ph, D., The University of Tokyo, Mar. 2002

Population genetics

Molecular genetics

Anthropology

Life Science, System genome science

Life Science, Genome biology

Life Science, Biodiversity and systematics

Life Science, Evolutionary biology

Bachelor's degree program, School of Engineering

Master's degree program, Graduate School of Information Science and Technology

Doctoral (PhD) degree program, Graduate School of Information Science and Technology

Jul. 2019, 日本学術振興会, 特別研究員等審査会専門委員（書面担当）の表彰
長田直樹

Sep. 2014, Genetic Society of Japan, The GSJ Award for Young Scientists
ゲノム情報と進化理論の統合による進化機構の解明
Naoki Osada

Oct. 2007, 日本遺伝学会, ベストペーパー賞
On the correlation between gene expression pattern and selection intensity in the human genome
長田直樹

Reproducible and Multi-Study Transcriptomic Integration with disint , Disease Integration and Clustering Toolkit, and Application to Drug Repositioning
Yi Cong; Naoki Osada; Toshinori Endo
OMICS: A Journal of Integrative Biology, SAGE Publications, 13 Jan. 2026, [Peer-reviewed]
English, Scientific journal, Integrating Big Data, such as large-scale transcriptomic datasets across diseases, continues to be a major challenge. This is in part due to inconsistent preprocessing and the lack of a standardized, reproducible analytical framework. Existing pipelines often rely on manual parameter tuning and fragmented scripts, which limits cross-dataset comparability and downstream interpretability. We developed disint (disease integration and clustering toolkit), an open-source Python framework for standardized cross-dataset expression integration, embedding, and clustering. The pipeline implements housekeeping gene-based normalization, disease-specific log ₂ fold-change computation, automated Uniform Manifold Approximation and Projection hyperparameter optimization, and adaptive K-means clustering. Building on its outputs, we further implemented a prototype downstream module, disease reposition , which extracts disease-specific gene signatures, evaluates their shared components, and explores potential drug repositioning candidates. The framework was validated on 28 transcriptomic datasets encompassing 34 disease categories and 386 samples, including 255 patient and 131 healthy control samples, covering 194,182 genes in total. These results highlight the reproducibility, scalability, and translational versatility of our proposed framework.

Genomic determinants of antibiotic resistance for Helicobacter pylori treatment: a retrospective phenotypic and genotypic observational study
Francisco José Martínez-Martínez; Álvaro Chiner-Oms; Victoria Furió; Francisco José Martínez-Martínez; Victoria Furió; Iñaki Comas; Álvaro Chiner-Oms; Yoshio Yamaoka; John P Dekker; Francis Megraud; Marine Jauvain; Christine Varon; Philippe Lehours; Quentin Jehanne; Lucie Bénéjat; Astrid Ducournau; Judith Romero-Gallo; Uma Krishna; Richard M Peek; M Blanca Piazuelo; Keith T Wilson; John T Loh; Timothy L Cover; Filipa F Vale; Naïma Raaf; Hafeza Aftab; Junko Akada; Takashi Matsumoto; Freddy Haesebrouck; Thais F Bartelli; Diana Noronha Nunes; Adriane Pelosof; Claudia Zitron Sztokfisz; Emmanuel Dias-Neto; Paulo Pimentel Assumpção; Petko Karagyozov; Ivan Tishkov; Karen J Goodman; Janis Geary; Taylor J Cromarty; Nancy L Price; Douglas Quilty; Alejandro H Corvalan; Robinson Gonzalez; Arnoldo Riquelme; Apolinaria García-Cancino; Cristian Parra-Sepúlveda; Francisco Castillo; Maria Mercedes Bravo; Alvaro Pazos; Luis E Bravo; James G Fox; Vanessa Ramírez-Mayorga; Silvia Molina-Castro; Sundry Durán-Bermúdez; Christian Campos-Núñez; Manuel Chaves-Cervantes; Evariste Tshibangu-Kabamba; Ghislain Disashi Tumba; Antoine Tshimpi-Wola; Patrick de Jesus Ngoma-Kisoko; Fabien Mbaya Tshibangu; Alain Cimuanga Mukanya; Tressy Kalenga Nkomba; Modesto Cruz; José Jiménez Abreu; Ousman Secka; Alexander Link; Peter Malfertheiner; Michael Buenor Adinortey; Ansumana Sandy Bockarie; Cynthia Ayefoumi Adinortey; Eric Gyamerah Ofori; Dionyssios N Sgouras; Beatriz Martinez-Gonzalez; Spyridon Michopoulos; Sotirios Georgopoulos; Elisa Hernandez; Ricardo L Dominguez; Douglas R Morgan; Hjördís Harðardóttir; Anna Ingibjörg Gunnarsdóttir; Hallgrímur Guðjónsson; Jón Gunnlaugur Jónasson; Einar S Björnsson; Mamatha Ballal; Vignesh Shetty; Muhammad Miftahussurur; Titong Sugihartono; Ricky Indra Alfaray; Langgeng Agung Waskito; Kartika Afrida Fauzia; Ari Fahrial Syam; Hasan Maulahela; Reza Malekzadeh; Avi Peretz; Maya Azrad; Avi On; Valli De Re; Stefania Zanussi; Renato Cannizzaro; Vincenzo Canzonieri; Takaya Shimura; Kengo Tokunaga; Takako Osaki; Shigeru Kamiya; Khaled Jadallah; Ismail Matalka; Nurbek Sagynbekuly Igissin; Mariia Satarovna Moldobaeva; Attokurova Rakhat; Il Ju Choi; Jae Gyu Kim; Nayoung Kim; Mārcis Leja; Reinis Vangravs; Ģirts Šķenders; Aiga Rūdule; Ilze Kikuste; Aigars Vanags; Dace Rudzīte; Juozas Kupcinskas; Edita Kiudeliene; Vytautas Kiudelis; Rolandas Gedgaudas; Paulius Jonaitis; Gediminas Kiudelis; Laimas Jonaitis; Jurgita Skieceviciene; Jamuna Vadivelu; Mun Fai Loke; Kumutha Malar Vellasamy; Roberto Herrera-Goepfert; Juan Octavio Alonso-Larraga; Than Than Yee; Kyaw Htet; Takeshi Matsuhisa; Pradeep Krishna Shrestha; Shamshul Ansari; Olumide Abiodun; Christopher Jemilohun; Kolawole Oluseyi Akande; Oluwatosin Olu-Abiodun; Francis Ajang Magaji; Ayodele Omotoso; Uchenna Okonkwo; Chukwuemeka Chukwunwendu Osuagwu; Opeyemi O Owoseni; Carlos Castaneda; Miluska Castillo; Billie Velapatino; Robert H Gilman; Paweł Krzyżek; Grażyna Gościniak; Dorota Pawełka; Izabela Korona-Glowniak; Halina Cichoz-Lach; Mónica Oleastro; Ceu Figueiredo; Jose C Machado; Rui M Ferreira; Dmitry S Bordin; Maria A Livzan; Vladislav V Tsukanov; Patrick Tan; Khay Guan Yeoh; Feng Zhu; Reid Ally; Rainer Haas; Wolfgang Fischer; Milagrosa Montes; María Fernández-Reyes; Esther Tamayo; Jacobo Lizasoain; Luis Bujanda; Sergio Lario; María José Ramírez-Lázaro; Xavier Calvet; Eduard Brunet-Mas; María José Domper-Arnal; Sandra García-Mateo; Daniel Abad-Baroja; Pedro Delgado-Guillena; Leticia Moreira; Josep Botargues; Isabel Pérez-Martínez; Eva Barreiro-Alonso; Virginia Flores; Javier P Gisbert; Edurne Amorena Muro; Pedro Linares; Laura Alcoba; Vicente Martin; Lars Engstrand; Helena Enroth; Peter M Keller; Karoline Wagner; Daniel Pohl; Yi-Chia Lee; Jyh-Ming Liou; Ming-Shiang Wu; Bekir Kocazeybek; Suat Sarıbas; İhsan Tasçı; Süleyman Demiryas; Nuray Kepil; Luis Quiel; Miguel Villagra; Morgan Norton; Deborah Johnson; Robert J Huang; Joo Ha Hwang; Wendy Szymczak; William R Jacobs; Haejin In; Roni Bollag; Aileen Lopez; Edward J Kruse; Joseph White; Charlotte Lane; Yang Gao; Benjamin D Gold; Marcia Cruz-Correa; María González-Pons; Luz M Rodriguez; Vo Phuoc Tuan; Ho Dang Quy Dung; Tran Thanh Binh; Tran Thi Huyen Trang; Vu Van Khien; Yukako Katsura; Patricio Gonzalez-Hormazabal; Eduardo Tarazona-Santos; Roxana Zamudio; Leonardo Mariño-Ramírez; Steffen Backert; Michael Naumann; Annemieke Smet; Douglas E Berg; Koji Yahara; Martin J Blaser; Tamas Vincze; Richard D Morgan; Richard J Roberts; Javier Torres; Roberto C Torres; Mehwish Noureen; Joshua L Cherry; Naoki Osada; Masaki Fukuyo; Masanori Arita; Santiago Sandoval-Motta; Rajiv Boscolo Agostini; Silvia Ghirotto; Zilia Y Muñoz-Ramírez; Daniel Falush; Kaisa Thorell; Ikuo Uchiyama; Ichizo Kobayashi; Difei Wang; Belynda Hicks; Meredith Yeager; Amy Hutchinson; Kedest Teshome; Kristie Jones; Wen Luo; Alisa M Goldstein; Nan Hu; Philip R Taylor; Minkyo Song; Kai Yu; Bin Zhu; Christian C Abnet; Charles S Rabkin; M Constanza Camargo; Yoshio Yamaoka; John P Dekker; Francis Mégraud; Lucie Bénéjat; Astrid Ducournau; Alban Giese; Quentin Jehanne; Marine Jauvain; M Constanza Camargo; Iñaki Comas; Philippe Lehours
The Lancet Microbe, 101217, 101217, Elsevier BV, Dec. 2025, [Peer-reviewed]
Scientific journal

Evolutionary dynamics of polymorphic endogenous retrovirus insertions across wild house mouse populations
Tomoki Yano; Toyoyuki Takada; Kazumichi Fujiwara; Dai Watabe; Shutaro Hirose; Hiroshi Masuya; Toshinori Endo; Naoki Osada
25 Sep. 2025

Helicobacter pylori base-excision restriction enzyme in stomach carcinogenesis
Masaki Fukuyo; Noriko Takahashi; Katsuhiro Hanada; Ken Ishikawa; Česlovas Venclovas; Koji Yahara; Hideo Yonezawa; Takeshi Terabayashi; Yukako Katsura; Naoki Osada; Atsushi Kaneda; M Constanza Camargo; Charles S Rabkin; Ikuo Uchiyama; Takako Osaki; Ichizo Kobayashi
PNAS Nexus, 7, 8, pgaf244, Oxford University Press (OUP), 05 Aug. 2025, [Peer-reviewed]
English, Scientific journal, Abstract

Many recent lines of evidence from the human microbiome and other fields indicate bacterial involvement in various types of cancer. Helicobacter pylori has been recognized as the major cause of stomach cancer (gastric cancer), but the mechanism by which it destabilizes the human genome to cause cancer remains unclear. Our recent studies have identified a unique family of toxic restriction enzymes that excise a base (A: adenine) from their recognition sequence (5’-GTAC). At the resulting abasic sites (5’-GT_C), its inherent endonuclease activity or that of a separate endonuclease may yield atypical strand breaks that resist repair by ligation. Here we present evidence demonstrating involvement of its H. pylori member, HpPabI, in stomach carcinogenesis: (i) Association of intact HpPabI gene with gastric cancer in the global Helicobacter pylori Genome Project and the open genomes; (ii) Frequent mutations at A in 5’-GTAC in the gastric cancer genomes as well as in H. pylori genomes; (iii) Its induction of chromosomal double-strand breaks in infected human cells and of mutagenesis in bacterial test systems. In addition, its unique regions that interact with DNA exhibit signs of diversifying selection. Our further analysis revealed similar oncogenic bacterium-restriction-enzyme pairs for other types of cancer. These results set another stage for cancer research and medicine around oncogenic restriction enzymes.

Copy Number Variation in the Amylase Gene (AMY) in the Brown Bear (Ursus arctos), Based on Whole Genome Resequencing Data
Naoko Kotani; Yu Endo; Naoki Osada; Tsutomu Mano; Alexei V. Abramov; Ryuichi Masuda
Zoological Science, 42, 4, 366, 373, Zoological Society of Japan, 14 Jul. 2025, [Peer-reviewed]
English, Scientific journal

Compensatory Evolution
Naoki Osada
Reference Module in Life Sciences, Elsevier, Jun. 2025, [Invited], [Lead author, Last author, Corresponding author]
English, In book

Population genetic structure of two mole species (Mogera imaizumii and M. wogura) in the Japanese Archipelago
Takeru Tsunoi; Gohta Kinoshita; Reiko Mitsuhashi; Masashi Harada; Jun J Sato; Shoji Tatsumoto; Yasuhiro Go; Hitoshi Suzuki; Naoki Osada
Journal of Mammalogy, Oxford University Press (OUP), 20 Jan. 2025, [Peer-reviewed], [Last author]
English, Scientific journal, Abstract

The Japanese Archipelago hosts a diverse group of mammalian species, including subterranean moles, whose migratory and dispersion patterns are believed to have been significantly influenced by environmental fluctuations during the Quaternary period. However, the genetic structure of these species has not been extensively studied using large-scale molecular data. In this study, we explored the population structure of 2 widely distributed mole species in Japan: the Lesser Japanese Mole (Mogera imaizumii), found mainly in eastern Honshu with a few isolated patches in western Honshu, and the Large Japanese Mole (M. wogura), distributed in western Honshu, Shikoku, and Kyushu. We constructed a genome sequence for M. wogura using the Chromium system and conducted a reduced genome representation analysis using multiplexed inter-simple sequence repeat genotyping by sequencing on M. imaizumii and M. wogura. Our findings indicate that M. imaizumii comprises 3 major genetic clusters (ncMim- 1 to 3) that are strongly differentiated (fixation index ranging from 0.376 to 0.478). We discovered genetic connections between populations in the southern Kinki area and isolated populations in western Japan. Mogera wogura consists of 5 main genetic clusters (ncMwo- 1 to 5). Evidence of introgression between 2 genetic clusters (ncMwo-2/ncMwo-3) was found among individuals from the Chugoku area, indicating secondary contact between the 2 differentiated populations. Both species shared a similar population boundary within the Kinki area, which may be associated with current and past geographic barriers. We confirmed that the Kinki region serves as an important site for the diversification of moles, where multiple factors (topographic barriers, interspecific interactions, and/or isolation related to vegetation) may have shaped their population genetic structures.

Population Genomics of Japanese Macaques (Macaca fuscata): Insights Into Deep Population Divergence and Multiple Merging Histories
Atsunori Higashino; Katsuki Nakamura; Naoki Osada
Genome Biology and Evolution, 17, 1, Oxford University Press (OUP), 06 Jan. 2025, [Peer-reviewed], [Last author, Corresponding author]
Scientific journal, Abstract

The influence of long-term climatic changes such as glacial cycles on the history of living organisms has been a subject of research for decades, but the detailed population dynamics during the environmental fluctuations and their effects on genetic diversity and genetic load are not well understood on a genome-wide scale. The Japanese macaque (Macaca fuscata) is a unique primate adapted to the cold environments of the Japanese archipelago. Despite the past intensive research for the Japanese macaque population genetics, the genetic background of Japanese macaques at the whole-genome level has been limited to a few individuals, and the comprehensive demographic history and genetic differentiation of Japanese macaques have been underexplored. We conducted whole-genome sequencing of 64 Japanese macaque individuals from 5 different regions, revealing significant genetic differentiation and functional variant diversity across populations. In particular, Japanese macaques have low genetic diversity and harbor many shared and population-specific gene loss, which might contribute to population-specific phenotypes. Our estimation of population demography using phased haplotypes suggested that, after the strong population bottleneck shared among all populations around 400 to 500 kya, the divergence among populations initiated around 150 to 200 kya, but there has been the time with strong gene flow between some populations after the split, indicating multiple population split and merge events probably due to habitat fragmentation and fusion during glacial cycles. These findings not only present a complex population history of Japanese macaques but also enhance their value as research models, particularly in neuroscience and behavioral studies. This comprehensive genomic analysis sheds light on the adaptation and evolution of Japanese macaques, contributing valuable insights to both evolutionary biology and biomedical research.

