Researcher Database

Hidemi Watanabe
Faculty of Information Science and Technology Bioengineering and Bioinformatics Bioinformatics

Researcher Profile and Settings


  • Faculty of Information Science and Technology Bioengineering and Bioinformatics Bioinformatics

Job Title

  • Professor

J-Global ID

Research Interests

  • ゲノム比較解析   比較解析   チンパンジーゲノム   チンパンジー   ヒト   ヒトゲノム   ゲノム進化   ヒト固有形質   ヒト固有遺伝情報   免疫系   種分化   染色体   分子進化   系統特異性   生物進化   地理的隔離   積分化   マッピング   非重複遺伝子   突然変異率   比較ゲノム   有効集団サイズ   大量情報処理   真核生物   地球史   ヒト特異的遺伝情報   継代培養   組換え   origins of life   comparative genomics   evolution   genome   

Research Areas

  • Life sciences / Evolutionary biology
  • Life sciences / Systems genomics
  • Life sciences / Genomics

Academic & Professional Experience

  • 2004/04 - Today  北海道大学 大学院・情報科学研究科教授
  • 2002/07 - 2004/03  National Institute of Informatics客員助教授
  • 2002/04 - 2004/03  理化学研究所 ゲノム科学総合研究センター客員主管研究員
  • 2002/04 - 2004/03  Nara Institute of Science and TechnologyGraduate School of Information Science助教授
  • 1999/05 - 2002/03  理化学研究所 ゲノム科学総合研究センター
  • 1997/05 - 1999/04  National Center for Biotechnology Information, National Institutes of Health
  • 1995/04 - 1997/03  National Institute of Genetics

Association Memberships

  • The Society for the Study of the Origin and Evolution of Life Japan   The American Association for the Advancement of Science (AAAS)   The Society for Molecular Biology and Evolution (SMBE)   

Research Activities

Published Papers

  • Gabriel Gonzalez, Camden R. Bair, Daryl M. Lamson, Hidemi Watanabe, Laura Panto, Michael J. Carr, Adriana E. Kajon
    Virology 538 11 - 23 2019 [Refereed][Not invited]
    Species Human mastadenovirus E (HAdV-E) comprises several simian types and a single human type: HAdV-E4, a respiratory and ocular pathogen. RFLP analysis for the characterization of intratypic genetic variability has previously distinguished two HAdV-E4 clusters: prototype (p)-like and a-like. Our analysis of whole genome sequences confirmed two distinct lineages, which we refer to as phylogroups (PGs). PGs I and II comprise the p- and a-like genomes, respectively, and differ significantly in their G + C content (57.7% ± 0.013 vs 56.3% ± 0.015). Sequence differences distinguishing the two clades map to several regions of the genome including E3 and ITR. Bayesian analyses showed that the two phylogroups diverged approximately 602 years before the present. A relatively faster evolutionary rate was identified for PG II. Our data provide a rationale for the incorporation of phylogroup identity to HAdV-E4 strain designation to reflect the identified unique genetic characteristics that distinguish PGs I and II.
  • Marcin Jąkalski, Kazutaka Takeshita, Mathieu Deblieck, Kanako O. Koyanagi, Izabela Makalowska, Hidemi Watanabe, Wojciech Makalowski
    Biology Direct 11 2016/08 [Refereed][Not invited]
    Retroposition, one of the processes of copying the genetic material, is an important RNA-mediated mechanism leading to the emergence of new genes. Because the transcription controlling segments are usually not copied to the new location in this mechanism, the duplicated gene copies (retrocopies) become pseudogenized. However, few can still survive, e.g. by recruiting novel regulatory elements from the region of insertion. Subsequently, these duplicated genes can contribute to the formation of lineage-specific traits and phenotypic diversity. Despite the numerous studies of the functional retrocopies (retrogenes) in animals and plants, very little is known about their presence in green algae, including morphologically diverse species. The current availability of the genomes of both uni- and multicellular algae provides a good opportunity to conduct a genome-wide investigation in order to fill the knowledge gap in retroposition phenomenon in this lineage.

