Naoki Osada, ph, D.

Education

 Work Experience

Research Interest

Every aspect of genome evolution.  Popultion genomics, molecular evolution, gene expression evolution.

Peer Reviewed Papers

• • Kazumichi Fujiwara, Shunpei Kubo, Toshinori Endo, Toyoyuki Takada, Toshihiko Shiroishi, Hitoshi Suzuki, Naoki Osada. Inference of selective force on house mouse genomes during secondary contact in East Asia. Genome Res. 2024 accepted
  • Sangeetha Ratnayake, Axel Martinelli, Toshinori Endo, Naoki Osada. Advancing antibody-antigen interface analysis in docking scoring functions for precision docking analysis. IPSJ Trans. Bioinfo. 2023 accepted
  • Sangeetha Ratnayake, Axel Martinelli, Toshinori Endo, Naoki Osada. Exploring the interplay between scoring functions and physico-chemical properties in antibody-antigen docking. IPSJ Trans. Bioinfo. 17: 10-17, 2023
  • Satoshi D. Ohdachi*, Kazumichi Fujiwara, Chandra Shekhar, Nguyễn Trường Sơn, Hitoshi Suzuki, Naoki Osada. Phylogenetics and population genetics of the Asian house shrew Suncus murinus–S. montanus complex inferred from whole-genome and mitochondrial DNA sequences, with special reference to the Ryukyu Archipelago, Japan. Zool. Sci.  41, 2024
  • (Consortium paper) The Helicobacter pylori Genome Project: insights into H. pylori population structure from analysis of a worldwide collection of complete genomes. Kaisa Thorell et al. Nature Communications 14(1) 2023
  • 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  2023
  • 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 2022
  • 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 2022
  • 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) 2022
  • 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 2022
  • 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 2022
  • 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 2022
  • 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  2021
  • 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 2021
  • (Review paper) Exploring models of human migration to the Japanese archipelago using genome-wide genetic data. Naoki Osada, Yosuke Kawai. Anthropological Science 129(1) 45-58 2021
  • 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 2021
  • 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 2020
  • 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
  • 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 2020
  • (Review paper) Achiasmy and sex chromosome evolution. Kazuhiro Satomura, Naoki Osada, Toshinori Endo. Ecological Genetics and Genomics 13 100045 2019 
  • 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 2019
  • 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 2019
  • 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 2018
  • 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 2018
  • 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 2018
  • 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
  • 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 2017
  • 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 2017
  • 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 2017
  • (Review paper) Compensatory Evolution. Naoki Osada. Encyclopedia of Evolutionary Biology 1 329-333 2016
  • 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 2015
  • 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 2015
  • Genetic diversity in humans and non-human primates and its evolutionary consequences. Naoki Osada. Genes and Genetic Systems 90(3) 133-145 2015
  • 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 2015
  • (Consortium paper) 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 2015
  • 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 2015
  • 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 2015
  • 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 2015
  • 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 2014
  • 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 2014
  • 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 2014
  • 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 2014
  • 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 2014
  • (Review paper)  Extracting population genetics information from a diploid genome sequence. Naoki Osada. Frontiers in Ecology and Evolution 2 7 2014
  • 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 2013
  • 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 2013
  • (Review paper)  Weak Selection and Protein Evolution. Hiroshi Akashi, Naoki Osada, Tomoko Ohta. GENETICS 192(1) 15-U43 2012
  • 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) 2012
  • 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 2012
  • 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 2012
  • 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 2012
  • 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 2012
  • 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 2011
  • 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 2011
  • 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 2011
  • 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 2011
  • Phylogenetic Inconsistency Caused by Ancient Sex-Biased Gene Migration. Naoki Osada. PLOS ONE 6(9) e25549-e25549 2011
  • 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 2011
  • The evolution of mammalian chemokine genes. Hisayuki Nomiyama, Naoki Osada, Osamu Yoshie. CYTOKINE & GROWTH FACTOR REVIEWS 21(4) 253-262 2010
  • 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 2010
  • 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 2010
  • 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
  • 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 2009
  • 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 2009
  • 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 2009
  • 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 2009
  • 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 2009
  • Duplication and Gene Conversion in the Drosophila melanogaster Genome. Naoki Osada, Hideki Innan. PLOS GENETICS 4(12) e1000305 2008
  • 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 2008
  • 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 2008
  • 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 2008年
  • 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 2007
  • 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 2007
  • Aberrant termination of reproduction-related TMEM30C transcripts in the hominoids. Naoki Osada, Katsuyuki Hashimoto, Momoki Hirai, Jun Kusuda. GENE 392(1-2) 151-156 2007
  • 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 2007
  • 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 2007
  • 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 2006年
  • 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 2006
  • 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 2005
  • 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 2005
  • Inferring the mode of speciation from genomic data: A study of the great apes. N Osada, CI Wu. GENETICS 169(1) 259-264 2005
  • 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 2003
  • 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 2003
  • 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 2003
  • 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 2002
  • Prediction of unidentified human genes on the basis of sequence similarity to novel cDNAs from cynomolgus monkey brain. Osada N, Hida M, Kusuda J, Tanuma R, Hirata M, Hirai M, Terao K, Suzuki Y, Sugano S, Hashimoto K.  Genome biology 3 RESEARCH0006 2002
  • 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
  • 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
  • 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 2001
  • 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, N Osada, K Hashimoto, T Tanaka, Y Nakamura, A Suyama, Y Sakaki, S Morishita, K Okubo, S Sugano. GENOME RESEARCH 11(5) 677-684 2001
  • 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

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