Gene content, phage cycle regulation model and prophage inactivation disclosed by prophage genomics in the Helicobacter pylori Genome Project
Filipa F. Vale; Richard J. Roberts; Ichizo Kobayashi; M. Constanza Camargo; Charles S. Rabkin
Gut Microbes, 16, 1, Informa UK Limited, 12 Aug. 2024, [Peer-reviewed]
Scientific journal

Genomic Evidence for the Complex Evolutionary History of Macaques (Genus Macaca)
Zhenxin Fan; Rusong Zhang; Anbo Zhou; Jody Hey; Yang Song; Naoki Osada; Yuzuru Hamada; Bisong Yue; Jinchuan Xing; Jing Li
Journal of Molecular Evolution, 92, 286, 299, Springer Science and Business Media LLC, 18 Apr. 2024, [Peer-reviewed]
Scientific journal

Inference of selective forces on house mouse genomes during secondary contact in East Asia
Kazumichi Fujiwara; Shunpei Kubo; Toshinori Endo; Toyoyuki Takada; Toshihiko Shiroishi; Hitoshi Suzuki; Naoki Osada
Genome Research, 34, 366, 375, Cold Spring Harbor Laboratory, 20 Mar. 2024, [Peer-reviewed], [Last author, Corresponding author]
Scientific journal, The house mouse (Mus musculus), which is commensal to humans, has spread globally via human activities, leading to secondary contact between genetically divergent subspecies. This pattern of genetic admixture can provide insights into the selective forces at play in this well-studied model organism. Our analysis of 163 house mouse genomes, with a particular focus on East Asia, revealed substantial admixture between the subspeciescastaneusandmusculus, particularly in Japan and southern China. We revealed, despite the different level of autosomal admixture among regions, that all Y Chromosomes in the East Asian samples belonged to themusculus-type haplogroup, potentially explained by genomic conflict under sex-ratio distortion owing to varying copy numbers of ampliconic genes on sex chromosomes,SlxandSly. Our computer simulations, designed to replicate the observed scenario, show that the preferential fixation ofmusculus-type Y Chromosomes can be achieved with a slight increase in the male-to-female birth ratio. We also investigated the influence of selection on the posthybridization of the subspeciescastaneusandmusculusin Japan. Even though the genetic background of most Japanese samples closely resembles the subspeciesmusculus, certain genomic regions overrepresented thecastaneus-like genetic components, particularly in immune-related genes. Furthermore, a large genomic block (∼2 Mbp) containing a vomeronasal/olfactory receptor gene cluster predominantly harboredcastaneus-type haplotypes in the Japanese samples, highlighting the crucial role of olfaction-based recognition in shaping hybrid genomes.

Exploring The Interplay Between Scoring Functions and Physico-chemical Properties in Antibody-antigen Docking
Sangeetha Ratnayake; Axel Martinelli; Toshinori Endo; Naoki Osada
IPSJ Transactions on Bioinformatics, 17, 10, 17, Information Processing Society of Japan, Feb. 2024, [Peer-reviewed], [Last author]
English, Scientific journal

Phylogenetics and Population Genetics of the Asian House Shrew, Suncus murinus–S. montanus Species Complex, Inferred From Whole-Genome and Mitochondrial DNA Sequences, with Special Reference to the Ryukyu Archipelago, Japan
Satoshi D. Ohdachi; Kazumichi Fujiwara; Chandra Shekhar; Nguyn Trưng Sơn; Hitoshi Suzuki; Naoki Osada
Zoological Science, 41, 2, Zoological Society of Japan, 30 Jan. 2024, [Peer-reviewed], [Last author]
Scientific journal

Advancing Antibody-antigen Interface Analysis in Docking Scoring Functions for Precision Docking Analysis
Sangeetha Ratnayake; Axel Martinelli; Toshinori Endo; Naoki Osada
IPSJ Transactions on Bioinformatics, 17, 40, 47, Information Processing Society of Japan, 2024, [Peer-reviewed], [Last author]
Scientific journal

The Helicobacter pylori Genome Project: insights into H. pylori population structure from analysis of a worldwide collection of complete genomes
Kaisa Thorell; Zilia Y. Muñoz-Ramírez; Difei Wang; Santiago Sandoval-Motta; Rajiv Boscolo Agostini; Silvia Ghirotto; Roberto C. Torres; Judith Romero-Gallo; Uma Krishna; Richard M. Peek; M. Blanca Piazuelo; Naïma Raaf; Federico Bentolila; Hafeza Aftab; Junko Akada; Takashi Matsumoto; Freddy Haesebrouck; Rony P. Colanzi; Thais F. Bartelli; Diana Noronha Nunes; Adriane Pelosof; Claudia Zitron Sztokfisz; Emmanuel Dias-Neto; Paulo Pimentel Assumpção; Ivan Tishkov; Laure Brigitte; Kouitcheu Mabeku; Karen J. Goodman; Janis Geary; Taylor J. Cromarty; Nancy L. Price; Douglas Quilty; Alejandro H. Corvalan; Carolina A. Serrano; Robinson Gonzalez; Arnoldo Riquelme; Apolinaria García-Cancino; Cristian Parra-Sepúlveda; Giuliano Bernal; Francisco Castillo; Alisa M. Goldstein; Nan Hu; Philip R. Taylor; Maria Mercedes Bravo; Alvaro Pazos; Luis E. Bravo; Keith T. Wilson; James G. Fox; Vanessa Ramírez-Mayorga; Silvia Molina-Castro; Sundry Durán-Bermúdez; Christian Campos-Núñez; Manuel Chaves-Cervantes; Evariste Tshibangu-Kabamba; Ghislain Disashi Tumba; Antoine Tshimpi-Wola; Patrick de Jesus; Ngoma-Kisoko; Dieudonné Mumba Ngoyi; Modesto Cruz; Celso Hosking; José Jiménez Abreu; Christine Varon; Lucie Beneja; Ousman Secka; Alexander Link; Peter Malfertheiner; Michael Buenor Adinortey; Ansumana Sandy Bockarie; Cynthia Ayefoumi Adinortey; Eric Gyamerah Ofori; Dionyssios N. Sgouras; Beatriz Martinez-Gonzalez; Spyridon Michopoulos; Sotirios Georgopoulos; Elisa Hernandez; Braulio Volga Tacatic; Mynor Aguilar; Ricardo L. Dominguez; Douglas R. Morgan; Hjördís Harðardóttir; Anna Ingibjörg Gunnarsdóttir; Hallgrímur Guðjónsson; Jón Gunnlaugur Jónasson; Einar S. Björnsson; Mamatha Ballal; Vignesh Shetty; Muhammad Miftahussurur; Titong Sugihartono; Ricky Indra Alfaray; Langgeng Agung Waskito; Kartika Afrida Fauzia; Ari Fahrial Syam; Hasan Maulahela; Reza Malekzadeh; Masoud Sotoudeh; Avi Peretz; Maya Azrad; Avi On; Valli De Re; Stefania Zanussi; Renato Cannizzaro; Vincenzo Canzonieri; Takaya Shimura; Kengo Tokunaga; Takako Osaki; Shigeru Kamiya; Khaled Jadallah; Ismail Matalka; Nurbek Igissinov; Mariia Satarovna Moldobaeva; Attokurova Rakha; Il Ju Choi; Jae Gyu Kim; Nayoung Kim; Minkyo Song; Mārcis Leja; Reinis Vangravs; Ģirts Šķenders; Dace Rudzīte; Aiga Rūdule; Aigars Vanags; Ilze Kikuste; Juozas Kupcinskas; Jurgita Skieceviciene; Laimas Jonaitis; Gediminas Kiudelis; Paulius Jonaitis; Vytautas Kiudelis; Greta Varkalaite; Jamuna Vadivelu; Mun Fai Loke; Kumutha Malar Vellasamy; Roberto Herrera-Goepfer; Juan Octavio Alonso-Larraga; Than Than Yee; Kyaw Hte; Takeshi Matsuhisa; Pradeep Krishna Shrestha; Shamshul Ansari; Olumide Abiodun; Christopher Jemilohun; Kolawole Oluseyi Akande; Oluwatosin Olu-Abiodun; Francis Ajang Magaji; Ayodele Omotoso; Chukwuemeka Chukwunwendu Osuagwu; Uchenna Okonkwo; Opeyemi O. Owoseni; Carlos Castaneda; Miluska Castillo; Billie Velapatino; Robert H. Gilman; Paweł Krzyżek; Grażyna Gościniak; Dorota Pawełka; Izabela Korona-Glowniak; Halina Cichoz-Lach; Monica Oleastro; Ceu Figueiredo; Jose C. Machado; Rui M. Ferreira; Dmitry S. Bordin; Maria A. Livzan; Vladislav V. Tsukanov; Patrick Tan; Khay Guan Yeoh; Feng Zhu; Reid Ally; Rainer Haas; Milagrosa Montes; María Fernández-Reyes; Esther Tamayo; Jacobo Lizasoain; Luis Bujanda; Sergio Lario; María José Ramírez-Lázaro; Xavier Calve; Eduard Brunet-Mas; María José Domper-Arnal; Sandra García-Mateo; Daniel Abad-Baroja; Pedro Delgado-Guillena; Leticia Moreira; Josep Botargues; Isabel Pérez-Martínez; Eva Barreiro-Alonso; Virginia Flores; Javier P. Gisber; Edurne Amorena Muro; Pedro Linares; Vicente Martin; Laura Alcoba; Tania Fleitas-Kanonnikoff; Hisham N. Altayeb; Lars Engstrand; Helena Enroth; Peter M. Keller; Karoline Wagner; Daniel Pohl; Yi-Chia Lee; Jyh-Ming Liou; Ming-Shiang Wu; Bekir Kocazeybek; Suat Sarıbas; İhsan Tasçı; Süleyman Demiryas; Nuray Kepil; Luis Quiel; Miguel Villagra; Morgan Norton; Deborah Johnson; Robert J. Huang; Joo Ha Hwang; Wendy Szymczak; Saranathan Rajagopalan; Emmanuel Asare; William R. Jacobs; Haejin In; Roni Bollag; Aileen Lopez; Edward J. Kruse; Joseph White; David Y. Graham; Charlotte Lane; Yang Gao; Patricia I. Fields; Benjamin D. Gold; Marcia Cruz-Correa; María González-Pons; Luz M. Rodriguez; Vo Phuoc Tuan; Ho Dang Quy Dung; Tran Thanh Binh; Tran Thi Huyen Trang; Vu Van Khien; Xiongfong Chen; Castle Raley; Bailey Kessing; Yongmei Zhao; Bao Tran; Andrés J. Gutiérrez-Escobar; Yunhu Wan; Belynda Hicks; Bin Zhu; Kai Yu; Bin Zhu; Meredith Yeager; Amy Hutchinson; Kedest Teshome; Kristie Jones; Wen Luo; Quentin Jehanne; Yukako Katsura; Patricio Gonzalez-Hormazabal; Xavier Didelo; Sam Sheppard; Eduardo Tarazona-Santos; Leonardo Mariño-Ramírez; John T. Loh; Steffen Backer; Michael Naumann; Christian C. Abne; Annemieke Sme; Douglas E. Berg; Álvaro Chiner-Oms; Iñaki Comas; Francisco José Martínez-Martínez; Roxana Zamudio; Philippe Lehours; Francis Megraud; Koji Yahara; Martin J. Blaser; Tamas Vincze; Richard D. Morgan; Richard J. Roberts; Stephen J. Chanock; John P. Dekker; Javier Torres; Timothy L. Cover; Mehwish Noureen; Wolfgang Fischer; Filipa F. Vale; Joshua L. Cherry; Naoki Osada; Masaki Fukuyo; Masanori Arita; Yoshio Yamaoka; Ichizo Kobayashi; Ikuo Uchiyama; Daniel Falush; M. Constanza Camargo; Charles S. Rabkin
Nature Communications, 14, 1, 8184, Springer Science and Business Media LLC, 11 Dec. 2023, [Peer-reviewed]
English, Scientific journal, Abstract

Helicobacter pylori, a dominant member of the gastric microbiota, shares co-evolutionary history with humans. This has led to the development of genetically distinct H. pylori subpopulations associated with the geographic origin of the host and with differential gastric disease risk. Here, we provide insights into H. pylori population structure as a part of the Helicobacter pylori Genome Project (HpGP), a multi-disciplinary initiative aimed at elucidating H. pylori pathogenesis and identifying new therapeutic targets. We collected 1011 well-characterized clinical strains from 50 countries and generated high-quality genome sequences. We analysed core genome diversity and population structure of the HpGP dataset and 255 worldwide reference genomes to outline the ancestral contribution to Eurasian, African, and American populations. We found evidence of substantial contribution of population hpNorthAsia and subpopulation hspUral in Northern European H. pylori. The genomes of H. pylori isolated from northern and southern Indigenous Americans differed in that bacteria isolated in northern Indigenous communities were more similar to North Asian H. pylori while the southern had higher relatedness to hpEastAsia. Notably, we also found a highly clonal yet geographically dispersed North American subpopulation, which is negative for the cag pathogenicity island, and present in 7% of sequenced US genomes. We expect the HpGP dataset and the corresponding strains to become a major asset for H. pylori genomics.

Genealogical characterization of regional populations and dorsal coat color variation in the house mouse Mus musculus from Asia based on haplotype structure analysis of a gene-rich region harboring Mc1r
Kazuhiro Zakoh; Kazumichi Fujiwara; Toyoyuki Takada; Naoki Osada; Hitoshi Suzuki
Genes & Genetic Systems, 98, 73, 87, Genetics Society of Japan, 2023, [Peer-reviewed]
Scientific journal

Whole-genome sequencing analysis of wild house mice (Mus musculus) captured in Madagascar
Kazumichi Fujiwara; Marie C. Ranorosoa; Satoshi D. Ohdachi; Satoru Arai; Yuki Sakuma; Hitoshi Suzuki; Naoki Osada
Genes & Genetic Systems, 97, 4, 193, 207, Genetics Society of Japan, 01 Aug. 2022, [Peer-reviewed], [Last author, Corresponding author]
Scientific journal

A New Approach to Drug Repurposing with Two-Stage Prediction, Machine Learning, and Unsupervised Clustering of Gene Expression
Yi Cong; Misaki Shintani; Fuga Imanari; Naoki Osada; Toshinori Endo
OMICS: A Journal of Integrative Biology, 26, 6, 339, 347, Mary Ann Liebert Inc, 01 Jun. 2022, [Peer-reviewed]
Scientific journal

Insights into Mus musculus Population Structure across Eurasia Revealed by Whole-Genome Analysis
Kazumichi Fujiwara; Yosuke Kawai; Toyoyuki Takada; Toshihiko Shiroishi; Naruya Saitou; Hitoshi Suzuki; Naoki Osada
Genome Biology and Evolution, 14, 5, Oxford University Press (OUP), 03 May 2022, [Peer-reviewed], [Last author, Corresponding author], [International Magazine]
English, Scientific journal, Abstract

For more than 100 years, house mice (Mus musculus) have been used as a key animal model in biomedical research. House mice are genetically diverse, yet their genetic background at the global level has not been fully understood. Previous studies have suggested that they originated in South Asia and diverged into three major subspecies, almost simultaneously, approximately 110,000–500,000 years ago; however, they have spread across the world with the migration of modern humans in prehistoric and historic times (∼10,000 years ago to the present day) and have undergone secondary contact, which has complicated the genetic landscape of wild house mice. In this study, we sequenced the whole-genome sequences of 98 wild house mice collected from Eurasia, particularly East Asia, Southeast Asia, and South Asia. Although wild house mice were found to consist of three major genetic groups corresponding to the three major subspecies, individuals representing admixtures between subspecies were more prevalent in East Asia than has been previously recognized. Furthermore, several samples exhibited an incongruent pattern of genealogies between mitochondrial and autosomal genomes. Using samples that likely retained the original genetic components of subspecies with the least admixture, we estimated the pattern and timing of divergence among the subspecies. The estimated divergence time of the three subspecies was 187,000–226,000 years ago. These results will help us to understand the genetic diversity of wild mice on a global scale, and the findings will be particularly useful in future biomedical and evolutionary studies involving laboratory mice established from such wild mice.

Whole-Genome Sequencing of Vero E6 (VERO C1008) and Comparative Analysis of Four Vero Cell Sublines
Kazuhiro Konishi; Toshiyuki Yamaji; Chisato Sakuma; Fumio Kasai; Toshinori Endo; Arihiro Kohara; Kentaro Hanada; Naoki Osada
Frontiers in Genetics, 13, 1, 9, 22 Mar. 2022, [Peer-reviewed], [Last author, Corresponding author]
English, Scientific journal

Predicting PRDM9 Binding Sites by a Convolutional Neural Network and Verification Using Genetic Recombination Map
Takahiro Nakamura; Toshinori Endo; Naoki Osada
IPSJ Transactions on Bioinformatics, 15, 9, 16, Information Processing Society of Japan, Mar. 2022, [Peer-reviewed], [Last author, Corresponding author]
English, Scientific journal

Phylogeographic study using nuclear genome sequences of Asip to infer the origins of ventral fur color variation in the house mouse Mus musculus
Toki Takeishi; Kazumichi Fujiwara; Naoki Osada; Akihiko Mita; Toyoyuki Takada; Toshihiko Shiroishi; Hitoshi Suzuki
Genes & Genetic Systems, 96, 1, 14, Genetics Society of Japan, Mar. 2022, [Peer-reviewed]
English, Scientific journal

Whole-genome sequencing analysis reveals the population history of Mus musculus in Madagascar
Kazumichi Fujiwara; Marie C Ranorosoa; Satoshi D Ohdachi; Satoru Arai; Yuki Sakuma; Hitoshi Suzuki; Naoki Osada
Cold Spring Harbor Laboratory, 10 Sep. 2021
In Madagascar, the house mouse (Mus musculus) is thought to have colonized along with humans and is now one of the most successfully colonized rodents on the island. In this study, we determined the whole-genome sequences of the Madagascar house mouse captured from the wild. We examined the evolutionary history of its population regarding the mitochondrial and autosomal genomes. We confirmed that in the mitochondrial genomes of Madagascar house mice, a monophyletic clade forms a basal origin within the species. An analysis of autosomal genomic sequences indicates that the Madagascar house mouse population is genetically a member of M. m. castaneus (CAS). It also contains genetic elements of M. m. domesticus (DOM) resulting from ancient hybridization. The signature of a strong population bottleneck 1000–3000 years ago was observed in the mitochondrial and autosomal genomic data. We also show that the divergence of the Madagascar population from the CAS population occurred approximately 50,000–99,000 years ago. Madagascar house mice show strong genetic affinity to many CAS samples across a wide range of Indian Ocean coastal regions. However, our results suggest that they would not have originated directly from the Indonesian islands, where Austronesian-speaking people in Madagascar originated. Because the ancient hybridization signature with DOM did not appear in the Indonesian and other CAS samples, we propose that Madagascar house mice were not directly brought by Austronesian-speaking people but came from somewhere around the Middle East or South Asia soon after the colonization of initial farmers.