    Here we present a comparative genomic analysis of uni- and multicellular algae, Chlamydomonas reinhardtii and Volvox carteri, respectively, to explore their retrogene complements. By adopting a computational approach, we identified 141 retrogene candidates in total in both genomes, with their fraction being significantly higher in the multicellular Volvox. Majority of the retrogene candidates showed signatures of functional constraints, thus indicating their functionality. Detailed analyses of the identified retrogene candidates, their parental genes, and homologs of both, revealed that most of the retrogene candidates were derived from ancient retroposition events in the common ancestor of the two algae and that the parental genes were subsequently lost from the respective lineages, making many retrogenes ‘orphan’.

    We revealed that the genomes of the green algae have maintained many possibly functional retrogenes in spite of experiencing various molecular evolutionary events during a long evolutionary time after the retroposition events. Our first report about the retrogene set in the green algae provides a good foundation for any future investigation of the repertoire of retrogenes and facilitates the assessment of the evolutionary impact of retroposition on diverse morphological traits in this lineage.

  • Gabriel Gonzalez, Kanako Ono Koyanagi, Koki Aoki, Hidemi Watanabe
    Journal of Virology 89 (12) 6209 - 6217 2015/06 [Refereed][Not invited]
    Human mastadenovirus D (HAdV-D) is exceptionally rich in type among the seven human adenovirus species. This feature is attributed to frequent intertypic recombination events that have reshuffled orthologous genomic regions between different HAdV-D types. However, this trend appears to be paradoxical, as it has been demonstrated that the replacement of some of the interacting proteins for a specific function with other orthologues causes malfunction, indicating that intertypic recombination events may be deleterious. In order to understand why the paradoxical trend has been possible in HAdV-D evolution, we conducted an inter-regional coevolution analysis between different genomic regions of 45 different HAdV-D types and found that ca. 70% of the genome has coevolved, even though these are fragmented into several pieces via short intertypic recombination hotspot regions. Since it is statistically and biologically unlikely that all of the coevolving fragments have synchronously recombined between different genomes, it is probable that these regions have stayed in their original genomes during evolution as a platform for frequent intertypic recombination events in limited regions. It is also unlikely that the same genomic regions have remained almost untouched during frequent recombination events, independently, in all different types, by chance. In addition, the coevolving regions contain the coding regions of physically interacting proteins for important functions. Therefore, the coevolution of these regions should be attributed at least in part to natural selection due to common biological constraints operating on all types, including protein-protein interactions for essential functions. Our results predict additional unknown protein interactions.
  • Gabriel Gonzalez, Kanako O. Koyanagi, Koki Aoki, Nobuyoshi Kitaichi, Shigeaki Ohno, Hisatoshi Kaneko, Susumu Ishida, Hidemi Watanabe
    GENE 547 (1) 10 - 17 0378-1119 2014/08 [Refereed][Not invited]
