1), 82-90, 2013. PMID:23388151.
Minamoto T, Hanai S, Kadota K, Oishi K, Matsumae H, Fujie M, Azumi K, Satoh N, Satake M, Ishida N. “Circadian clock in Ciona intestinalis revealed by microarray analysis and oxygen consumption.” J Biochem. 147(2), 175-84, 2010. PMID:19855119.
COSOPT is an algorithm to detect periodic gene expression and described in (Panda et al. 2002) and (Straume 2004). Our implementations (both R and C versions are available) on Github.
2020, Information Processing Society of Japan, IPSJ Yamashita SIG Research Award
2003, Pre-Patent contest for undergraduate students, co-organized by MEXT, Japan Patent Office, Japan Patent Attorneys Association, and Japan Institute of Invention and Innovation. 2003.
JST FOREST (Fusion Oriented REsearch for disruptive Science and Technology)(Yagi Panel), anthropological informatics, 2021.04-2027.03
KAKEN Wakate, population genomics of a disease-related fungus, 2020.04-2022.03
KAKEN Grants-in-Aid for Scientific Research, Evolinguistics, 2020.04-2022.03
KAKEN Grants-in-Aid for Scientific Research, Evolinguistics 2018.04-2020.03
Pilot Project, School of Medicine, Tokai University, 2020
Pilot Project, School of Medicine, Tokai University, 2019
ROIS-DS-JOINT Research Grant, 2019
the Joint Research Grant, Medical Mycology Research Center (MMRC), Chiba University. 2019.
SOKEN Project grant, Tokai University, 2019-2021.
Workshop for genes and languages in Northeast Asia, supported by URPPs Evolution in Action and Language and Space, University of Zurich, 2016
URPP Evolution in Action pilot study, University of Zurich, 2015