Demographic history of the brown bear (Ursus arctos) on Hokkaido island, Japan, based on whole-genomic sequence analysis.
Yu Endo; Naoki Osada; Tsutomu Mano; Ryuichi Masuda
Genome Biology and Evolution, Oxford University Press (OUP), 2021, [Peer-reviewed], [International Magazine]
English, Scientific journal,
Previous studies of the brown bear (Ursus arctos) on Hokkaido Island, Japan, have detected three geographically distinct subpopulations representing different mitochondrial lineages and shown that gene flow between subpopulations has occurred due to male-biased dispersal. In this study, we determined whole-genomic sequences for six Hokkaido brown bears and analyzed these data along with previously published genomic sequences of 17 brown bears from other parts of the world. We found that the Hokkaido population is genetically distinct from the other populations, keeping genetic diversity higher than the endangered populations in Western Europe but lower than most populations on the continents. A reconstruction of historical demography showed no increase in population size for the Hokkaido population during the Eemian interglacial period (130,000–114,000 years ago). In a phylogenetic analysis of the autosomal data, the Hokkaido population formed a clade distinct from North American and European populations, showing that it has maintained genetic diversity independently from continental populations following geographical isolation on the island. This autosomal genetic similarity contrasts with the geographically separate mitochondrial lineages on Hokkaido and indicates the occurrence of male-driven gene flow between subpopulations.

House mouse Mus musculus dispersal in East Eurasia inferred from 98 newly determined complete mitochondrial genome sequences
Yue Li; Kazumichi Fujiwara; Naoki Osada; Yosuke Kawai; Toyoyuki Takada; Alexey P. Kryukov; Kuniya Abe; Hiromichi Yonekawa; Toshihiko Shiroishi; Kazuo Moriwaki; Naruya Saitou; Hitoshi Suzuki
Heredity, 126, 1, 132, 147, Springer Science and Business Media LLC, Jan. 2021, [Peer-reviewed]
English, Scientific journal, The Eurasian house mouse Mus musculus is useful for tracing prehistorical human movement related to the spread of farming. We determined whole mitochondrial DNA (mtDNA) sequences (ca. 16,000 bp) of 98 wild-derived individuals of two subspecies, M. m. musculus (MUS) and M. m. castaneus (CAS). We revealed directional dispersals reaching as far as the Japanese Archipelago from their homelands. Our phylogenetic analysis indicated that the eastward movement of MUS was characterised by five step-wise regional extension events: (1) broad spatial expansion into eastern Europe and the western part of western China, (2) dispersal to the eastern part of western China, (3) dispersal to northern China, (4) dispersal to the Korean Peninsula and (5) colonisation and expansion in the Japanese Archipelago. These events were estimated to have occurred during the last 2000–18,000 years. The dispersal of CAS was characterised by three events: initial divergences (ca. 7000–9000 years ago) of haplogroups in northernmost China and the eastern coast of India, followed by two population expansion events that likely originated from the Yangtze River basin to broad areas of South and Southeast Asia, including Sri Lanka, Bangladesh and Indonesia (ca. 4000–6000 years ago) and to Yunnan, southern China and the Japanese Archipelago (ca. 2000–3500). This study provides a solid framework for the spatiotemporal movement of the human-associated organisms in Holocene Eastern Eurasia using whole mtDNA sequences, reliable evolutionary rates and accurate branching patterns. The information obtained here contributes to the analysis of a variety of animals and plants associated with prehistoric human migration.

Exploring models of human migration to the Japanese archipelago using genome-wide genetic data
NAOKI OSADA; YOSUKE KAWAI
Anthropological Science, 129, 1, 45, 58, Anthropological Society of Nippon, 2021, [Peer-reviewed], [Invited], [Lead author, Corresponding author]
English, Scientific journal,

The origins of people in the Japanese archipelago are of long-standing interest among anthropologists, archeologists, linguists, and historians studying the history of Japan. While the 'dual-structure' model proposed by Hanihara in 1991 has been considered the primary working hypothesis for three decades, recent advances in DNA typing and sequencing technologies provide an unprecedented amount of present-day and ancient human nuclear genome data, which enable us to refine or extend the dual-structure model. In this review, we summarize recent genome sequencing efforts of present-day and ancient people in Asia, mostly focusing on East Asia, and we discuss the possible migration routes and admixture patterns of Japanese ancestors. We also report on a meta-analysis we performed by compiling publicly available datasets to clarify the genetic relationships of present-day and ancient Japanese populations with surrounding populations. Because the ancient genetic data from the Japanese archipelago have not yet been fully analyzed, we have to corroborate models of prehistoric human movement using not only new genetic data but also linguistic and archeological data to reconstruct a more comprehensive history of the Japanese people.

, 12290829

Testing sex-biased admixture origin of macaque species using autosomal and X-chromosomal genomic sequences
Naoki Osada; Kazunari Matsudaira; Yuzuru Hamada; Suchinda Malaivijitnond
Genome Biology and Evolution, 13, evaa233, Oxford University Press (OUP), 2021, [Peer-reviewed], [Lead author, Corresponding author]
English, Scientific journal,
The role of sex-specific demography in hybridization and admixture of genetically diverged species and populations is essential to understand the origins of the genomic diversity of sexually reproducing organisms. In order to infer how sex-linked loci have been differentiated undergoing frequent hybridization and admixture, we examined 17 whole-genome sequences of seven species of the genus Macaca, which shows frequent inter-specific hybridization and predominantly female philopatry. We found that hybridization and admixture were prevalent within these species. For three cases of suggested hybrid origin of species/subspecies, M. arctoides, M. fascicularis ssp. aurea, and Chinese M. mulatta, we examined the level of admixture of X chromosomes, which is less affected by male-biased migration than that of autosomes. In one case, we were able to determine that M. cyclopis and M. fuscata was genetically closer to Chinese M. mulatta than to the Indian M. mulatta, and the admixture level of Chinese M. mulatta and M. fuscata/cyclopis was more pronounced on the X chromosome than on autosomes. Since the mitochondrial genomes of Chinese M. mulatta, M. cyclopis, and M. fuscata were found to cluster together, and the mitochondrial genome of Indian M. mulatta is more distantly related, the observed pattern of genetic differentiation on X-chromosomal loci is consistent with the nuclear swamping hypothesis, in which strong, continuous male-biased introgression from the ancestral Chinese M. mulatta population to a population related to M. fuscata and M. cyclopis generated incongruencies between the genealogies of the mitochondrial and autosomal genomes.

Identification of Characteristic Genomic Markers in Human Hepatoma HuH-7 and Huh7.5.1-8 Cell Lines
Masaki Kawamoto; Toshiyuki Yamaji; Kyoko Saito; Yoshitaka Shirasago; Kazuhiro Satomura; Toshinori Endo; Masayoshi Fukasawa; Kentaro Hanada; Naoki Osada
Frontiers in Genetics, 11, Frontiers Media SA, 09 Oct. 2020, [Peer-reviewed], [Last author, Corresponding author]
Scientific journal

Comparative characterization of flavivirus production in two cell lines: Human hepatoma-derived Huh7.5.1-8 and African green monkey kidney-derived Vero.
Kyoko Saito; Masayoshi Fukasawa; Yoshitaka Shirasago; Ryosuke Suzuki; Naoki Osada; Toshiyuki Yamaji; Takaji Wakita; Eiji Konishi; Kentaro Hanada
PloS one, 15, 4, e0232274, 2020, [Peer-reviewed], [International Magazine]
English, Scientific journal, The Flaviviridae is a family of enveloped viruses with a positive-sense single-stranded RNA genome. It contains many viruses that threaten human health, such as Japanese encephalitis virus (JEV) and yellow fever virus (YFV) of the genus Flavivirus as well as hepatitis C virus of the genus Hepacivirus. Cell culture systems highly permissive for the Flaviviridae viruses are very useful for their isolation, propagation, and diagnosis, an understanding of their biology, and the development of vaccines and antiviral agents. Previously, we isolated a human hepatoma HuH-7-derived cell clone, Huh7.5.1-8, which is highly permissive to hepatitis C virus infection. Here, we have characterized flavivirus infection in the Huh7.5.1-8 cell line by comparing with that in the African green monkey kidney-derived Vero cell line, which is permissive for a wide spectrum of viruses. Upon infection with JEV, Huh7.5.1-8 cells produced a higher amount of virus particles early in infection and were more susceptible to virus-induced cell death than Vero cells. Similar outcomes were obtained when the cells were infected with another flavivirus, YFV (17D-204 strain). Quantification of cellular and extracellular viral RNA revealed that high JEV production in Huh7.5.1-8 cells can be attributed to rapid viral replication kinetics and efficient virus release early in infection. In a plaque assay, Huh7.5.1-8 cells developed JEV plaques more rapidly than Vero cells. Although this was not the case with YFV plaques, Huh7.5.1-8 cells developed higher numbers of YFV plaques than Vero cells. Sequence analysis of cDNA encoding an antiviral RNA helicase, RIG-I, showed that Huh7.5.1-8 cells expressed not only a full-length RIG-I mRNA with a known dominant-negative missense mutation but also variants without the mutation. However, the latter mRNAs lacked exon 5/6-12, indicating functional loss of RIG-I in the cells. These characteristics of the Huh7.5.1-8 cell line are helpful for flavivirus detection, titration, and propagation.

Dysfunctional missense variant of OAT10/SLC22A13 decreases gout risk and serum uric acid levels.
Toshihide Higashino; Keito Morimoto; Hirofumi Nakaoka; Yu Toyoda; Yusuke Kawamura; Seiko Shimizu; Takahiro Nakamura; Kazuyoshi Hosomichi; Akiyoshi Nakayama; Keiko Ooyama; Hiroshi Ooyama; Toru Shimizu; Miki Ueno; Toshimitsu Ito; Takashi Tamura; Mariko Naito; Hiroshi Nakashima; Makoto Kawaguchi; Mikiya Takao; Yosuke Kawai; Naoki Osada; Kimiyoshi Ichida; Ken Yamamoto; Hiroshi Suzuki; Nariyoshi Shinomiya; Ituro Inoue; Tappei Takada; Hirotaka Matsuo
Annals of the rheumatic diseases, 79, 1, 164, 166, Jan. 2020, [Peer-reviewed], [International Magazine]
English, Scientific journal

Achiasmy and sex chromosome evolution
Kazuhiro Satomura; Naoki Osada; Toshinori Endo
Ecological Genetics and Genomics, 13, 100045, Sep. 2019, [Peer-reviewed]
English, Scientific journal

Genetic diversity and population structure of Glossina morsitans morsitans in the active foci of human African trypanosomiasis in Zambia and Malawi
Yukiko Nakamura; Junya Yamagishi; Kyoko Hayashida; Naoki Osada; Elisha Chatanga; Cornelius Mweempwa; Kalinga Chilongo; John Chisi; Jenelisa Musaya; Ryosuke Omori; Noboru Inoue; Boniface Namangala; Chihiro Sugimoto
PLoS Negl. Trop. Dis., 13, 7, e0007568, Jul. 2019, [Peer-reviewed]
English, Scientific journal

Key metabolic gene for recurrent freshwater colonization and radiation in fishes
Asano Ishikawa; Naoki Kabeya; Koki Ikeya; Ryo Kakioka; Jennifer N. Cech; Naoki Osada; Miguel C. Leal; Jun Inoue; Manabu Kume; Atsushi Toyoda; Ayumi Tezuka; Atsushi J. Nagano; Yo Y. Yamasaki; Yuto Suzuki; Tomoyuki Kokita; Hiroshi Takahashi; Kay Lucek; David Marques; Yusuke Takehana; Kiyoshi Naruse; Seiichi Mori; Oscar Monroig; Nemiah Ladd; Carsten J. Schubert; Blake Matthews; Catherine L. Peichel; Ole Seehausen; Goro Yoshizaki; Jun Kitano
Science, 364, 6443, 886, 889, May 2019, [Peer-reviewed], [International Magazine]
English, Scientific journal, Colonization of new ecological niches has triggered large adaptive radiations. Although some lineages have made use of such opportunities, not all do so. The factors causing this variation among lineages are largely unknown. Here, we show that deficiency in docosahexaenoic acid (DHA), an essential ω-3 fatty acid, can constrain freshwater colonization by marine fishes. Our genomic analyses revealed multiple independent duplications of the fatty acid desaturase gene Fads2 in stickleback lineages that subsequently colonized and radiated in freshwater habitats, but not in close relatives that failed to colonize. Transgenic manipulation of Fads2 in marine stickleback increased their ability to synthesize DHA and survive on DHA-deficient diets. Multiple freshwater ray-finned fishes also show a convergent increase in Fads2 copies, indicating its key role in freshwater colonization.

Novel endogenous simian retroviral integrations in Vero cells: Implications for quality control of a human vaccine cell substrate
Chisato Sakuma; Tsuyoshi Sekizuka; Makoto Kuroda; Fumio Kasai; Kyoko Saito; Masaki Ikeda; Toshiyuki Yamaji; Naoki Osada; Kentaro Hanada
Scientific Reports, 8, 1, 644, Nature Publishing Group, 01 Dec. 2018, [Peer-reviewed], [Corresponding author]
English, Scientific journal

Comprehensive phylogenomic analysis reveals a novel cluster of simian endogenous retroviral sequences in Colobinae monkeys
Masaki Ikeda; Kazuhiro Satomura; Tsuyoshi Sekizuka; Kentaro Hanada; Toshinori Endo; Naoki Osada
American Journal of Primatology, e22882, Jun. 2018, [Peer-reviewed], [Last author, Corresponding author]
English, Scientific journal

Development of genotyping method for functionally relevant variants of cytochromes P450 in cynomolgus macaques
Y. Uno; N. Osada; S. Sakurai; N. Shimozawa; T. Iwata; K. Ikeo; H. Yamazaki
Journal of Veterinary Pharmacology and Therapeutics, 41, 1, e30, e34, Blackwell Publishing Ltd, 01 Feb. 2018, [Peer-reviewed]
English, Scientific journal

Ancient hybridization and admixture in macaques (genus Macaca) inferred from whole genome sequences.
Fan, Zhenxin; Anbo Zhou; Naoki Osada; Jianqiu Yu; Juan Jiang; Peng Li; Lianming Du; Lili Niu; Jiabo Deng; Huailiang Xu; Jinchuan Xing; Bisong Yue; Jing Li
Molecular Phylogenetics and Evolution, 127, 376, 387, 2018, [Peer-reviewed]
English, Scientific journal

Cis- and Trans-regulatory Effects on Gene Expression in a Natural Population of Drosophila melanogaster
Naoki Osada; Ryutaro Miyagi; Aya Takahashi
GENETICS, 206, 4, 2139, 2148, Aug. 2017, [Peer-reviewed], [Lead author]
English, Scientific journal

A Generalized Linear Model for Decomposing Cis-regulatory, Parent-of-Origin, and Maternal Effects on Allele-Specific Gene Expression
Yasuaki Takada; Ryutaro Miyagi; Aya Takahashi; Toshinori Endo; Naoki Osada
G3-GENES GENOMES GENETICS, 7, 7, 2227, 2234, Jul. 2017, [Peer-reviewed], [Corresponding author]
English, Scientific journal

Translational Repression of a Splice Variant of Cynomolgus Macaque CXCL1L by Its C-Terminal Sequence
Hisayuki Nomiyama; Naoki Osada; Ichiro Takahashi; Keiji Terao; Kazuya Yamagata; Osamu Yoshie
JOURNAL OF INTERFERON AND CYTOKINE RESEARCH, 37, 3, 129, 138, Mar. 2017, [Peer-reviewed]
English, Scientific journal

Compensatory Evolution
Naoki Osada
Encyclopedia of Evolutionary Biology, 1, 329, 333, May 2016, [Peer-reviewed], [Invited], [Lead author, Last author, Corresponding author]
English, Scientific journal

Complex patterns of cis-regulatory polymorphisms in ebony underlie standing pigmentation variation in Drosophila melanogaster
Ryutaro Miyagi; Noriyoshi Akiyama; Naoki Osada; Aya Takahashi
MOLECULAR ECOLOGY, 24, 23, 5829, 5841, Dec. 2015, [Peer-reviewed]
English, Scientific journal

An Individual-Based Diploid Model Predicts Limited Conditions Under Which Stochastic Gene Expression Becomes Advantageous
Tomotaka Matsumoto; Katsuhiko Mineta; Naoki Osada; Hitoshi Araki
FRONTIERS IN GENETICS, 6, 336, Nov. 2015, [Peer-reviewed]
English, Scientific journal

Genetic diversity in humans and non-human primates and its evolutionary consequences
Naoki Osada
Genes and Genetic Systems, 90, 3, 133, 145, Genetics Society of Japan, 27 Oct. 2015, [Peer-reviewed], [Invited], [Lead author, Last author, Corresponding author]
English, Scientific journal