    Human adenovirus species D (HAdV-D), which is composed of clinically and epidemiologically important pathogens worldwide, contains more taxonomic "types" than any other species of the genus Mastadenovirus, although the mechanisms accounting for the high level of diversity remain to be disclosed. Recent studies of known and new types of HAdV-D have indicated that intertypic recombination between distant types contributes to the increasing diversity of the species. However, such findings raise the question as to how homologous recombination events occur between diversified types since homologous recombination is suppressed as nucleotide sequences diverge. In order to address this question, we investigated the distribution of the recombination boundaries in comparison with the landscape of intergenomic sequence conservation assessed according to the synonymous substitution rate (d(s)). The results revealed that specific genomic segments are conserved between even the most distantly related genomes; we call these segments "universally conserved segments" (UCSs). These findings suggest that UCSs facilitate homologous recombination, resulting in intergenomic segmental exchanges of UCS-flanking genomic regions as recombination modules. With the aid of such a mechanism, the haploid genomes of HAdV-Ds may have been reshuffled, resulting in chimeric genomes out of diversified repertoires in the HAdV-D population analogous to the MHC region reshuffled via crossing over in vertebrates. In addition, some HAdVs with chimeric genomes may have had the opportunity to avoid host immune responses thereby causing epidemics. (C) 2014 Elsevier B.V. All rights reserved.
  • Tsuguto Fujimoto, Shotaro Yamane, Tomoko Ogawa, Nozomu Hanaoka, Atsushi Ogura, Chiemi Hotta, Takeshi Niwa, Yakou Chiba, Gabriel Gonzalez, Koki Aoki, Kanako Ono Koyanagi, Hidemi Watanabe
    Japanese Journal of Infectious Diseases 67 (4) 282 - 287 2014/07 [Refereed][Not invited]
    Recently, new genotypes of human adenoviruses (HAdVs) have been reported and many of them have been found to be recombinant forms of different known types of HAdV species D (HAdV-D). The objective of this study was to document the evolutionary features of a novel isolate (HAdV_Chiba_E086/2012) obtained from the eye swab of a patient with conjunctivitis in Japan. Viral DNA was extracted from the isolate to sequence the whole genome by the Sanger method and aligned with available genome sequences of HAdV-Ds. The phylogenetic trees of the nucleotide sequences of the penton base, hexon, and fiber genes and the E3 region showed that HAdV_Chiba_E086/2012 is closest to HAdV genotype 65 (HAdV-GT65), HAdV-48, HAdV-GT60 and HAdV-22 at 98%, 99%, 95% and 98% identity, respectively, suggesting that this isolate is a novel recombinant form to be designated as P65H48F60. Further phylogenetic and recombination analyses of the genome alignment of the new isolate implied that nested recombination events involving HAdV-GT59, GT65, 48, GT60, 22, and some ancestral lineages or their close relatives have shaped its genome. These results showed that HAdV_Chiba_E086/2012 is the first HAdV-48-related HAdV found in Japan, which has the most complicated evolutionary history among the known HAdVs so far.
  • Koki Aoki, Hisatosi Kaneko, Nobuyoshi Kitaichi, Hidemi Watanabe, Susumu Ishida, Shigeaki Ohno
    Nippon Ganka Gakkai Zasshi 117 (9) 721 - 726 2013/09 [Refereed][Not invited]
    Human adenovirus causing epidemic keratoconjunctivitis is limited to D and E species. Recent progress of bioinformatics revealed that these viruses attach to the host with fiber, infiltrate to the host cells via RGD motif of penton base, and show their serological reaction by hexon. Loop 1 and 2 are the variable region of hexon. The recombination of above three hot spots introduces the novel types such as HAdV-53, -54, and -56. Boinformatics may promise the rapid genotyping in the case of nosocomial infection, predicting the future epidemic, and the estimate of the therapeutic target molecules in the near future.