CYP2D44 polymorphisms in cynomolgus and rhesus macaques
Yasuhiro Uno; Shotaro Uehara; Sakae Kohara; Naoki Osada; Norie Murayama; Hiroshi Yamazaki
MOLECULAR BIOLOGY REPORTS, 42, 7, 1149, 1155, Jul. 2015, [Peer-reviewed]
English, Scientific journal

Model-Based Verification of Hypotheses on the Origin of Modern Japanese Revisited by Bayesian Inference Based on Genome-Wide SNP Data
Shigeki Nakagome; Takehiro Sato; Hajime Ishida; Tsunehiko Hanihara; Tetsutaro Yamaguchi; Ryosuke Kimura; Shuhei Mano; Hiroki Oota
MOLECULAR BIOLOGY AND EVOLUTION, 32, 6, 1533, 1543, Jun. 2015, [Peer-reviewed]
English, Scientific journal

Population genetics of non-genetic traits: Evolutionary roles of stochasticity in gene expression
Katsuhiko Mineta; Tomotaka Matsumoto; Naoki Osada; Hitoshi Araki
GENE, 562, 1, 16, 21, May 2015, [Peer-reviewed]
English, Scientific journal

Ecological genomics in Xanthomonas: the nature of genetic adaptation with homologous recombination and host shifts
Chao-Li Huang; Pei-Hua Pu; Hao-Jen Huang; Huang-Mo Sung; Hung-Jiun Liaw; Yi-Min Chen; Chien-Ming Chen; Ming-Ban Huang; Naoki Osada; Takashi Gojobori; Tun-Wen Pai; Yu-Tin Chen; Chi-Chuan Hwang; Tzen-Yuh Chiang
BMC GENOMICS, 16, 188, Mar. 2015, [Peer-reviewed]
English, Scientific journal

Whole-Genome Sequencing of Six Mauritian Cynomolgus Macaques (Macaca fascicularis) Reveals a Genome-Wide Pattern of Polymorphisms under Extreme Population Bottleneck
Naoki Osada; Nilmini Hettiarachchi; Isaac Adeyemi Babarinde; Naruya Saitou; Antoine Blancher
GENOME BIOLOGY AND EVOLUTION, 7, 3, 821, 830, Mar. 2015, [Peer-reviewed]
English, Scientific journal

Adaptive divergence with gene flow in incipient speciation of Miscanthus floridulus/sinensis complex (Poaceae)
Chao-Li Huang; Chuan-Wen Ho; Yu-Chung Chiang; Yasumasa Shigemoto; Tsai-Wen Hsu; Chi-Chuan Hwang; Xue-Jun Ge; Charles Chen; Tai-Han Wu; Chang-Hung Chou; Hao-Jen Huang; Takashi Gojobori; Naoki Osada; Tzen-Yuh Chiang
PLANT JOURNAL, 80, 5, 834, 847, Dec. 2014, [Peer-reviewed]
English, Scientific journal

The Genome Landscape of the African Green Monkey Kidney-Derived Vero Cell Line
Naoki Osada; Arihiro Kohara; Toshiyuki Yamaji; Noriko Hirayama; Fumio Kasai; Tsuyoshi Sekizuka; Makoto Kuroda; Kentaro Hanada
DNA RESEARCH, 21, 6, 673, 683, Dec. 2014, [Peer-reviewed]
English, Scientific journal

Dopamine Receptor Genes and Evolutionary Differentiation in the Domestication of Fighting Cocks and Long-Crowing Chickens
Tomoyoshi Komiyama; Hisakazu Iwama; Naoki Osada; Yoji Nakamura; Hiroyuki Kobayashi; Yoshio Tateno; Takashi Gojobori
PLOS ONE, 9, 7, e101778, Jul. 2014, [Peer-reviewed]
English, Scientific journal

Prdm9 Polymorphism Unveils Mouse Evolutionary Tracks
Hiromitsu Kono; Masaru Tamura; Naoki Osada; Hitoshi Suzuki; Kuniya Abe; Kazuo Moriwaki; Kunihiro Ohta; Toshihiko Shiroishi
DNA RESEARCH, 21, 3, 315, 326, Jun. 2014, [Peer-reviewed]
English, Scientific journal

Whole-Genome Sequencing of Tibetan Macaque (Macaca thibetana) Provides New Insight into the Macaque Evolutionary History
Zhenxin Fan; Guang Zhao; Peng Li; Naoki Osada; Jinchuan Xing; Yong Yi; Lianming Du; Pedro Silva; Hongxing Wang; Ryuichi Sakate; Xiuyue Zhang; Huailiang Xu; Bisong Yue; Jing Li
MOLECULAR BIOLOGY AND EVOLUTION, 31, 6, 1475, 1489, Jun. 2014, [Peer-reviewed]
English, Scientific journal

Extracting population genetics information from a diploid genome sequence
Naoki Osada
Frontiers in Ecology and Evolution, 2, 7, Apr. 2014, [Peer-reviewed]
English, Scientific journal

Finding the Factors of Reduced Genetic Diversity on X Chromosomes of Macaca fascicularis: Male-Driven Evolution, Demography, and Natural Selection
Naoki Osada; Shigeki Nakagome; Shuhei Mano; Yosuke Kameoka; Ichiro Takahashi; Keiji Terao
GENETICS, 195, 3, 1027, +, Nov. 2013, [Peer-reviewed]
English, Scientific journal

Systematic classification of vertebrate chemokines based on conserved synteny and evolutionary history
Hisayuki Nomiyama; Naoki Osada; Osamu Yoshie
GENES TO CELLS, 18, 1, 1, 16, Jan. 2013, [Peer-reviewed]
English, Scientific journal

Weak Selection and Protein Evolution
Hiroshi Akashi; Naoki Osada; Tomoko Ohta
GENETICS, 192, 1, 15, U43, Sep. 2012, [Peer-reviewed], [Invited]
English, Scientific journal

Whole-genome sequencing and analysis of the Malaysian cynomolgus macaque (Macaca fascicularis) genome
Atsunori Higashino; Ryuichi Sakate; Yosuke Kameoka; Ichiro Takahashi; Makoto Hirata; Reiko Tanuma; Tohru Masui; Yasuhiro Yasutomi; Naoki Osada
Genome Biology, 13, 7, R58, 02 Jul. 2012, [Peer-reviewed]
English, Scientific journal

Footprints of natural and artificial selection for photoperiod pathway genes in Oryza
Chao-Li Huang; Cheng-Yu Hung; Yu-Chung Chiang; Chi-Chuan Hwang; Tsai-Wen Hsu; Chi-Chun Huang; Kuo-Hsiang Hung; Kun-Chan Tsai; Kuo-Hsiung Wang; Naoki Osada; Barbara Anna Schaal; Tzen-Yuh Chiang
PLANT JOURNAL, 70, 5, 769, 782, Jun. 2012, [Peer-reviewed]
English, Scientific journal

Evolutionary rates of commonly used nuclear and organelle markers of Arabidopsis relatives (Brassicaceae)
Chi-Chun Huang; Kuo-Hsiang Hung; Wei-Kuang Wang; Chuan-Wen Ho; Chao-Li Huang; Tsai-Wen Hsu; Naoki Osada; Chi-Chuan Hwang; Tzen-Yuh Chiang
GENE, 499, 1, 194, 201, May 2012, [Peer-reviewed]
English, Scientific journal

Mitochondrial-Nuclear Interactions and Accelerated Compensatory Evolution: Evidence from the Primate Cytochrome c Oxidase Complex
Naoki Osada; Hiroshi Akashi
MOLECULAR BIOLOGY AND EVOLUTION, 29, 1, 337, 346, Jan. 2012, [Peer-reviewed]
English, Scientific journal

Characterization of MHC class I transcripts of a Malaysian cynomolgus macaque by high-throughput pyrosequencing and EST libraries
Alice Aarnink; Pol-Andre Apoil; Ichiro Takahashi; Naoki Osada; Antoine Blancher
IMMUNOGENETICS, 63, 11, 703, 713, Nov. 2011, [Peer-reviewed]
English, Scientific journal

CpG site degeneration triggered by the loss of functional constraint created a highly polymorphic macaque drug-metabolizing gene, CYP1A2
Yasuhiro Uno; Naoki Osada
BMC EVOLUTIONARY BIOLOGY, 11, 283, 283, Oct. 2011, [Peer-reviewed]
English, Scientific journal

Novel DNA sequence isolated from blood donors with high transaminase levels
Koei Satoh; Akiko Iwata-Takakura; Naoki Osada; Akira Yoshikawa; Yuji Hoshi; Keiko Miyakawa; Yuko Gotanda; Masahiro Satake; Kenji Tadokoro; Hideaki Mizoguchi
HEPATOLOGY RESEARCH, 41, 10, 971, 981, Oct. 2011, [Peer-reviewed]
English, Scientific journal

Population Genetics in Nonmodel Organisms: II. Natural Selection in Marginal Habitats Revealed by Deep Sequencing on Dual Platforms
Renchao Zhou; Shaoping Ling; Wenming Zhao; Naoki Osada; Sufang Chen; Meng Zhang; Ziwen He; Hua Bao; Cairong Zhong; Bing Zhang; Xuemei Lu; David Turissini; Norman C. Duke; Jian Lu; Suhua Shi; Chung-I Wu
MOLECULAR BIOLOGY AND EVOLUTION, 28, 10, 2833, 2842, Oct. 2011, [Peer-reviewed]
English, Scientific journal

Phylogenetic Inconsistency Caused by Ancient Sex-Biased Gene Migration
Naoki Osada
PLOS ONE, 6, 9, e25549, e25549, Sep. 2011, [Peer-reviewed]
English, Scientific journal

A family tree of vertebrate chemokine receptors for a unified nomenclature
Hisayuki Nomiyama; Naoki Osada; Osamu Yoshie
DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY, 35, 7, 705, 715, Jul. 2011, [Peer-reviewed]
English, Scientific journal

The evolution of mammalian chemokine genes
Hisayuki Nomiyama; Naoki Osada; Osamu Yoshie
CYTOKINE & GROWTH FACTOR REVIEWS, 21, 4, 253, 262, Aug. 2010, [Peer-reviewed]
English

Ancient genome-wide admixture extends beyond the current hybrid zone between Macaca fascicularis and M. mulatta
Naoki Osada; Yasuhiro Uno; Katsuhiko Mineta; Yosuke Kameoka; Ichiro Takahashi; Keiji Terao
MOLECULAR ECOLOGY, 19, 14, 2884, 2895, Jul. 2010, [Peer-reviewed]
English, Scientific journal

Genetic Variants of CYP3A4 and CYP3A5 in Cynomolgus and Rhesus Macaques
Yasuhiro Uno; Akinori Matsushita; Naoki Osada; Shotaro Uehara; Sakae Kohara; Ryoichi Nagata; Koichiro Fukuzaki; Masahiro Utoh; Norie Murayama; Hiroshi Yamazaki
DRUG METABOLISM AND DISPOSITION, 38, 2, 209, 214, Feb. 2010, [Peer-reviewed]
English, Scientific journal

Multilocus analysis of genetic divergence between outcrossing Arabidopsis species: evidence of genome-wide admixture
Wei-Kuang Wang; Chuan-Wen Ho; Kuo-Hsiang Hung; Kuo-Hsiung Wang; Chi-Chun Huang; Hitoshi Araki; Chi-Chuan Hwang; Tsai-Wen Hsu; Naoki Osada; Tzen-Yuh Chiang
NEW PHYTOLOGIST, 188, 2, 488, 500, 2010, [Peer-reviewed]
English, Scientific journal

Collection of Macaca fascicularis cDNAs derived from bone marrow, kidney, liver, pancreas, spleen, and thymus.
Naoki Osada; Makoto Hirata; Reiko Tanuma; Yutaka Suzuki; Sumio Sugano; Keiji Terao; Jun Kusuda; Yosuke Kameoka; Katsuyuki Hashimoto; Ichiro Takahashi
BMC research notes, 2, 199, 199, 29 Sep. 2009, [Peer-reviewed], [International Magazine]
English, BACKGROUND: Consolidating transcriptome data of non-human primates is essential to annotate primate genome sequences, and will facilitate research using non-human primates in the genomic era. Macaca fascicularis is a macaque monkey that is commonly used for biomedical and ecological research. FINDINGS: We constructed cDNA libraries of Macaca fascicularis, derived from tissues obtained from bone marrow, liver, pancreas, spleen, and thymus of a young male, and kidney of a young female. In total, 5'-end sequences of 56,856 clones were determined. Including the previously established cDNA libraries from brain and testis, we have isolated 112,587 cDNAs of Macaca fascicularis, which correspond to 56% of the curated human reference genes. CONCLUSION: These sequences were deposited in the public sequence database as well as in-house macaque genome database http://genebank.nibio.go.jp/qfbase/. These data will become valuable resources for identifying functional parts of the genome of macaque monkeys in future studies.

IL-10 is a negative regulatory factor of CAWS-vasculitis in CBA/J mice as assessed by comparison with Bruton's tyrosine kinase-deficient CBA/N mice.
Noriko N Miura; Motohiko Komai; Yoshiyuki Adachi; Naoki Osada; Yosuke Kameoka; Kazuo Suzuki; Naohito Ohno
Journal of immunology (Baltimore, Md. : 1950), 183, 5, 3417, 24, 5, 01 Sep. 2009, [Peer-reviewed], [International Magazine]
English, Candida albicans water-soluble fraction (CAWS), a mannoprotein-beta-glucan complex obtained from the culture supernatant of C. albicans NBRC1385, exhibits vasculitis-inducing activity (CAWS-vasculitis) in mice. The sensitivity to CAWS-vasculitis varies greatly among mouse strains. This study examined the factors contributing to or inhibiting CAWS-vasculitis using CAWS-vasculitis-resistant CBA/J mice and Bruton's tyrosine kinase-deficient CBA/N mice, which is a CAWS-vasculitis-sensitive strain that has the same origin as CBA/J mice. After stimulation with various kinds of pathogen-associated molecular patterns, the production of inflammatory cytokines IL-6 and IFN-gamma was induced in CBA/N mice, whereas that of immunosuppressive IL-10 was induced in CAWS-vasculitis-resistant CBA/J mice. Furthermore, the production of tissue inhibitor of metalloproteinase 1, an endogenous matrix metalloproteinase inhibitor, was observed in CBA/J mice. The results strongly suggest that the difference in the production of these cytokines is closely linked to the development of CAWS-vasculitis.

Development of an integrative database with 499 novel microsatellite markers for Macaca fascicularis
Atsunori Higashino; Naoki Osada; Yumiko Suto; Makoto Hirata; Yosuke Kameoka; Ichiro Takahashi; Keiji Terao
BMC GENETICS, 10, 24, Jun. 2009, [Peer-reviewed]
English, Scientific journal

Multiple duplication of the bucentaur gene family, which recruits the APE-like domain of retrotransposon: Identification of a novel homolog and distinct cellular expression
Shintaro Iwashita; Kentaro Nakashima; Motoki Sasaki; Naoki Osada; Si-Young Song
GENE, 435, 1-2, 88, 95, Apr. 2009, [Peer-reviewed]
English, Scientific journal

Quantifying dominance and deleterious effect on human disease genes
Naoki Osada; Shuhei Mano; Jun Gojobori
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 106, 3, 841, 846, Jan. 2009, [Peer-reviewed]
English, Scientific journal

Duplication and Gene Conversion in the Drosophila melanogaster Genome
Naoki Osada; Hideki Innan
PLOS GENETICS, 4, 12, e1000305, Dec. 2008, [Peer-reviewed]
English, Scientific journal

Extensive expansion and diversification of the chemokine gene family in zebrafish: Identification of a novel chemokine subfamily CX
Hisayuki Nomiyama; Kunio Hieshima; Naoki Osada; Yoko Kato-Unoki; Kaori Otsuka-Ono; Sumio Takegawa; Toshiaki Izawa; Akio Yoshizawa; Yutaka Kikuchi; Sumio Tanase; Retsu Miura; Jun Kusuda; Miki Nakao; Osamu Yoshie
BMC GENOMICS, 9, 222, May 2008, [Peer-reviewed]
English, Scientific journal

Large-scale analysis of Macaca fascicularis transcripts and inference of genetic divergence between M.fascicularis and M. mulatta
Naoki Osada; Katsuyuki Hashimoto; Yosuke Kameoka; Makoto Hirata; Reiko Tanuma; Yasuhiro Uno; Itsuro Inoue; Munetomo Hida; Yutaka Suzuki; Sumio Sugano; Keiji Terao; Jun Kusuda; Ichiro Takahashi
BMC GENOMICS, 9, 90, Feb. 2008, [Peer-reviewed]
English, Scientific journal

Expressed sequence tags from cynomolgus monkey (Macaca fascicularis) liver: A systematic identification of drug-metabolizing enzymes
Yasuhiro Uno; Yutaka Suzuki; Hiroyuki Wakaguri; Yoshiko Sakamoto; Hitomi Sano; Naoki Osada; Katsuyuki Hashimoto; Sumio Sugano; Ituro Inoue
FEBS LETTERS, 582, 2, 351, 358, Jan. 2008, [Peer-reviewed]
English, Scientific journal

Inference of expression-dependent negative selection based on polymorphism and divergence in the human genome
Naoki Osada
MOLECULAR BIOLOGY AND EVOLUTION, 24, 8, 1622, 1626, Aug. 2007, [Peer-reviewed]
English, Scientific journal

Positive and negative regulation of adenovirus infection by CAR-like soluble protein, CLSP
K. Kawabata; K. Tashiro; F. Sakurai; N. Osada; J. Kusuda; T. Hayakawa; K. Yamanishi; H. Mizuguchi
GENE THERAPY, 14, 16, 1199, 1207, Aug. 2007, [Peer-reviewed]
English, Scientific journal

Aberrant termination of reproduction-related TMEM30C transcripts in the hominoids
Naoki Osada; Katsuyuki Hashimoto; Momoki Hirai; Jun Kusuda
GENE, 392, 1-2, 151, 156, May 2007, [Peer-reviewed]
English, Scientific journal

Rate of evolution in brain-expressed genes in humans and other primates
Hurng-Yi Wang; Huan-Chieh Chien; Naoki Osada; Katsuyuki Hashimoto; Sumio Sugano; Takashi Gojobori; Chen-Kung Chou; Shih-Feng Tsai; Chung-I Wu; C. -K. James Shen
PLOS BIOLOGY, 5, 2, 335, 342, Feb. 2007, [Peer-reviewed]
English, Scientific journal

Identification of a novel CXCL1-like chernokine gene in macaques and its inactivation in hominids
Hisayuki Nomiyama; Kaori Otsuka-Ono; Retsu Miura; Naoki Osada; Keiji Terao; Osamu Yoshie; Jun Kusuda
JOURNAL OF INTERFERON AND CYTOKINE RESEARCH, 27, 1, 32, 37, Jan. 2007, [Peer-reviewed]
English, Scientific journal

Genomic inferences of the cis-regulatory nucleotide polymorphisms underlying gene expression differences between Drosophila melanogaster mating races
Naoki Osada; Michael H. Kohn; Chung-I Wu
MOLECULAR BIOLOGY AND EVOLUTION, 23, 8, 1585, 1591, Aug. 2006, [Peer-reviewed]
English, Scientific journal

A tandem gene duplication followed by recruitment of a Retrotransposon created the paralogous bucentaur gene (bcnt(p97)) in the ancestral ruminant
S Iwashita; S Ueno; K Nakashima; SY Song; K Ohshima; K Tanaka; H Endo; J Kimura; M Kurohmaru; K Fukuta; L David; N Osada
MOLECULAR BIOLOGY AND EVOLUTION, 23, 4, 798, 806, Apr. 2006, [Peer-reviewed]
English, Scientific journal

Substitution rate and structural divergence of 5'UTR evolution: Comparative analysis between human and cynomolgus monkey cDNAs
N Osada; M Hirata; R Tanuma; J Kusuda; M Hida; Y Suzuki; S Sugano; T Gojobori; CKJ Shen; CI Wu; K Hashimoto
MOLECULAR BIOLOGY AND EVOLUTION, 22, 10, 1976, 1982, Oct. 2005, [Peer-reviewed]
English, Scientific journal

Evolution of sexual isolation during secondary contact: Genotypic versus phenotypic changes in laboratory populations
JA Alipaz; S Fang; N Osada; CI Wu
AMERICAN NATURALIST, 165, 4, 420, 428, Apr. 2005, [Peer-reviewed]
English, Scientific journal

Inferring the mode of speciation from genomic data: A study of the great apes
N Osada; CI Wu
GENETICS, 169, 1, 259, 264, Jan. 2005, [Peer-reviewed]
English, Scientific journal

A transposable element-mediated gene divergence that directly produces a novel type bovine Bcnt protein including the endonuclease domain of RTE-1
S Iwashita; N Osada; T Itoh; M Sezaki; K Oshima; E Hashimoto; Y Kitagawa-Arita; Takahashi, I; T Masui; K Hashimoto; W Makalowski
MOLECULAR BIOLOGY AND EVOLUTION, 20, 9, 1556, 1563, Sep. 2003, [Peer-reviewed]
English, Scientific journal

Molecular cloning, genomic characterization and over-expression of a novel gene, XRRA1, identified from human colorectal cancer cell HCT116(Clone2_XRR) and macaque testis
FM Mesak; N Osada; K Hashimoto; QY Liu; CE Ng
BMC GENOMICS, 4, 32, Aug. 2003, [Peer-reviewed]
English, Scientific journal

Analysis of 5'-end sequences of chimpanzee cDNAs
R Sakate; N Osada; M Hida; S Sugano; Hayasaka, I; N Shimohira; S Yanagi; Y Suto; K Hashimoto; M Hirai
GENOME RESEARCH, 13, 5, 1022, 1026, May 2003, [Peer-reviewed]
English, Scientific journal

Search for genes positively selected during primate evolution by 5 '-end-sequence screening of cynomolgus monkey cDNAs
N Osada; J Kusuda; M Hirata; R Tanuma; M Hida; S Sugano; M Hirai; K Hashimoto
GENOMICS, 79, 5, 657, 662, May 2002, [Peer-reviewed]
English, Scientific journal

Cynomolgus monkey testicular cDNAs for discovery of novel human genes in the human genome sequence
N Osada; M Hida; J Kusuda; R Tanuma; M Hirata; Y Suto; M Hirai; K Terao; S Sugano; K Hashimoto
BMC GENOMICS, 3, 36, 2002, [Peer-reviewed]
English, Scientific journal

Prediction of unidentified human genes on the basis of sequence similarity to novel cDNAs from cynomolgus monkey brain
Naoki Osada; Munetomo Hida; Jun Kusuda; Reiko Tanuma; Makoto Hirata; Momoki Hirai; Keiji Terao; Yutaka Suzuki; Sumio Sugano; Katsuyuki Hashimoto
GENOME BIOLOGY, 3, 1, 2002, [Peer-reviewed]
English, Scientific journal

Assignment of 118 novel cDNAs of cynomolgus monkey brain to human chromosomes
N Osada; M Hida; J Kususda; R Tanuma; K Iseki; M Hirata; Y Suto; M Hirai; K Terao; Y Suzuki; S Sugano; K Hashimoto
GENE, 275, 1, 31, 37, Sep. 2001, [Peer-reviewed]
English, Scientific journal

Identification and characterization of the potential promoter regions of 1031 kinds of human genes
Y Suzuki; T Tsunoda; J Sese; H Taira; J Mizushima-Sugano; H Hata; T Ota; T Isogai; T Tanaka; Y Nakamura; A Suyama; Y Sakaki; S Morishita; K Okubo; S Sugano
GENOME RESEARCH, 11, 5, 677, 684, May 2001, [Peer-reviewed]
English, Scientific journal

Sequence analysis, gene expression, and chromosomal assignment of mouse Borg4 gene and its human orthologue
N Osada; J Kusuda; Y Suzuki; S Sugano; K Hashimoto
JOURNAL OF HUMAN GENETICS, 45, 6, 374, 377, 2000, [Peer-reviewed]
English, Scientific journal

Simulated short-read sequence dataset of Fictus yaponesiae
Naoki Osada, Zenodo, Mar. 2025
English, Others, 12290829

日本列島域先史時代の人類と動物
長田直樹, 細胞, 56, 34, 35, Nov. 2024, [Invited]
Japanese, Introduction other

東アジアのハツカネズミにおける亜種間交雑によるゲノム進化
藤原一道; 長田直樹, 実験医学, 42, 2549, 2552, Oct. 2024, [Invited], [Last author]
Japanese, Introduction commerce magazine

De novo Gene Birth:ゲノムの非コード領域から新たに誕生する遺伝子
細川竜聡; 里村和浩; 長田直樹; 遠藤俊徳, 日本遺伝学会大会プログラム・予稿集, 95th (CD-ROM), 2023

ソフトウェア紹介13：SLiM－前向きシミュレーターについて
長田直樹, Yaponesian, 4, はる, 12, 13, Jun. 2022, [Invited]
Japanese, Introduction other

オミックスデータを用いたde novo gene birthメカニズムの探索
細川竜聡; 里村和浩; 長田直樹; 遠藤俊徳, 日本遺伝学会大会プログラム・予稿集, 94th (CD-ROM), 2022

最先端医療の今 ヤポネシア人の人口・歴史推定
長田 直樹, Medical Science Digest, 47, 9, 476, 478, Aug. 2021
(株)ニュー・サイエンス社, Japanese

現代・古代人ゲノム情報を用いた日本列島への移住経路と混合様式の推定
長田直樹, 日本人類遺伝学会大会(CD-ROM), 66th, 2021

栽培アワの日本への伝播と野生種との相互作用の歴史
里村和浩; 長田直樹; 遠藤俊徳, 日本進化学会大会プログラム・講演要旨集(Web), 23rd, 2021

Exploring off-target drug efficacy using non-linear dimensionality reduction on diseasespecific gene expression data
YI Cong; 新谷美咲; 今成楓河; 長田直樹; 遠藤俊徳, 日本分子生物学会年会プログラム・要旨集(Web), 44th, 2021

東アジアから俯瞰する二重構造説
Yaponesian, 3, ふゆ, 2021, [Invited]
Japanese, Book review

ソフトウェア紹介9：TreeMixとqpGraph
長田直樹, Yaponesian, 3, はる, 37, 39, 2021
Japanese, Introduction other

論文紹介4：ゲノム規模の遺伝子データを用いた日本列島への人類の移動モデルの探索
長田直樹, Yaponesian, 3, はる, 17, 21, 2021, [Invited]
Japanese, Book review

ソフトウェア紹介6：PLINK
長田直樹, Yaponesian, 2, なつ, 9, 10, Sep. 2020, [Invited], [Lead author]
Japanese, Introduction other, 12290829

栽培植物アワおよびキビの系統化の歴史
里村和浩; 長田直樹; 遠藤俊徳, 日本遺伝学会大会プログラム・予稿集, 92nd, 2020

膜翅目の多様性に影響を与えた遺伝子重複進化の解析
津田康太朗; 里村和浩; 長田直樹; 遠藤俊徳, 情報処理学会研究報告(Web), 2020, BIO-64, 2020

組織特異的な遺伝子発現に影響を与えた転移因子の同定
島野桂伍; 里村和浩; 長田直樹; 遠藤俊徳, 情報処理学会研究報告(Web), 2020, BIO-64, 2020

Quantification for the genetic and epigenetic effects on mouse allele-specific gene expression and evaluation
滝澤紘樹; 里村和浩; 遠藤俊徳; 長田直樹, 日本進化学会大会プログラム・講演要旨集(Web), 22nd, 2020

Comparison of whole genome sequences of Vero cell sub-lines
小西一弘; 里村和浩; 遠藤俊徳; 花田賢太郎; 長田直樹, 日本進化学会大会プログラム・講演要旨集(Web), 22nd, 2020

History of the domestication of foxtail millet (Setaria italica)
里村和浩; 長田直樹; 遠藤俊徳, 日本進化学会大会プログラム・講演要旨集(Web), 22nd, 2020

膜翅目の多様性に影響を与えた遺伝子重複進化のビッグデータ解析
津田康太朗; 里村和浩; 長田直樹; 遠藤俊徳, 日本分子生物学会年会プログラム・要旨集(Web), 43rd, 2020

ソフトウェア紹介1：FastQC
長田直樹, Yaponesian, 1, はる, 20, 21, May 2019, [Invited]
Japanese, Introduction other

ヤポネシア人の歴史の解明が医学にもたらすもの
長田直樹, 実験医学, 37, 926, 936, Apr. 2019
Japanese, Introduction other

ソフトウェア紹介はじまります
Naoki Osada, Yaponesian, 0, 0, 27, 28, Mar. 2019
Japanese, Others

研究計画B03班の紹介
Naoki Osada, Yaponesian, 0, 0, 16, 17, Mar. 2019
Japanese, Meeting report

哺乳類の遺伝子における多重置換に対する自然選択
里村和浩; 長田直樹; 遠藤俊徳, 日本遺伝学会大会プログラム・予稿集, 91st, 2019

ヒョウタンゲノムからみる古代の植物栽培伝播
渡部大; 里村和浩; 長田直樹; 遠藤俊徳, 日本遺伝学会大会プログラム・予稿集, 91st, 2019

出アフリカ後のヒトミトコンドリアタンパク質複合体IVのタンパク質熱力学的構造安定性の経時変化
藤原一道; 里村和浩; 遠藤俊徳; 長田直樹, 日本進化学会大会プログラム・講演要旨集(Web), 21st, 2019

転移因子の転移とゲノム進化の関係
島野桂伍; 里村和浩; 長田直樹; 遠藤俊徳, 日本進化学会大会プログラム・講演要旨集(Web), 21st, 2019

霊長類ミトコンドリア遺伝子における多重置換に対する自然選択
里村和浩; 長田直樹; 遠藤俊徳, 日本遺伝学会大会プログラム・予稿集, 90th, 2018

旧世界ザルゲノムに存在する内在性サルレトロウィルス(SERV)配列の探索と分子系統解析
池田昌輝; 里村和浩; 関塚剛史; 花田賢太郎; 遠藤俊徳; 長田直樹, 日本遺伝学会大会プログラム・予稿集, 90th, 2018

霊長類ミトコンドリアゲノムにおける補償的復帰突然変異
里村和浩; 長田直樹; 遠藤俊徳, 情報処理学会研究報告(Web), 2017, BIO-51, 2017

Genome-wide analysis of cis- and trans-regulatory effects on gene expression using allele samples from a natural population of Drosophila melanogaster
Naoki Osada; Ryutaro Miyagi; Aya Takahashi, GENES & GENETIC SYSTEMS, 91, 6, 372, 372, Dec. 2016
English, Summary international conference

Revisiting the Relationship between Evolutionary Conservation and Disease Causality: A Case Study of Beta Globin Gene
Sangeetha Udani Ratnayake; Toshinori Endo; Naoki Osada, GENES & GENETIC SYSTEMS, 91, 6, 345, 345, Dec. 2016
English, Summary international conference

The cause of gene expression changes in reciprocal crosses of Drosophila melanogaster by measuring allele-specific gene expression
Yasuaki Takada; Aya Takahashi; Ryutaro Miyagi; Toshinori Endo; Naoki Osada, GENES & GENETIC SYSTEMS, 91, 6, 372, 372, Dec. 2016
English, Summary international conference

古代ゲノムの解析手法（情報編）
長田直樹, 細胞工学, 34, 1092, 1095, Nov. 2015, [Invited]
Japanese, Introduction commerce magazine

Genome-scale approaches for studying human and non-human primate evolution
Naoki Osada, Genes and Genetic Systems, 90, 3, 121, 122, 27 Oct. 2015
Genetics Society of Japan, English, Report scientific journal

ポスドクからの留学先の選び方
長田直樹, 実験医学Webコラム, Aug. 2015, [Invited]
Japanese, Others

ゲノム情報から生物進化の過程に迫る
長田直樹, 北海道大学大学院情報科学研究科ネットジャーナル, 40, Jun. 2015
Japanese, Others

Lineage-specific genome evolution in the Drosophila melanogaster subgroup
Neha Mishra; Tomotaka Matsumoto; Naoki Osada; Hiroshi Akashi, GENES & GENETIC SYSTEMS, 89, 6, 277, 277, Dec. 2014
English, Summary international conference

Discovery of species-specific genomic information of a Macaca fuscate by whole-genome sequencing
FUKUTA Kentaro; NOGUCHI Hideki; TOYODA Atsushi; OSADA Naoki; GO Yasuhiro; ISHIDA Takahumi; ISA Tadashi; FUJIYAMA Asao, Primate Research Supplement, 30, 0, 49, 49, 2014
ニホンザルは他のマカク属サルには見られない形態的特徴・社会的特徴を有しているとされ，運動学的，生理学的，認知学的，あるいは病理学的な様々な研究が進められている．
マカク属の比較ゲノム解析には，2007年に公開されたインド産アカゲザルの全ゲノム配列（rheMac2）が参照配列として広く使われてきたが，ニホンザルを対象にした地域間ないし個体間の比較を行うためには，高精度かつ大規模な配列情報を元にしたニホンザル固有の参照配列を用いることが望ましい．そのため，我々はゲノムの200倍以上の被覆度を持つ配列（Illumina Hiseq2000による大阪府箕面産の個体の配列）を用いて参照配列の作成を進めているが，これと並行して，青森県下北半島産・長野県北部産・宮崎県幸島産の3個体のニホンザル，タイワンザル1個体*，タイ産カニクイザル1個体，中国産アカゲザル1個体*について，それぞれ約50倍の被覆度の配列データを用意し，rheMac2を参照配列とした比較ゲノム解析を実施した（*京大霊長類研究所共同利用研究）．
ニホンザルは比較した他の個体に比べてホモ接合性が極めて高く，他のマカク属サルではヘテロ接合で有しているSNVs（single nucleotide variants）の多くがニホンザルではホモ接合となっていることが明らかとなった．分子系統学的解析の結果から，ニホンザルのゲノムの分岐年代（約144万年前）や有効集団サイズの歴史が推定され，これによって，ニホンザルが大陸から渡ってきた年代（約60万年前）や，ニホンザルに普遍的と思われる共通の強いボトルネックが約10万年前に存在することが推定できた．さらにSNVsの詳細な解析から，ニホンザルに特有なSNVsやニホンザルで有意に進化速度が速いと思われる遺伝子候補を見出した．本会では，全ゲノムレベルの大規模解析によって得られたニホンザルゲノムの特性について報告する．, Primate Society of Japan