  • Jun YAMAMOTO, Toshihiro IWAMORI, Naoki HOSHI, Takuzo ABE, Keiichiro SAKAOKA, Yoshihiko KAMEI, Shogo TAKAGI, Osamu NUMAMOTO, Yukihiro SAKA, Kazuhisa SUEOKA, Hiroki ARIMURA, Hidemi WATANABE
    Journal of Fisheries Technology 5 (2) 171 - 174 2013/02 [Refereed][Not invited]
    We developed a battery powered compact 2000m class ROV (Remotely Operated Vehicle) system with a High-Definition video camera. It does not require specialized equipment to operate. It can be operated using only general purpose equipment. This system mainly consists of a shipboard controller, a vehicle and a launcher. A thin, light optical fiber cable (diameter 9mm, length 2,500m), the primary cable, transfers control data and video images between the shipboard controller and the launcher. The secondary cable, a composite cable (diameter 14.2mm, length 50m), transfers control data and video images and supplies power to the vehicle from the six packs of lithium-ion batteries, which are mounted in the launcher. The launcher is suspended by a rope from the support ship, and the depth of the launcher is adjusted by changing the length of the rope using a general purpose rewinder.
    Although initially, we had some trouble due to the launcher rope and the primary cable getting tangled, a newly-designed instrument that restricts the movement of the carabiner, and the use of a low expansion rope, facilitated smoother operation and an easier recovery of the ROV.
  • Yamane S, Lee AW, Hanaoka N, Gonzalez G, Kaneko H, Ishida S, Kitaichi N, Ohno S, Koyanagi KO, Aoki K, Fujimoto T, Yawata N, Watanabe H
    Journal of virology 2 87 (2) 1285 - 1286 0022-538X 2013/01 [Refereed][Not invited]
    電子情報通信学会技術研究報告 111 (442(IE2011 105-132)) 73 - 78 0913-5685 2012/02 [Not refereed][Not invited]
  • Yamada A, Koyanagi KO, Watanabe H
    Gene 2 491 (2) 232 - 236 0378-1119 2012/01 [Refereed][Not invited]
  • Hayashida K, Hara Y, Abe T, Yamasaki C, Toyoda A, Kosuge T, Suzuki Y, Sato Y, Kawashima S, Katayama T, Wakaguri H, Inoue N, Homma K, Tada-Umezaki M, Yagi Y, Fujii Y, Habara T, Kanehisa M, Watanabe H, Ito K, Gojobori T, Sugawara H, Imanishi T, Weir W, Gardner M, Pain A, Shiels B, Hattori M, Nene V, Sugimoto C
    mBio 5 3 e00204 - 12 2012 [Refereed][Not invited]
  • Kaneko H, Aoki K, Ishida S, Ohno S, Kitaichi N, Ishiko H, Fujimoto T, Ikeda Y, Nakamura M, Gonzalez G, Koyanagi KO, Watanabe H, Suzutani T
    The Journal of general virology Pt 6 92 (6) 1251 - 1259 0022-1317 2011/06 [Refereed][Not invited]
  • Kaneko H, Aoki K, Ohno S, Ishiko H, Fujimoto T, Kikuchi M, Harada S, Gonzalez G, Koyanagi KO, Watanabe H, Suzutani T
    Journal of clinical microbiology 2 49 484 - 490 0095-1137 2011/02 [Refereed][Not invited]
  • Itoh M, Watanabe H
    Bioinformatics (Oxford, England) 7 25 958 - 959 1367-4803 2009/04 [Refereed][Not invited]
  • Innan H, Watanabe H
    Molecular biology and evolution 5 23 1040 - 1047 0737-4038 2006/05 [Refereed][Not invited]
  • Satta Y, Hickerson M, Watanabe H, O'hUigin C, Klein J
    Journal of molecular evolution 4 59 478 - 487 0022-2844 2004/10 [Refereed][Not invited]
  • International Human, Genome Sequencing Consortium
    Nature 431 931 - 945 2004/10 [Refereed][Invited]
    The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ~99% of the euchromatic genome and is accurate to an error rate of ~1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human genome seems to encode only 20,000–25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead.