進化学者に聞く！学生からの10の質問
長田直樹, 日本進化学会ニュース, 15, 2, 6, 7, 2014
Japanese, Others

Expression variation analyses of the dopamine biosynthesis pathway genes within Drosophila melanogaster wild population using PCR and 454 GS Junior
Ryutaro Miyagi; Naoki Osada; Aya Takahashi, GENES & GENETIC SYSTEMS, 88, 6, 367, 367, Dec. 2013
English, Summary international conference

t-haplotype and molecular evolution of mouse Prdm9 gene
Hiromitsu Kono; Masaru Tamura; Naoki Osada; Kunihiro Ohta; Toshihiko Shiroishi, GENES & GENETIC SYSTEMS, 88, 6, 368, 368, Dec. 2013
English, Summary international conference

有害な変異と偶然の効果―中立説とほぼ中立説
長田直樹, 遺伝, 5, 322, 326, May 2013, [Invited]
Japanese, Introduction other

Polymorphism analysis of mouse speciation / recombination hotspots activator gene Prdm9
Hiromitsu Kono; Masaru Tamura; Naoki Osada; Hitoshi Suzuki; Kazuo Moriwaki; Kunihiro Ohta; Toshihiko Shiroishi, GENES & GENETIC SYSTEMS, 87, 6, 401, 401, Dec. 2012
English, Summary international conference

Genome-wide expression analyses using allelic samples from a natural population of Drosophila melanogaster
Aya Takahashi; Naoki Osada, GENES & GENETIC SYSTEMS, 87, 6, 416, 416, Dec. 2012
English, Summary international conference

Whole-genome sequencing and analysis of Malaysian cynomolgus macaque (Macaca fascicularis) genome
HIGASHINO Atsunori; SAKATE Ryuichi; KAMEOKA Yosuke; TAKAHASHI Ichiro; HIRATA Makoto; TANUMA Reiko; MASUI Tohru; YASUTOMI Yasuhiro; OSADA Naoki, Primate Research Supplement, 28, 0, 61, 61, 2012
目的，カニクイザルは主要な実験動物の一種であるが種内での遺伝的差異が大きい上に，交配可能なアカゲザルとの遺伝子交流の頻度は産地ごとに異なると予想される．我々は産地による遺伝的差異を解明し，実験動物としてのカニクイザルの利用価値を高めるために，今回はマレーシア産カニクイザルの全ゲノム配列の決定を行った．
方法，独立行政法人医薬基盤研究所・霊長類医科学研究センターで飼育管理されているマレーシア産カニクイザル（F1，オス）末梢血から抽出したゲノミックDNAをサンプルとした．カニクイザル全ゲノム配列にはSOLiD 3 Plusシステムを用いて約4.9 × 109リードを得た．ゲノムマッピングにはBioScopeを用い，リファレンス配列としてインド産アカゲザルゲノムを用いた．
結果，インド産アカゲザルゲノムへのマッピングの結果，マッピング率は69.8％，合計1.1 × 1011 bpがマッピングされ，平均41.5倍のカバレージを持つマレーシア産カニクイザルゲノムデータを得た．インド産アカゲザルに対する1塩基多型（SNP）解析はSamtoolsを用いて行った．その結果およそ960万のSNPが検出された．更に，得られたゲノム配列をこれまでに決定されたベトナム産カニクイザル，中国産アカゲザル，インド産アカゲザルと比較することにより，カニクイザル-アカゲザル間で完全に分離しているSNPを同定した．免疫関連遺伝子群，薬剤代謝遺伝子群にかかわる遺伝子の中では60個の非同義置換が種特異的変異の候補として見つかった．全SNPデータはcDNAライブラリ，BACクローン，マイクロサテライトデータとともにデータベースを構築して公開している．
考察，非同義置換SNPはカニクイザルとアカゲザルにおける薬剤や病原体に対する種特異的な反応を規定する候補因子を探索する際に有用なデータとなる．高カバレージのカニクイザル全ゲノム配列はマカク種内での遺伝的差異の解明のための基礎データとして，さらに実験動物リソースとしての価値を高めると考えられる．, Primate Society of Japan, Japanese

遺伝子発現の確率的な挙動が生物集団へ与える影響
峯田克彦; 松本知高; 長田直樹; 荒木仁志, 日本分子生物学会年会プログラム・要旨集(Web), 35th, 1P-0013 (WEB ONLY), 2012
Japanese

Gene expression and protein evolution in Drosophila
Hiroshi Akashi; Naoki Osada, GENES & GENETIC SYSTEMS, 86, 6, 388, 388, Dec. 2011
English, Summary international conference

Functional loss and CpG site degeneration created a high genetic diversity of macaque CYP1A2
Naoki Osada; Yasuhiro Uno, GENES & GENETIC SYSTEMS, 86, 6, 443, 443, Dec. 2011
English, Summary international conference

Compensatory mutation model between mitochondrial and nuclear genomes: an example of COX evolution in primates
Naoki Osada; Hiroshi Akashi, GENES & GENETIC SYSTEMS, 85, 6, 439, 439, Dec. 2010
English, Summary international conference

次世代シークエンサーを用いたカニクイザルにおける遺伝子発現解析
東濃篤徳; 長田直樹; 坂手龍一; 平田誠; 亀岡洋祐; 保富康弘; 高橋一朗, 生化学, ROMBUNNO.1P-0709, 2010
Japanese

Genetic admixture and differentiation between laboratory macaques
Naoki Osada; Yosuke Kameoka; Ichiro Takahashi; Keiji Terao, GENES & GENETIC SYSTEMS, 83, 6, 523, 523, Dec. 2008
English, Summary international conference

系統特異的重複および欠失によるケモカイン遺伝子ファミリーの急速な進化
野見山 尚之; 長田 直樹; 楠田 潤; 義江 修, 日本生化学会大会・日本分子生物学会年会合同大会講演要旨集, 81回・31回, 1T2, 11, Nov. 2008
(公社)日本生化学会, Japanese

JCRB遺伝子バンク： 疾患研究と創薬にむけた遺伝子バンク
長田直樹; 高橋一朗, 細胞工学, 26, 1307, 1308, 2007, [Invited]
Japanese, Introduction other

Mitochondrial DNA diversity of the Philippine Negrito populations.
Y Suto; N Osada; M Hirai; S Misawa; K Omoto, ANTHROPOLOGICAL SCIENCE, 111, 1, 74, 74, Jan. 2003
English, Summary international conference

Isolation and sequence analysis of newly identified clones from full-length cynomolgus monkey brain cDNA library
N Osada; Y Suto; M Hida; M Hirai; J Kusuda; R Tanuma; K Iseki; M Hirata; K Hashimoto, ANTHROPOLOGICAL SCIENCE, 110, 1, 81, 81, Jan. 2002
English, Summary international conference

Assignment of 118 novel cDNAs of cynomolgus monkey brain to human chromosomes (vol 275, pg 31, 2001)
N Osada; M Hida; J Kusuda; R Tanuma; K Iseki; M Hirata; Y Suto; M Hirai; K Terao; Y Suzuki; S Sugano; K Hashimoto, GENE, 278, 1-2, 267, 267, Oct. 2001
English, Others

第24回日本分子生物学会年会 The 24th Annual Meeting of the Molecular Biology Society of Japan
長田直樹; 山下順範; 川崎勝己, バイオサイエンスとインダストリー = Bioscience & industry, 60, 41, 42, 2001
Japanese, Meeting report

第23回日本分子生物学会年会 The 23th Annual Meeting of the Molecular Biology Society of Japan
和地正明; 長田直樹; 山下康治, バイオサイエンスとインダストリー = Bioscience & industry, 59, 40, 41, 2000
Japanese, Meeting report

Analysis of DNA replication timing using FISH: A comparative study in primates
N Osada; F Kasai; K Terao; Y Mori; Hayasaka, I; M Hirai, ANTHROPOLOGICAL SCIENCE, 107, 1, 56, 56, Jan. 1999
English, Summary international conference

DNA replication timing of human chromosome 11p15 analyzed by FISH
OSADA Naoki; KASAI Fumio; ISEKI Kanako; KUSUDA Jun; HASHIMOTO Katuyuki; HIRAI Momoki, 日本分子生物学会年会プログラム・講演要旨集, 21, 363, 363, 01 Dec. 1998
Japanese

Analysis of replication timing of chromosomal DNA by FISH-based assay
N Osada; M Hirai, ANTHROPOLOGICAL SCIENCE, 106, 2, 166, 166, Apr. 1998
English, Summary international conference

ヤポネシアの動植物ゲノム = Deciphering plant and animal genomes in Yaponesia
鈴木, 仁; 長田, 直樹
朝倉書店, Aug. 2025, 9784254177930, xv, 218p, 図版4p(ページ付なし), Japanese, [Editor]

ヤポネシアの現代人ゲノム = Deciphering modern human genomes in Yaponesia
斎藤, 成也, 第2章 二重構造モデルの検証
朝倉書店, Apr. 2025, 9784254177916, xi, 173p, 図版4p(ページ付なし), Japanese, 12290829, [Contributor]

ゲノム多様性解析 = Genome diversity analysis
長田, 直樹; 藤本, 明洋; 河合, 洋介; 五條堀, 淳; 東野, 俊英; 木村, 亮介, 理学; 松波, 雅俊
森北出版, Mar. 2025, 9784627261716, vii, 242p, Japanese, [Editor]

Evaluating the Interesting Journey of Taro Plant Varieties to Japan Using Phylogenetic Analysis
Reiko Motohashi; Yuina Saitou; Natsuki Shinomura; Tatsuo Konishi; Hiroshi Fujii; Mitsuo Omura; Naoki Osada, Chapter 7
Springer Nature, Oct. 2024, 9789819768868, 210, 95–106, English, Scholarly book, 12290829, [Contributor]

Human Impacts on the Evolution of Rats and Mice in East Asia
Naoki Osada; Hitoshi Suzuki, Chapter 2
Springer Nature, Oct. 2024, 9789819768875, [Contributor]

Phylogeographic History of Plants and Animals Coexisting with Humans in Asia
Naoki Osada; Masahiko Kumagai; Hitoshi Suzuki; Mitsuaki Endo
Springer Nature, Oct. 2024, 9789819768875, 210, English, Scholarly book, [Joint editor]

霊長類学の百科事典 = The encyclopedia of primatology
日本霊長類学会
丸善出版, Jul. 2023, 9784621308042, xxii, 716p, 図版 [8] p, Japanese, [Contributor]

Encyclopedia of genetics : origin of inheritance and diversity
日本遺伝学会, pp42-43, 418-419
丸善出版, Jan. 2022, 9784621306604, xvii, 668p, Japanese, [Contributor]

進化で読み解く バイオインフォマティクス入門
長田 直樹
森北出版, 28 Jun. 2019, 4627261411, 232, Japanese, [Single work]

ヒトは病気とともに進化した (シリーズ認知と文化)
太田博樹; 長谷川真理子, 第二章
勁草書房, Dec. 2013, 4326199458, 212, Japanese, Textbook, [Single work]

遺伝子図鑑
国立遺伝学研究所「遺伝子図鑑」編集委員会; 国立遺伝学研究所
悠書館, 01 Oct. 2013, 4903487792, 263, Japanese

Post-Genome Biology of Primates (Primatology Monographs)
Hirohisa Hirai; Hiroo Imai; Yasuhiro Go
Springer, 19 Mar. 2012, 4431540105, 280

Handbook of human molecular evolution
Cooper, David N., Dr; Kehrer-Sawatzki, Hildegard; Dawkins, Richard
John Wiley & Sons, 2008, 9780470517468, 2 v. (xxxii, 1717 p.), English, [Contributor]

ハツカネズミから知る人類の歴史
長田直樹
第79回日本人類学会大会, 12 Oct. 2025, Japanese, Invited oral presentation
42300527, [Invited]

集団遺伝学基礎講義・「ゲノム多様性解析」ハンズオンセミナー
長田直樹,木村亮介,河合洋介
27 Sep. 2025, Japanese, Public discourse
[Invited]

次世代シークエンサーを用いたゲノム多様性解析の概要
長田直樹
第26回日本進化学会神奈川大会, 24 Aug. 2024, Japanese, Public discourse
[Invited]

Inference of population history and selective force on house mouse genomes during secondary contact in East Asia
Naoki Osada
SMBE Regional Meeting in Taiwan, 29 Mar. 2024, English, Invited oral presentation
27 Mar. 2024 - 30 Mar. 2024, 42300527, [Invited]

ゲノムデータのQC，マッピング，バリアントコール，フィルタリング
長田直樹
第一回統合生物考古学セミナー, 09 Dec. 2023, Japanese, Public discourse
42300548

東アジアにおいて野生ハツカネズミが辿った歴史と進化
長田 直樹
第33回モロシヌス研究会, 23 Nov. 2023, Japanese, Oral presentation
42300527

ほぼ中立説と弱有害変異について―霊長類・げっ歯類ゲノム研究の視点から
長田直樹
日本遺伝学会第95回大会, 07 Sep. 2023, Japanese, Nominated symposium
[Invited]

人類の移動に伴う小型げっ歯類の拡散と進化
長田直樹
日本進化学会第25回沖縄大会, 31 Aug. 2023, Japanese, Nominated symposium
42300527, [Invited]

ゲノム多様性のバイオインフォマティクス解析：野生ハツカネズミの歴史とゲノム進化
長田直樹
第一回北海道バイオ”Mix up”, 09 Aug. 2023, Japanese, Invited oral presentation

Genomic Insights into the Hybridization of House Mouse Subspecies in East Asia
Naoki Osada
SMBE2023, 25 Jul. 2023, English, Poster presentation

Hybrids meet in Japan: pattern and mode of genomic admixture between subspecies of wild house mice (Mus musculus) in East Asia
Kazumichi Fujiwara; Shunpei Kubo; Tomoki Yano; Toshinori Endo; Toyoyuki Takada; Toshihiko Shiroishi; Hitoshi Suzuki; Naoki Osada
IMGC2023, 01 Mar. 2023, English, Oral presentation

日本産野生ハツカネズミの混合過程における選択について
久保俊平; 藤原一道; 長田直樹
第4回ヤポネシアくにうみミーティング, 01 Mar. 2023, Japanese, Poster presentation

時をかけるゲノム～膨大な遺伝情報からたどるヤポネシア人の起源
長田直樹
サイエンスカフェ, 18 Oct. 2022, Japanese, Public discourse
[Invited]

ゲノムから探る人類と野生ハツカネズミの歴史
長田直樹
第94回日本遺伝学会大会, 16 Oct. 2022, Japanese, Invited oral presentation

人類の多様性と歴史を解明するバイオインフォマティクス
長田直樹
第二回名古屋産学官・医連携研究会（NJK）, 09 Aug. 2022, Japanese, Public discourse
[Invited]

くにうみやわらか講座：ゲノム解析の基礎と考え方
長田直樹
第3回ヤポネシアゲノムくにうみミーティング, 15 Mar. 2022, Japanese, Public discourse
[Invited]

東アジア人の分化と歴史
長田直樹
第3回ヤポネシアゲノムくにうみミーティング, 15 Mar. 2022, Japanese, Public discourse

東アジアから俯瞰する二重構造説
長田直樹
埴原和郎二重構造モデル論文発表30周年記念公開シンポジウム, 28 Nov. 2021, Japanese, Public discourse
[Invited]

現代・古代人ゲノム情報を用いた日本列島への移住経路と混合様式の推定
長田直樹
日本人類遺伝学会第67回大会, 15 Oct. 2021, Japanese, Nominated symposium
[Invited]

古代・現代人ゲノムデータをもとにしたヤポネシアへの人類移住経路の考察
長田直樹
第75回日本人類学会, 11 Oct. 2021, Japanese, Nominated symposium
[Invited]

現代・古代東アジア人の遺伝的構造について
長田直樹
第2回ヤポネシアゲノムくにうみミーティング, 02 Mar. 2021, Japanese, Nominated symposium
[Invited]

Genome-wide genetic diversity of wild house mice across Eurasia
Naoki Osada
Genome Concept Centennial Symposium, 17 Feb. 2021, English, Public discourse
[Invited]

マカク属7種のゲノム解析による進化モデルの構築
長田直樹; 松平一成; 濱田穣; Malaivijitnond Suchinda
第36回日本霊長類学会, 06 Dec. 2020, Japanese, Oral presentation

Inference of East and Northeast Asian Population Histories using Present-day and Ancient Genome Sequence Data
Naoki Osada
The First Meeting of the Academic Year 2020 Joint Research Project on “Studies in Asian and African Geolinguistics”, ILCAA, 10 Oct. 2020, English, Nominated symposium
[Invited]

ゲノム配列データからヤポネシア人の起源について考える
長田直樹
第22回日本進化学会オンライン大会, 08 Sep. 2020, Japanese, Nominated symposium
[Invited]

Big data in biology: perspectives of genomic diversity studies
Naoki Osada
2019 Winter International Symposium on Big-Data, Cybersecurity and IoT, 06 Dec. 2019, English, Invited oral presentation
[Invited]

ソフトウェア講習
長田直樹
第3回木村資生記念進化学セミナー, 04 Aug. 2019, Japanese, Public discourse
[Invited]

霊長類種間における遺伝子浸透様式の解析
長田直樹
ヤポネシアゲノム若手研究集会, 23 Jan. 2019, Japanese, Oral presentation
[Domestic Conference]

移住率の性による偏りをゲノムデータから探る
長田直樹
ヤポネシアゲノムB02班班会議, 23 Jan. 2019, Japanese, Public discourse

ゲノムからたどる人類進化の歴史
長田直樹
名古屋大学遺伝子実験施設公開セミナー「ゲノム解析が見える化する生命の成り立ち」, 10 Dec. 2018, Japanese, Public discourse
[Invited], [Domestic Conference]

性による移住率の偏りをゲノムデータから推定する
長田直樹
日本人類学会大会公開シンポジウム：DNAからみたヒトの進化, 22 Oct. 2018, Japanese, Invited oral presentation
静岡県三島市, [Invited], [Domestic Conference]

旧世界ザルゲノムに存在する内在性サルレトロウィルス（SERV）配列の探索と分子系統解析
池田昌輝; 里村和浩; 関塚剛史; 花田賢太郎; 遠藤俊徳; 長田直樹
第90回日本遺伝学会, 21 Sep. 2018, Japanese, Oral presentation
[Domestic Conference]

Dissecting genetic and epigenetic gene expression regulatory variations in diploid organisms
Naoki Osada
14th Japanese-German Frontiers of Science Symposium, 08 Sep. 2018, English, Poster presentation
[Invited], [International presentation]

ゲノム進化解析ソフトウェアの使い方
長田直樹
第2回木村資生記念進化学セミナー, 02 Sep. 2018, Japanese, Public discourse
[Domestic Conference]

集団遺伝学とゲノム進化学
長田直樹
第11回生物学基礎論研究会特別講演, 10 Sep. 2017, Japanese, Invited oral presentation
[Invited], [Domestic Conference]

環境変動と集団サイズ変動の関係を考える
Naoki Osada
日本列島（ヤポネシア）人のゲノム歴史学, 17 Aug. 2017, Japanese, Oral presentation
[Domestic Conference]

Quantifying genetic and epigenetic control of gene expression in Drosophila and mice
Naoki Osada
The 5th international symposium “Frontier Science in Ecology, Genetics and Genomics”, 19 Mar. 2017, English, Invited oral presentation
[Invited], [International presentation]

集団遺伝学データ解析
長田直樹
ゲノム多様性データの統計解析ワークショップ, 05 Dec. 2016, Japanese, Public discourse
[Invited], [Domestic Conference]

Genomics of non-human primates: application to biomedical studies
Naoki Osada
2016 HU/SNU joint symposium, 25 Nov. 2016, English, Invited oral presentation
[Invited], [International presentation]

Population genomics of non-human primates: a case of Mauritian cynomolgus macaques (Macaca fascicularis)
Naoki Osada; Soichi Sakurai
5th Asian Primate Symposium, 20 Oct. 2016, English, Oral presentation
[International presentation]

An impact of population bottleneck on genomes: a case of Mauritian cynomolgus macaques (Macaca fascicularis)
Naoki Osada
13th Japanese-German Frontiers of Science Symposium, 07 Oct. 2016, English, Poster presentation
[Invited], [International presentation]

集団遺伝学データ解析
長田直樹
ゲノム多様性データの統計解析ワークショップ, 17 Dec. 2015, Japanese, Public discourse
総合研究大学院大学葉山キャンパス, [Domestic Conference]

Genetic architecture of gene expression variation in fruit flies
Naoki Osada
12th Japanese-German Frontiers of Science Symposium, 03 Oct. 2015, English, Poster presentation
[International presentation]

モーリシャス島産カニクイザルの全ゲノムシークエンス解析
長田直樹; Hettiarachchi Nilmini; Babarinde Isaac Adeyemi; 斎藤成也; Blancher Antoine
第31回日本霊長類学会大会, 19 Jul. 2015, Japanese, Oral presentation
[Domestic Conference]

Effect of strong population bottleneck on genomes: a case of Mauritian cynomolgus macaques
Naoki Osada
遺伝研研究集会「ビッグデータ時代の分子進化」, 26 Jun. 2015, Japanese, Invited oral presentation
[Domestic Conference]

集団遺伝学データ解析：ABCのABC
長田直樹
ゲノム多様性データの統計解析ワークショップ, 05 Dec. 2014, Japanese, Public discourse
[Domestic Conference]

Challenge of population genomics in non-model organisms
長田直樹
Frontiers in Genomic Research, 02 Dec. 2014, English, Keynote oral presentation
[International presentation]

木村先生の研究に関連した、私の二つの研究トピック: 優性度による選択圧の違いと補完的進化
長田直樹
木村資生博士生誕90周年記念シンポジウム, 14 Nov. 2014, Japanese, Nominated symposium
[Domestic Conference]

Compensatory Evolution
長田直樹
EvoDevo・PopGenの融合アプローチから明らかになる適応進化の新局面, 26 Oct. 2014, Japanese, Nominated symposium
[Domestic Conference]

日本遺伝学会奨励賞受賞講演「ゲノム情報と進化理論の統合による進化機構の解明」
長田直樹
第86回日本遺伝学会大会, 18 Sep. 2014, Japanese, Invited oral presentation
[Domestic Conference]

Allele-specific gene expression among Drosophila melanogaster hybrid lines revealed abundant cis-regulatory mutations
長田直樹
国立遺伝学研究所研究会：ゲノム進化分野におけるビッグデータ情報解析の新展開, 20 Mar. 2014, English, Oral presentation
[Domestic Conference]

Finding evidence for weak compensatory evolution
Naoki Osada; Hiroshi Akashi
SMBE Satellite Meeting/NIG International Workshop: The Causes of Genome Evolution, 15 Mar. 2014, English, Invited oral presentation
[International presentation]

帰無モデルとしての中立説と歴史推定
長田直樹
統計数理研究所研究集会：ゲノム多様性のデータ解析, 21 Dec. 2013, Japanese, Invited oral presentation
[Domestic Conference]

Dissecting regulatory mechanisms of transcriptome variation in Drosophila melanogaster
Naoki Osada
Seminar at Academia Sinica, 11 Nov. 2013, English, Invited oral presentation
[International presentation]

Dissecting regulatory mechanisms of transcriptome variation in Drosophila melanogaster
Naoki Osada
ISEGB2013, 08 Nov. 2013, English, Invited oral presentation
[International presentation]

霊長類のゲノム進化
長田直樹
日本人類学会大会, 02 Nov. 2013, Japanese, Oral presentation
[Domestic Conference]

キイロショウジョウバエにおける集団内でのcisおよびtrans遺伝子発現変異の定量
長田直樹; 宮城竜太郎; 高橋文
日本遺伝学会大会, 20 Sep. 2013, Japanese, Oral presentation
[Domestic Conference]

Finding the factors of reduced genetic diversity on X chromosomes of Macaca fascicularis
Naoki Osada; Shigeki Nakagome; Shuhei Mano; Yosuke Kameoka; Ichiro Takahashi; Keiji Terao
SMBE2013, Jul. 2013, English, Poster presentation
[International presentation]

Finding evidence for weak compensatory evolution
長田直樹
NIG Collaborative Workshop: Evolution of Junk DNAs, 23 Jun. 2013, English, Oral presentation
[Domestic Conference]

ヒトゲノムの進化における自然選択と遺伝的浮動の役割
長田直樹
インシリコ・メガバンク研究会, 24 May 2013, Japanese, Invited oral presentation
[Domestic Conference]

Evolution of rice photoperiod genes
長田直樹
NIG collaborative research meeting: Evolutionary Genetics and Proteomics of Natural Resources in Asia, 04 Feb. 2013, English, Oral presentation
[Domestic Conference]

Ecological and Evolutionary Genomics of non-model organisms in Asia
長田直樹
CKJ meeting: Genomics, Proteomics, and Bioinformatics with the Asian Perspective, 11 Dec. 2012, English, Oral presentation
[International presentation]

実験用霊長類のゲノムとその多様性
長田直樹
霊長類医科学研究フォーラム, 29 Nov. 2012, Japanese, Invited oral presentation
[Domestic Conference]

霊長類でのX染色体と常染色体との遺伝的多様性の比について
長田直樹
日本人類学会大会, 04 Nov. 2012, Japanese, Oral presentation
[Domestic Conference]

ゲノムの分岐パターンから探る-歴史，種分化，適応
長田直樹
みちのく進化生物セミナー, 19 Oct. 2012, Japanese, Invited oral presentation
[Domestic Conference]

Genetic diversity of humans and nonhuman primates and its evolutionary implications
Naoki Osada
Seminar at Academia Sinica, 28 Sep. 2012, English, Invited oral presentation
[International presentation]

Inference of population history from genomic data
Naoki Osada
Arabidopsis symposium, 25 Sep. 2012, English, Invited oral presentation
[International presentation]

ゲノム情報を用いた集団の歴史の推定：霊長類や植物の例
長田直樹
統計数理研究所研究集会：生物集団に関する遺伝データと集団遺伝学, 30 Aug. 2012, Japanese, Oral presentation
[Domestic Conference]

Compensatory Evolution between Mitochondrial and Nuclear Genomes
Naoki Osada
Okazaki Biological Conference 8 (OBC8), 20 Mar. 2012, English, Invited oral presentation
[International presentation]

Inference of natural selection by stratifying individual genome sequences
長田直樹
国立遺伝学研究所研究会：ゲノム多様性研究における革新的な知的発見のための戦略～次世代シーケンサーを用いたゲノム多様性研究における今後の課題～, Mar. 2012, Japanese, Oral presentation
[Domestic Conference]

Genetic diversity and population history of macaque monkeys
Naoki Osada
Genomic Conservation and Diversity of Organisms: Beyond the NGS time of Life Science, Dec. 2011, English, Invited oral presentation
[International presentation]

Inference of population history using a single genome data
長田直樹
日本分子生物学会年会, Dec. 2011, Japanese, Oral presentation
[Domestic Conference]

多座位データを用いたゲノムヒストリーの推定
長田直樹
統計数理研究所共同利用重点型研究による研究集会：ゲノムの多様性，進化，疾患に関わる話題についての講演, Dec. 2011, Japanese, Invited oral presentation
[Domestic Conference]

メタゲノム解析とその応用
長田直樹
メタゲノム解析を利用した下水道情報網基盤構築に関する研究集会, Nov. 2011, Japanese, Oral presentation
[Domestic Conference]

機能喪失とCpGサイトの崩壊による旧世界ザルCYP1A2遺伝子の高い遺伝的多様性
長田直樹; 宇野泰広
日本遺伝学会大会, Sep. 2011, Japanese, Oral presentation
[Domestic Conference]

Compensatory evolution between mitochondrial and nuclear genomes: evidence from primate respiratory chain complex genes
Naoki Osada
SMBE2011, Jul. 2011, English, Invited oral presentation
[International presentation]

Compensatory Evolution between Mitochondrial and Nuclear Genomes: Evidence from Primate Respiratory Chain Complex Genes
Naoki Osada
Seminar at National Taiwan University, Jul. 2011, English, Invited oral presentation
[International presentation]

霊長類の中のヒト:ゲノム多様性の種間比較
長田直樹
遺伝研共同研究集会：ヒト形質のゲノム発掘による新しい進化人類学の創成, Jul. 2011, Japanese, Oral presentation
[Domestic Conference]

ヒトの遺伝的多様性―進化生物学的視点から
長田直樹
日本赤十字第6回学術講演会, Jun. 2011, Japanese, Invited oral presentation
[Domestic Conference]

Compensatory Evolution between Mitochondrial and Nuclear Genomes: Evidence from Primate Respiratory Chain Complex Genes
Naoki Osada
Seminar at National Cheng-Kung University, Mar. 2011, English, Invited oral presentation
[International presentation]

人類集団における自然淘汰
長田直樹
現生人類の拡散による遺伝子と文化の多様性創出に関する総合的研究, Mar. 2011, Japanese, Oral presentation
[Domestic Conference]

Genetic analysis using multi-locus DNA sequence data for ecology and evolution research
長田直樹
NIG Collaborative Research Meeting: Toward Next Generation Studies of Biodiversity and Bioresources, Nov. 2010, English, Oral presentation
[Domestic Conference]

ヒトの遺伝的多様性とゲノムにかかる自然選択について
長田直樹
遺伝研共同研究集会：個人ゲノム時代におけるヒトゲノムDNA多型研究, Nov. 2010, Japanese, Oral presentation
[Domestic Conference]

Population Genetics of Non-human Primates: How Are We Diverse?
Naoki Osada
International Primatological Society Congress, 13 Sep. 2010, English, Oral presentation
[International presentation]

ミトコンドリア・核遺伝子間の弱有害補完モデル：霊長類COX遺伝子群の進化を例に
長田直樹; 明石裕
日本遺伝学会大会, Aug. 2010, Japanese, Oral presentation
[Domestic Conference]

マルチローカスデータを用いた進化生態学研究について
長田直樹
日本進化学会大会, Aug. 2010, Japanese, Oral presentation
[Domestic Conference]

Polymorphism, Divergence, and Speciation: Genomic Perspective
Naoki Osada
Seminar at National Cheng-Kung University, Mar. 2010, English, Invited oral presentation
[International presentation]

実験用霊長類の種差・個体差について：ゲノム解析の視点から
長田直樹
日本薬学会大会融合型シンポジウム, Mar. 2010, Japanese, Invited oral presentation
[Domestic Conference]

カニクイザルのトランスクリプトーム解析
長田直樹
国際生物多様性会議：霊長類のゲノム多様性研究, Mar. 2010, Japanese, Oral presentation
[Domestic Conference]

進化生物学への次世代シークエンサーの応用について
長田直樹
国立遺伝学研究所研究集会：次世代シーケンサーを活用したゲノム多様性の研究, 14 Jan. 2010, Japanese, Oral presentation
[Domestic Conference]

カニクイザルcDNAライブラリーの解析とゲノム統合データベースの開発
長田直樹; 平田誠; 田沼玲子; 亀岡洋祐; 高橋一朗; 東濃篤範; 鈴木穣; 菅野純夫; 寺尾恵治; 楠田潤; 橋本雄之
日本分子生物学会年会, Dec. 2009, Japanese, Poster presentation
[Domestic Conference]

有害な突然変異とその優性度の推定について：ヒト疾患遺伝子の解析
長田直樹
日本遺伝学会大会, Sep. 2009, Japanese, Oral presentation
[Domestic Conference]

Ecological adaptation and speciation: genomic perspective
Naoki Osada
Eawag CEEB joint workshop: Beyond the gaps among ecology, evolution and biogeochemistry, Aug. 2009, English, Invited oral presentation
[International presentation]

Analysis of gene duplication and conversion in the Drosophila melanogaster genome.
Naoki Osada; Hideki Innan
JSPS Japan-Germany International Colloquium, Mar. 2009, English, Invited oral presentation
[International presentation]

Polymorphism, Divergence, and Speciation: Genomic Perspective
長田直樹
国立遺伝学研究所 Biological symposium, Mar. 2009, English, Invited oral presentation
[Domestic Conference]

カニクイザル骨髄・脾臓・膵臓由来cDNAライブラリーの解析
長田直樹; 亀岡洋祐; 平田誠; 田沼玲子; 鈴木穣; 菅野純夫; 高橋一朗
日本分子生物学会年会, Dec. 2008, Japanese, Poster presentation
[Domestic Conference]

ヒトゲノム中の塩基置換多型と疾患関連遺伝子について
長田直樹
日本人類学会大会, Nov. 2008, Japanese, Oral presentation
[Domestic Conference]

Deleterious Mutations and Human Diseases: Genomic Perspective
長田直樹
日本進化学会大会, Aug. 2008, Japanese, Oral presentation
[Domestic Conference]

ヒト疾患とほぼ中立説
長田直樹
国立遺伝学研究所研究集会：中立進化論の現在, Jul. 2008, Japanese, Invited oral presentation
[Domestic Conference]

実験用マカク間における遺伝的分化と交雑についてのゲノム解析
長田直樹; 亀岡洋祐; 高橋一朗; 寺尾恵治
日本霊長類学会大会, Jul. 2008, Japanese, Oral presentation
[Domestic Conference]

Pattern of genetic admixture and differentiation between Macaca fascicularis and M. mulatta genome
Naoki Osada; Yosuke Kameoka; Ichiro Takahashi; Keiji Terao
SMBE2008, Jun. 2008, English, Oral presentation
[International presentation]

Primate speciation: genes and genome
Naoki Osada
Seminar at National Taiwan University, May 2008, English, Invited oral presentation
[International presentation]

Primate speciation: genes and genome
Naoki Osada
Seminar at National Cheng-Kung University, May 2008, English, Invited oral presentation
[International presentation]

カニクイザルcDNAライブラリーコレクションの拡充とその解析
長田直樹; 橋本雄之; 楠田潤; 亀岡洋祐; 田沼玲子; 平田誠; 高橋一朗
日本分子生物学会年会, Dec. 2007, Japanese, Poster presentation
[Domestic Conference]

突然変異にかかる淘汰圧と遺伝子発現の関係について
長田直樹
北海道大学バイオインフォマティクスセミナー, Oct. 2007, Japanese, Invited oral presentation
[Domestic Conference]

ヒトゲノム中での遺伝子発現パターンと淘汰圧との関係について
長田直樹
日本遺伝学会大会, Sep. 2007, Japanese, Oral presentation
[Domestic Conference]

遺伝子配列と発現パターンから見た霊長類進化
長田直樹
京都大学霊長類研究所共同利用プログラム/京都大学グローバルCOEプログラム：霊長類ゲノムと脳・感覚研究の最前線, Jul. 2007, Japanese, Invited oral presentation
[Domestic Conference]