  • Watanabe Hidemi, Fujiyama A, Hattori M, Taylor TD, Toyoda A, Kuroki Y, Noguchi H, BenKahla A, Lehrach H, Sudbrak R, Kube M, Taenzer S, Galgoczy P, Platzer M, Scharfe M, Nordsiek G, Blöcker H, Hellmann I, Khaitovich P, Pääbo S, Reinhardt R, Zheng HJ
    Nature 429 (6990) 382 - 388 0028-0836 2004/05 [Refereed][Not invited]
  • Yamada Y, Watanabe H, Miura F, Soejima H, Uchiyama M, Iwasaka T, Mukai T, Sakaki Y, Ito T
    Genome research 2 14 247 - 266 1088-9051 2004/02 [Refereed][Not invited]
  • Human versus chimpanzee chromosome-wide sequence comparison and its evolutionary implication.
    Sakaki Y, Watanabe H, Taylor T, Hattori M, Fujiyama A, Toyoda A, Kuroki Y, Itoh T, Saitou N, Oota S, Kim CG, Kitano T, Lehrach H, Yaspo ML, Sudbrak R, Kahla A, Reinhardt R, Kube M, Platzer M, Taenzer S, Galgoczy P, Kel A
    Cold Spring Harb Symp Quant Biol. 68 455 - 460 2003 [Refereed][Not invited]
  • Akman L, Yamashita A, Watanabe H, Oshima K, Shiba T, Hattori M, Aksoy S
    Nature genetics 3 32 (3) 402 - 407 1061-4036 2002/11 [Refereed][Not invited]
  • Fujiyama A, Watanabe H, Toyoda A, Taylor TD, Itoh T, Tsai SF, Park HS, Yaspo ML, Lehrach H, Chen Z, Fu G, Saitou N, Osoegawa K, de Jong PJ, Suto Y, Hattori M, Sakaki Y
    Science (New York, N.Y.) 5552 295 (5552) 131 - 134 0036-8075 2002/01 [Refereed][Not invited]
  • Codon and base biases after the initiation codon of the open reading frames in the Escherichia coli genome and their influence on the translation efficiency.
    Sato T, Terabe M, Watanabe H, Gojobori T, Hori-Takemoto C, Miura Ki
    J Biochem 129 (6) 851 - 860 2001/06 [Refereed][Not invited]
  • Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, Kann L, Lehoczky J, LeVine R, McEwan P, McKernan K, Meldrim J, Mesirov JP
    Nature 509 (6822) 860 - 921 2001/02 [Refereed][Not invited]
  • Shigenobu S, Watanabe H, Sakaki Y, Ishikawa H
    J Mol Evol 53 (4/5) 377 - 386 0022-2844 2001 [Refereed][Not invited]
  • Shigenobu S, Watanabe H, Hattori M, Sakaki Y, Ishikawa H
    Nature 407 (6800) 81 - 86 0028-0836 2000/09 [Refereed][Not invited]
  • Yatsuki H, Watanabe H, Hattori M, Joh K, Soejima H, Komoda H, Xin Z, Zhu X, Higashimoto K, Nishimura M, Kuratomi S, Sasaki H, Sakaki Y, Mukai T
    DNA Res 7 (3) 195 - 206 1340-2838 2000/06 [Refereed][Not invited]
  • Hattori M, Fujiyama A, Taylor TD, Watanabe H, Yada T, Park HS, Toyoda A, Ishii K, Totoki Y, Choi DK, Groner Y, Soeda E, Ohki M, Takagi T, Sakaki Y, Taudien S, Blechschmidt K, Polley A, Menzel U, Delabar J, Kumpf K, Lehmann R
    Nature 405 (6784) 311 - 319 2000/05 [Refereed][Not invited]
  • Bellgard MI, Itoh T, Watanabe H, Imanishi T, Gojobori T
    Ann N Y Acad Sci 870 293 - 300 0077-8923 1999/05 [Refereed][Not invited]
  • Characteristic distribution of bases and codons around the initiation and termination codons in whole reading frames in bacteria and yeast genomes.
    Watanabe H, Gojobori T, Terabe M, Wakiyama M, Miura K
    Nucleic Acids Symp Ser 37 297 - 298 1997 [Refereed][Not invited]
  • Tateno Y, Ikeo K, Imanishi T, Watanabe H, Endo T, Yamaguchi Y, Suzuki Y, Takahashi K, Tsunoyama K, Kawai M, Kawanishi Y, Naitou K, Gojobori T
    J Mol Evol 44 (Suppl 1) S38 - S43 1997 [Refereed][Not invited]
  • Watanabe H, Mori H, Itoh T, Gojobori T
    J Mol Evol 44 (Suppl 1) S57 - S64 1997 [Refereed][Not invited]
  • A comprehensive representation of extensive similarity linkage between large numbers of proteins.
    Watanabe H, Otsuka J
    Comput Appl Biosci 11 (2) 159 - 166 1995/04 [Refereed][Not invited]
  • Escherichia coli K12 genomic database.
    Kunisawa T, Nakamura M, Watanabe H, Otsuka J, Tsugita A, Yeh LS, George DG, Barker WC
    Protein Seq Data Anal 3 (2) 157 - 162 1990/06 [Refereed][Not invited]