カニクイザル由来cDNAデータベースの構築，アカゲザルとの比較解析
長田直樹; 橋本雄之; 平田誠; 田沼玲子; 亀岡洋祐; 楠田潤; 寺尾恵治; 高橋一朗
日本霊長類学会大会, Jul. 2007, Japanese, Oral presentation
[Domestic Conference]

高等霊長類でのTMEM30C遺伝子転写の進化
長田直樹
日本進化学会大会, Aug. 2006, Japanese, Poster presentation
[Domestic Conference]

Collection and analysis of primate disease-related homologs
Naoki Osada; Reiko Tanuma; Makoto Hirata; Ichirou Takahashi; Yousuke Kameoka; Katsuyuki Hashimoto; Jun Kusuda
20th International congress of biochemistry and molecular biology and 11th FAOBMB congress, Jun. 2006, English, Poster presentation
[International presentation]

Divergence between human and macaque beyond the protein evolution
Naoki Osada; Katsuyuki Hashimoto; Reiko Tanuma; Makoto Hirata; Jun Kusuda
Human Genome Meeting 2006, May 2006, English, Oral presentation
[International presentation]

カニクイザルcDNAの解析とデータベース構築
長田直樹; 平田誠; 田沼玲子; 高橋一朗; 亀岡洋祐; 橋本雄之; 楠田潤
日本分子生物学会年会, Dec. 2005, Japanese, Poster presentation
[Domestic Conference]

カニクイザルcDNAデータベースの紹介と応用: ミトコンドリア蛋白で起こった正の淘汰
長田直樹
日本遺伝学会大会, 29 Sep. 2005, Japanese, Oral presentation
[Domestic Conference]

ゲノムレベルでわかる霊長類進化
長田直樹
遺伝研生命情報センターCIBセミナー, 03 Jun. 2005, Japanese, Invited oral presentation
[Domestic Conference]

Cynomolgus monkey cDNA libraries: Rate and Pattern of 5’UTR evolution in primates
Naoki Osada; Makoto Hirata; Reiko Tanuma; Jun Kusuda; Katsuyuki Hashimoto
Human Genome Meeting 2005, Apr. 2005, English, Poster presentation
[International presentation]

Rate and pattern of 5’ UTR evolution: comparative analysis between human and cynomolgus monkey
Naoki Osada; Makoto Hirata; Jun Kusuda; Reiko Tanuma; Katsuyuki Hashimoto
International Workshop on Encoding Information in DNA Sequences, Feb. 2005, English, Poster presentation
[International presentation]

9. Gene expression of Drosophila melanogaster head with sexual isolation - cis-associated difference and pattern of sex, virginity and genotype
Naoki Osada
日本分子生物学会年会, Dec. 2004, English, Poster presentation
[Domestic Conference]

Testing the mode of speciation with genomic data
Naoki Osada; Chung-I Wu
Keystone symposia, Natural variation and quantitative genetics in model organism, Mar. 2004, English, Poster presentation
[International presentation]

Prediction of novel human genes applying cDNA sequence of cynomolgus monkey brain
長田直樹長田直樹; 肥田宗友; 楠田潤; 田沼玲子; 平田誠; 平井百樹; 橋本雄之
Dec. 2002, Japanese, Oral presentation
[Domestic Conference]

Identification of human homologs for novel cynomolgus monkey cDNAs
Naoki Osada
Gordon Research Conference: GENOMICS & STRUCTURAL/EVOLUTIONARY BIOINFORMATICS, Aug. 2002, English, Poster presentation
[International presentation]

カニクイザル完全長cDNAの分離ーヒトゲノム配列での新規ヒト遺伝子同定および既知ヒト遺伝子との配列比較
長田直樹
哺乳動物遺伝学研究会, Jun. 2002, Japanese, Oral presentation
[Domestic Conference]

Isolation and sequence analysis of newly identified clones from full-length cynomolgus monkey brain cDNA library
長田直樹; 肥田宗友; 楠田潤; 田沼玲子; 伊関可奈子; 平田誠; 平井百樹; 数藤由美子; 橋本雄之
日本人類学会大会, Aug. 2001, Japanese, Oral presentation
[Domestic Conference]

Analysis of full-length cynomolgus monkey cDNA library from brain and isolation of unidentified clones
長田直樹; 肥田宗友; 楠田潤; 田沼玲子; 伊関可奈子; 平田誠; 平井百樹; 数藤由美子; 橋本雄之
日本分子生物学会年会, Nov. 2000, Japanese, Poster presentation
[Domestic Conference]

Isolation and analysis of unidentified mouse cDNA clones containing CpG islands
田直樹; 楠田潤; 田沼玲子; 伊藤亜紀子; 平田誠; 平井百樹; 橋本雄之
日本分子生物学会年会, Nov. 1999, Japanese, Poster presentation
[Domestic Conference]

DNA replication timing of human chromosome 11p15 analyzed by FISH
長田直樹; 笠井文生; 伊関可奈子; 楠田潤; 橋本雄之
日本分子生物学会年会, Nov. 1998, Japanese, Poster presentation
[Domestic Conference]

Analysis of DNA replication timing using FISH : A comparative study in primates
長田直樹; 笠井文生; 寺尾恵治; 森祐介; 早坂郁夫
日本人類学会大会, Sep. 1998, Japanese, Poster presentation
[Domestic Conference]

Analysis of DNA replication timing using FISH method
長田直樹; 平井百樹
日本人類学会大会, Nov. 1997, Japanese, Poster presentation
[Domestic Conference]

情報生物学特論, 2024年, 修士課程, 情報科学院

情報生物学特論, 2024年, 博士後期課程, 情報科学研究科

情報生物学特論, 2024年, 博士後期課程, 情報科学院

情報学 Ⅰ, 2024年, 学士課程, 全学教育

生命情報解析学, 2024年, 学士課程, 工学部

一般教育演習(ﾌﾚｯｼｭﾏﾝｾﾐﾅｰ), 2024年, 学士課程, 全学教育

生体医工学基礎, 2024年, 学士課程, 工学部

生体工学概論, 2024年, 学士課程, 工学部

生体情報工学実験Ⅰ, 2024年, 学士課程, 工学部

生体情報工学演習Ⅱ, 2024年, 学士課程, 工学部

生体情報工学実験Ⅱ, 2024年, 学士課程, 工学部

先史人類による人為的環境形成（動物相）に関する研究
科学研究費助成事業 学術変革領域研究(A)
01 Apr. 2023 - 31 Mar. 2028
長田 直樹
日本学術振興会, 学術変革領域研究(A), 北海道大学, 23H04846

Integrative Bioarcheology: Reconstruction of Human Prehistory around the Japanese Archipelago
Grants-in-Aid for Scientific Research
Apr. 2023 - Mar. 2028
山田 康弘
Japan Society for the Promotion of Science, Grant-in-Aid for Transformative Research Areas (A), Tokyo Metropolitan University, 23H04836

Comprehensive search and population genetic analysis of virus-like sequences in human genomes
Grants-in-Aid for Scientific Research
01 Apr. 2022 - 31 Mar. 2026
長田 直樹; 河合 洋介
令和5年度は引き続き野生ハツカネズミの内在性レトロウイルス解析を行うと同時に，ヒトゲノム解析へ向けたパイプライン構築と，倫理申請について進めた．ヒトゲノムの大量解析については令和6年に始めることとし，条件検討およびパイプライン構築に努めた．野生ハツカネズミの解析では，ゲノム中に大量の非リファレンス型の内在性ウイルス様配列が存在していることが明らかになった．特に日本由来および韓国由来の野生ハツカネズミにおいて配列の異常な増幅を発見した．また，すでにウイルスへの防御機能をもつことが知られている内在性レトロウイルス由来遺伝子，Fv-1およびFv-4を含むゲノム領域において，日本産のハツカネズミのゲノムが南方型のcastaneus亜種由来のゲノムを多く持つことが示された．特に，Fv-1領域においては何らかの自然選択によってこのようなゲノムの特徴が出来上がったことが示唆された．また，Fv-4は以前より日本由来の個体とcastaneus亜種個体での存在が示唆されていたが，domesticus亜種がもととなっているリファレンス配列には存在しないことが知られていた．本解析では，日本由来個体とcastaneus亜種個体において，Fv-4が予想される位置に挿入されていることを示す証拠を確認することができた．これらのことから，ヒトゲノムとほぼ同じサイズと似たような構造をもつハツカネズミゲノム解析において，解析手法がうまく働くことが示された．
Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research (B), Hokkaido University, 23K23970

Comprehensive search and population genetic analysis of virus-like sequences in human genomes
Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (B)
01 Apr. 2022 - 31 Mar. 2026
長田 直樹; 河合 洋介
Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research (B), Hokkaido University, 22H02707

Thousands of adaptive changes emerging from thousands of genomes within a species
Grants-in-Aid for Scientific Research
Apr. 2023 - Mar. 2026
小林 一三; 長田 直樹; 内山 郁夫; 大崎 敬子; 印南 秀樹
Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research (C), National Institute for Basic Biology, Coinvestigator, 23K05735

血中exosome内circRNA発現解析による膵癌の診断・予後関連マーカー探索
科学研究費助成事業 基盤研究(C)
01 Apr. 2022 - 31 Mar. 2025
柿坂 達彦; 蒲池 浩文; 長田 直樹; 神山 俊哉; 折茂 達也
日本学術振興会, 基盤研究(C), 北海道大学, 22K08789

Deciphering Origin and Establishment of Japonesians mainly based on genome sequence data
Grants-in-Aid for Scientific Research
Jun. 2018 - Mar. 2023
長田 直樹; 五條堀 淳; 河合 洋介; 藤本 明洋
当初の計画に沿って研究を進行したが，その他の関連する研究も行った．ヤポネシア人ゲノムの解析については，東アジア人におけるアミラーゼ遺伝子のコピー数推定を行った．その際，コピー数推定のバラツキが少なくなるような手法を開発し，従来手法よりもよい精度で東アジア人集団のアミラーゼ遺伝子コピー数推定を行った．その結果，縄文人が現代東アジア人で典型的な8コピーのAMY1遺伝子をもっていることが示された．また，ハプロタイプ情報を用いてヤポネシア人と他の人類集団との分岐年代を推定した．その他，新規手法に基づいて同定されたマイクロサテライト配列の多型を用いて人類集団の解析を行い，従来手法よりもSNP解析に近い結果を得ることができた．さらに，9850人のヤポネシア人全ゲノムシークエンスデータの解析を行い，日本列島内での現代人の遺伝的構造を高解像度で示すことに成功した．他に，希少変異解析を用いて複数の縄文人個体ゲノムや弥生人ゲノムを解析し，別の手法を用いて解析を行った結果と比較した．
その他，マダガスカル産ハツカネズミの全ゲノム解析による渡来経路の推定，北海道産ヒグマの全ゲノム解析による集団動態の解析，日本列島におけるハツカネズミの亜種間交雑過程の全ゲノム規模での解析，ハイイロオオカミ，ニホンオオカミ，イヌなどのゲノム解析に関する研究など，ヤポネシア人に関する研究だけでなく，動植物のゲノム解析などについての解析を他研究班と共同で進めた．
Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area), Hokkaido University, Principal investigator, 18H05511

Origin and formation of Yaponesians based on genome sequences
Grants-in-Aid for Scientific Research
Jun. 2018 - Mar. 2023
斎藤 成也; 藤尾 慎一郎; 木部 暢子; 篠田 謙一; 遠藤 光暁; 鈴木 仁; 長田 直樹
リースしているサーバー(すさのを)および国立遺伝学研究所のスーパーコンピュータを用いて、現代人ゲノムの解析環境をととのえた。2019年度に購入したサーバー2台(うみさちとやまさち)を用いて、古代人や公開されている現代人ゲノムや動植物ゲノムデータの格納をおこない、それらデータの解析環境を整えた。季刊誌Yaponesianの2021年はる号、なつ号、あき号、2022年ふゆ号を編集刊行した。新学術領域研究ヤポネシアゲノムのウェブサイトを運営した。2021年6月12-13日に、オンラインにて総括班会議と全体会議を開催した。2021年11月28日に、国際日本文化研究センターと共催で「埴原和郎の二重構造モデル論文発表３０周年記念公開シンポジウム」をハイブリッド方式で開催した。2022年2月12-13日に、オンラインにて全体会議と総括班会議をハイブリッド方式で開催した。2022年3月15-17日に、 「第3回くにうみミーティング」(若手研究者育成の一環)を開催した。
Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area), National Institute of Genetics, 18H05505

Theoretical and empirical studies for compensatory molecular evolution
Grants-in-Aid for Scientific Research
Apr. 2014 - Mar. 2017
Osada Naoki
Compensatory molecular evolution refers to the process where the fixation of multiple mutation that are singly deleterious maintain organismal fitness by compensating their effects. In this research project, we mainly focus on the compensatory weak selection model, where the fixation of slightly advantageous mutations follow the fixation of slightly deleterious mutations in a variety of molecular systems, including protein-protein interaction and gene expression.
Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research (C), Principal investigator, 26440202

Integrative study of nucleotide sequence evolution using primate genomes as model
Grants-in-Aid for Scientific Research
Apr. 2014 - Mar. 2017
SAITOU NARUYA
Evolutionarily conserved noncoding sequences (CNSs) were analyzed for whole Eukaryotes, Amniotes, Hominoids, and Hominidae by comparing many genome sequences, and series of new CNS characteristics were discovered (mainly conduced by Saitou). Repeat sequence evolution of New World monkeys were analyzed (mainly conduced by Koga). Genomic structure of chimpanzee Rh blood group gene region was analyzed (mainly conduced by Kitano). Whole-genome sequences of Mauritian cynomolgus macaques and Tibetan macaque were analyzed (mainly conduced by Osada). Substitution type mutation pattens were analyzed by using ENU-induced mice (mainly conduced by OOta). Gene annotation of cynomolgus macaque genome was conducted (mainly conduced by Ikeo). These studies deciphered various facets of genome evolution, in particular, of primates.
Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research (A), National Institute of Genetics, Coinvestigator, 26251040

Analyses of behavior incompatibility triggered by expression changes of pigmentation genes
Grants-in-Aid for Scientific Research
Apr. 2011 - Mar. 2016
Takahashi Aya; OSADA Naoki
This study focused on dopamine biosynthesis pathway genes, which has a pleiotropic effect on both body pigmentation and behavior, as genes potentially involved in reproductive isolation triggered by environmental adaptation. We found unexpectedly complex cis-regulatory polymorphisms in these genes and a genetic variant that is likely to change both pigmentation and behavior.
From a wider viewpoint of the “Correlative gene systems”, another contribution of this study was to elucidate various associations between cis/trans-regulatory variations and genomic factors by conducting a novel type of genome-wide transcriptome analysis.
Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area), 23113008

Analysis of gene expression network of natural and artificial allotetraploids using next generation sequencers
Grants-in-Aid for Scientific Research
Apr. 2010 - Mar. 2014
OSADA Naoki
Understanding the interaction between two different genomes is important issue in evolutionary biology research, especially when the two genomes were incorporated into the same organisms. I analyzed the genomic and expression properties of recently established natural allotetraploid plants, of which parental species are relative to the model species Arabidopsis thaliana. Using massively parallel sequencers, genome sequences of parental species and transcriptome data of allotetraploid species were studied.
Japan Society for the Promotion of Science, Grant-in-Aid for Young Scientists (A), National Institute of Genetics, Principal investigator, 22687021

動物資源の安定供給に向けた繁殖および品質管理技術の高度化に関する研究
生物資源研究事業
May 2007 - Mar. 2010
寺尾恵治
厚生労働省, Competitive research funding

Birth and Death of Chemokine Family Genes and Gain of Novel Functions
Grants-in-Aid for Scientific Research
2007 - 2008
NOMIYAMA Hisayuki; SETOYAMA Chiaki; OSADA Naoki
ケモカインファミリー遺伝子は進化速度が特に早い. そのメンバーであるカニクイザル特異的CXCL1L遺伝子は, mRNAは発現するにもかかわらず, タンパク質はほとんど合成しない. その翻訳抑制機構を解析し, ケモカイン遺伝子進化との関係において考察した.
Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research (C), Kumamoto University, Coinvestigator not use grants, Competitive research funding, 19510197

Inter- and Intra-specific Genetic Diversity in Genus Macaca.
Grants-in-Aid for Scientific Research
2007 - 2008
OSADA Naoki
感染症などの医学研究、創薬などの薬学研究において、哺乳類実験動物、特に霊長類はヒトと遺伝的に非常に近く、重要な位置を占める.ところが、医薬学の実験にサル類の遺伝的多様性がどのような影響を及ぼすかは全くの未知数である.また、これらの実験用霊長類のなかにどれだけの種間・種内の遺伝的多様性があるのかもはっきりとはわかっていないのが現状である.これらを明らかにするため、マカク属の中でも実験用霊長類としてメジャーなアカゲザルとカニクイザルの個体より得られたDNAの多型解析を行った.その結果、1)カニクイザルの遺伝的多様性は現生人類よりも4-5倍高い値を示す、2)カニクイザルとアカゲザルでは、種がわかれた後に遺伝子交流があったかもしれない、3)薬剤代謝にかかわる遺伝子のいくつかは種間の遺伝子での分化度が非常に高い、ということが示された.
Japan Society for the Promotion of Science, Grant-in-Aid for Young Scientists (B), National Institute of Biomedical Innovation, Principal investigator, Competitive research funding, 19770073