Awards & Honors

  • 2012/06 画像電子学会 優秀論文賞
    受賞者: 方 明;髙氏 秀則;金子 俊一;渡邉 日出海

Research Grants & Projects

  • 単一細胞シークエンスデータに基づく細胞社会学のための情報手法の開発とデータ解析
    Date (from‐to) : 2017 -2021 
    Author : 池尾 一穂
  • 文部科学省:科学研究費補助金(新学術領域研究(研究領域提案型))
    Date (from‐to) : 2010 -2014 
    Author : 渡邉 日出海
  • Ministry of Education, Culture, Sports, Science and Technology:Grants-in-Aid for Scientific Research(基盤研究(B))
    Date (from‐to) : 2006 -2008 
    Author : Watanabe WATANABE
  • 文部科学省:科学研究費補助金(特定領域研究)
    Date (from‐to) : 2006 -2007 
    Author : 渡邉 日出海, 小柳 香奈子
  • 文部科学省:科学研究費補助金(特定領域研究)
    Date (from‐to) : 2005 -2005 
    Author : 渡邉 日出海
  • Ministry of Education, Culture, Sports, Science and Technology:Grants-in-Aid for Scientific Research(基盤研究(C))
    Date (from‐to) : 2003 -2005 
    Author : Hidemi WATANABE
    To address the issue on the speciation process in the primate lineages, several studies were conducted with collaborators, Dr.Satta at Sokendai, and Dr.Innan at the University of Texas Health Science Center at Houston, with large numbers of sequence fragments randomly selected from the chimpanzee genome and the human genome as well as additional data sets of other primates. In these studies, the ancestral population sizes of primates and the divergence times of major primate lineages were carefully estimated, and it was suggested that the ancestral population sizes of primates were several ...
  • 文部科学省:科学研究費補助金(特定領域研究)
    Date (from‐to) : 2004 -2004 
    Author : 渡邉 日出海, 小柳 香奈子
    理化学研究所が中心となって日独中韓台の9センターで編成したコンソーシアムにおいて、霊長類の染色体としては世界で初めてのチンパンジー22番染色体(PTR22)の完成配列を決定し、Nature誌のArticleとして発表した。この論文において本研究代表者は比較解析全般を担当し、ヒト相同染色体であるヒト21番染色体(HSA21)および他の類人猿との間で種間比較解析を行った。本研究の目的は、500-700万年前にヒトとチンパンジーが分岐した後に、それぞれの系統において生じてきたゲノムの構造変化の詳細を明らかにすることである。同コンソーシアムによる先行研究(Fujiyama et al.,2002)において両ゲノムは塩基配列レベルで平均1.23%の塩基置換が起きていることをあきらかにしていたが、PTR22-HSA21間では若干高い1.44%の平均塩基置換率になっていた。これは主としてテロメア側半分ではGC含量が高くCpGのメチル化脱アミノ化による塩基置換(C:G→T:A)が高頻度で起こっていることによることがわかった。他に、PTR22はHSA21よりも約1%小さいこと、多くの挿入・欠失が存在し短いものほど頻度が高いこと、300bp以上の長さの挿入は大部分が散在性反復配列の挿入によるものであること、挿入はHSA21で高頻度で起こっている一方、欠失は両染色体で完全に同じ傾向をしめしているこ...
  • 文部科学省:科学研究費補助金(特定領域研究)
    Date (from‐to) : 2003 -2003 
    Author : 渡邉 日出海
    国際コンソーシアムにおいて、類人猿あるいは霊長類の染色体としては世界で初めてチンパンジーの22番染色体(PTR22)の完成配列を決定し、そのヒト相同染色体であるヒト21番染色体(HSA21)との間で種間比較を行った。本研究の目的は、ヒトとチンパンジーの染色体塩基配列を比較することによって、約500万年前にヒトとチンパンジーが分岐した後に、それぞれの系統において生じてきたゲノムの構造変化の詳細を明らかにすることである。両ゲノムは塩基配列レベルでは僅かに1.23%程度しか異なっていないことを同コンソーシアムが先行研究(Fujiyama et al.,2002)で明らかにしていたため、概要配列ではなく高精度の完成配列の形でチンパンジーゲノム配列の決定を行うことが必要であると考えられた。しかし、そのためには膨大な作業が必要になるため、まず染色体レベルでの解析を行うことにし、同様のメンバーで構成された国際コンソーシアムによってその完成配列が決定されたヒト21番染色体(Hattori et al.,2000)の相同染色体を解析の対象に選んだ。配列決定の結果、(1)PTR22はHSA21よりも約1%小さい、(2)多くの挿入・欠失(INDEL)が存在し、短いものほど頻度が高い、(3)300bp以上の長さの挿入は、大部分が散在性反復配列の挿入によるものである、(4)HSA21、PTR22それぞ...
  • 文部科学省:科学研究費補助金(特定領域研究)
    Date (from‐to) : 2002 -2002 
    Author : 渡邉 日出海
    本研究課題において、2つの研究を具体的に行った。ツェツェバエの細胞内共生微生物であるWigglesworthia glossinidiaのゲノムを他の共同研究者と共に決定し、そのゲノム配列を、本研究代表者らが既に決定し報告してあったアブラムシの細胞内共生微生物であるBuchnera APSのゲノム配列(Shigenobu, et al.,2000)と比較し、共生微生物の進化過程についての様々な情報を得た(Akman, et al.,2002)。Buchneraのゲノムは、共生生物としては世界で初めて配列決定されたものであったため、その解析によって明らかになった様々な特徴が共生生物の特徴であると我々は考えた。しかし、系統的にBuchneraに極めて近い関係にあると考えられているWigglesworthiaのゲノムと比較してみた結果、予想に反して、多くの点で異なっていることが明らかになった。例えば、これら2つのゲノムは最も小さい部類に属しているため、その中に存在する遺伝子は生存にとって必要不可欠なものに限られているであろうと考えられていたが、実際には、2者に共通している遺伝子は僅かに7割弱であった。したがって、生物は一定の生活環境に置かれると、その環境に適応するかたちで短期間のうちにゲノムの中身が大きく変わることが明らかになった。もう1つの研究は、チンパンジー22番染色体(PTR...
  • 文部科学省:科学研究費補助金(特定領域研究(C))
    Date (from‐to) : 2001 -2001 
    Author : 渡邉 日出海
  • 文部科学省:科学研究費補助金(特定領域研究(C))
    Date (from‐to) : 2000 -2000 
    Author : 渡邉 日出海
    初めに、大量のゲノムDNA配列を短時間で比較するために、備品として購入したAlphaStation DS20E上に、最新のゲノムDNA配列データを公共データベースから定期的に自動で収集管理するシステムを構築した。この自動データ収集システムを用いて、ヒト、類人猿、霊長類、マウスなどを含むその他の哺乳類、ニワトリ、アフリカツメガエル、フグ、ショウジョウバエ、線虫、酵母、植物等の、真核生物のゲノムデータを定期的に収集し種毎に整理する。現在のところ、ヒトを除いた脊椎動物に限った場合、800メガ塩基対相当のデータが蓄積されている。この収集されたゲノムDNA配列データを種内・種間で高速で自動比較するために、配列データを一旦加工した後、BLASTを用いて総当りの比較を行い、保存領域に関する情報を蓄積するシステムを構築した。比較解析データには、保存領域に関する、配列、保存度、ゲノム上あるは配列データ上での位置と方向などが含まれる。比較解析結果から生物学的意味を抽出するために、まず、保存領域を含む遺伝子に関する情報をゲノムデータから抽出する。遺伝子に関する情報には、遺伝子内での位置、エクソン/イントロンの区別、遺伝子の機能が含まれる。保存領域の、遺伝子との関係を見ることにより、保存領域が持つ機能の範囲を限定する。続いて、保存領域の中から、遺伝子内に見出されないもの、つまり遺伝子によって機能が限...

Educational Activities

Teaching Experience

  • Bioengineering
    開講年度 : 2018
    課程区分 : 修士課程
    開講学部 : 情報科学研究科
    キーワード : 遺伝情報, genetic information, バイオインフォマティクス, bioinformatics, イメージング, imaging, 生体医工学, biomedical engineering, 細胞力学, cell mechanics
  • Inter-Graduate School Classes(General Subject):Inter-Disciplinary Sciences
    開講年度 : 2018
    課程区分 : 修士課程
    開講学部 : 大学院共通科目
  • Genome Informatics
    開講年度 : 2018
    課程区分 : 修士課程
    開講学部 : 情報科学研究科
    キーワード : ゲノム, 複製, 転写, 翻訳, 塩基配列決定, 分子進化解析, ゲノム配列解析, ゲノム発現解析
  • Bioengineering
    開講年度 : 2018
    課程区分 : 博士後期課程
    開講学部 : 情報科学研究科
    キーワード : 遺伝情報, genetic information, バイオインフォマティクス, bioinformatics, イメージング, imaging, 生体医工学, biomedical engineering, 細胞力学, cell mechanics
  • Genome Informatics
    開講年度 : 2018
    課程区分 : 博士後期課程
    開講学部 : 情報科学研究科
    キーワード : ゲノム, 複製, 転写, 翻訳, 塩基配列決定, 分子進化解析, ゲノム配列解析, ゲノム発現解析
  • Biochemistry
    開講年度 : 2018
    課程区分 : 学士課程
    開講学部 : 工学部
    キーワード : アミノ酸、タンパク質、糖、脂質、核酸、酵素、反応速度、生体エネルギー、代謝
  • Bioinformatics
    開講年度 : 2018
    課程区分 : 学士課程
    開講学部 : 工学部
    キーワード : 遺伝情報、ゲノム、染色体、遺伝子、遺伝子型、表現型、突然変異、メンデル遺伝学、分子進化
  • Molecular Biology I
    開講年度 : 2018
    課程区分 : 学士課程
    開講学部 : 工学部
    キーワード : 遺伝情報、ゲノム、染色体、遺伝子、遺伝子型、表現型、突然変異、メンデル遺伝学、分子進化
  • Molecular Biology I
    開講年度 : 2018
    課程区分 : 学士課程
    開講学部 : 工学部
    キーワード : アミノ酸、タンパク質、糖、脂質、核酸、酵素、反応速度、生体エネルギー、代謝
  • Molecular Biology II
    開講年度 : 2018
    課程区分 : 学士課程
    開講学部 : 工学部
    キーワード : 遺伝情報、ゲノム、染色体、遺伝子、遺伝子型、表現型、突然変異、メンデル遺伝学、分子進化

Committee Membership

  • 2016/07 - Today   International Committee on Taxonomy of Viruses   Adenoviridae Study Group

Social Contribution

Social Contribution

Media Coverage

  • Associate Editor
    Date : 2009/01/01
    Publisher, broadcasting station: Oxford University Press
    Program, newspaper magazine: Genome Biology and Evolution


  • 2017/09 -2017/09 日本学術振興会表彰

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