ゲノム科学の総合的推進に向けた大規模ゲノム情報生産・高度情報解析支援

2015 Fiscal Year Annual Research Report

• Project Area: ゲノム科学の総合的推進に向けた大規模ゲノム情報生産・高度情報解析支援
• Project/Area Number: 221S0002
• Research Institution: National Institute of Genetics
• Principal Investigator: 小原 雄治 国立遺伝学研究所, 系統生物研究センター, 特任教授 (70135292)
• Co-Investigator(Kenkyū-buntansha): 久原 哲 九州大学, (連合)農学研究科(研究院), 教授 (00153320) ; 井ノ上 逸朗 国立遺伝学研究所, 総合遺伝研究系, 教授 (00192500) ; 林 哲也 九州大学, 医学(系)研究科(研究院), 教授 (10173014) ; 加藤 和人 大阪大学, 医学(系)研究科(研究院), 教授 (10202011) ; 豊田 敦 国立遺伝学研究所, 生命情報研究センター, 特任准教授 (10267495) ; 榊原 康文 慶應義塾大学, 理工学部, 教授 (10287427) ; 矢田 哲士 九州工業大学, 大学院情報工学研究院, 教授 (10322728) ; 黒木 陽子 東北大学, 東北メディカルメガバンク機構, 非常勤講師 (10344037) ; 黒川 顕 東京工業大学, 地球生命研究所, 教授 (20343246) ; 浅井 潔 東京大学, 新領域創成科学研究科, 教授 (30356357) ; 鈴木 穣 東京大学, 新領域創成科学研究科, 教授 (40323646) ; 岩崎 渉 東京大学, 大学院理学系研究科, 准教授 (50545019) ; 菅野 純夫 東京大学, 新領域創成科学研究科, 教授 (60162848) ; 山本 健 久留米大学, 医学部, 教授 (60274528) ; 中村 保一 国立遺伝学研究所, 生命情報研究センター, 教授 (60370920) ; 笠原 雅弘 東京大学, 新領域創成科学研究科, 講師 (60376605) ; 辻 省次 東京大学, 医学部附属病院, 教授 (70150612) ; 田畑 哲之 公益財団法人かずさDNA研究所, その他部局等, 所長 (70197549) ; 森下 真一 東京大学, 新領域創成科学研究科, 教授 (90292854) ; 瀬々 潤 国立研究開発法人産業技術総合研究所, 創薬基盤研究部門, 主任研究員 (40361539) ; 高橋 弘喜 千葉大学, 真菌医学研究センター, 准教授 (60548460)
• Project Period (FY): 2010-04-01 – 2016-03-31
• Keywords: 次世代DNAシーケンサ / RNA-seq / ChIP-seq / de novo配列決定 / 個人ゲノム / リシーケンシング / GWAS / インフォームドコンセント

Outline of Annual Research Achievements

支援課題公募では211件の応募があり、74件を選定し支援した。中～大型ゲノムの新規配列決定は本年度11種に上った。成果論文は、支援成果の査読有論文108報（発表論文欄は班員が加わっているもの38報をあげた）及び班員の高度化研究等論文27報である。
今年度の主な論文発表成果としては、新規配列決定支援では原始的な多細胞生物ゴニウム（野崎ら）、ベネズエラ糞線虫（丸山ら、英国サンガーセンターと共同研究）のゲノム解読と比較研究等があった。再シーケンス支援では、マウスの1世代あたりの変異率の測定に成功（八木ら）、苔類ゼニゴケの多型情報を取得データベース化することによって新たなモデル生物化（河内ら）等がある。RNA、エピゲノム解析支援では、免疫担当細胞におけるRegnase1の作用機序の詳細の解明が論文化された（竹内ら）。微生物支援では、芳香族化合物による汚染土壌のメタゲノム解析が微生物による環境浄化の分野を先導する研究となった（津田ら）。大腸菌に近縁の病原細菌であるE. albertii 29株のゲノム配列を決定し、病原遺伝子の網羅的な同定に成功した（林ら）。ゲノム医科学支援では、長年のGWAS解析から痛風の発症リスクに有意な5つの遺伝子領域を見出した（松尾ら）。ゲノム解析技術開発においては、1分子シーケンシング手法、1細胞解析技術の開発整備をさらに進めた。情報解析支援では、開発したソフトウェアの支援への活用を進めるとともに、GMcloser（高精度ギャップ修復、平川ら）、Sharaku（機能性RNA解析、榊原ら）、MOCCS（ChIP-Seqデータから配列モチーフ列挙、岩崎ら）、DomSign（タンパク質の機能予測ツール、黒川ら）、FuncTree（機能的特徴の視覚化、黒川ら）、COSMOS（大規模構造変異検出、瀬々ら）等の開発も進めた。ゲノム支援講習会を開催した。ゲノムELSIユニットでは個人ゲノム解読の倫理問題への実務的支援を引き続き推進した。

Research Progress Status

27年度が最終年度であるため、記入しない。

Strategy for Future Research Activity

27年度が最終年度であるため、記入しない。

Research Products

• [Journal Article] The Gonium pectorale genome demonstrates cooption of cell cycle regulation during the evolution of multicellularity (2016)
  • Author(s): Erik R. Hanschen, Tara N. Marriage, Patrick J. Ferris, Takashi Hamaji, Atsushi Toyoda, Asao Fujiyama, Rafik Neme, Hideki Noguchi, Yohei Minakuchi, Masahiro Suzuki, Hiroko Kawai-Toyooka, David R. Smith, Halle Sparks, Jaden Anderson, Robert Bakaric, Victor Luria, Amir Karger, Marc Kirschner, et al.
  • Journal Title: Nature Communications Volume: 7 Pages: 11370
  • DOI: 10.1038/ncomms11370
  • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] Ezh2 regulates the Lin28/let-7 pathway to restrict activation of fetal gene signature in adult hematopoietic stem cells. (2016)
  • Author(s): Oshima M, Hasegawa N, Mochizuki-Kashio M, Muto T, Miyagi S, Koide S, Yabata S, Wendt G, Saraya A, Wang C, Shimoda K, Suzuki Y, Iwama A.
  • Journal Title: Exp Hematol Volume: 44(4) Pages: 282-296.e3.
  • DOI: 10.1016/j.exphem.2015.12.009.
  • Peer Reviewed
• [Journal Article] Histone H3K36 trimethylation is essential for multiple silencing mechanism in fission yeast. (2016)
  • Author(s): Shota Suzuki, Hiroaki Kato, Yutaka Suzuki, Yuji Chikashige, Yasushi Hiraoka, Hiroshi Kimura, Koji Nagao, Chikashi Obuse, Shinya Takahata and Yota Murakami
  • Journal Title: Nucleic Acids Research Volume: 44 (9) Pages: 4147-4162
  • DOI: 10.1093/nar/gkw008
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] COSMOS: accurate detection of somatic structural variations through asymmetric comparison between tumor and normal samples. (2016)
  • Author(s): Yamagata, Koichi; Yamanishi, Ayako; Kokubu, Chikara; Takeda, Junji; Sese, Jun
  • Journal Title: Nucleic Acids Research Volume: 44 (8) Pages: e78
  • DOI: 10.1093/nar/gkw026
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] The complete genome sequencing of Prevotella intermedia strain OMA14 and a subsequent finescale, intra-species genomic comparison re an unusual amplification of conjugative and mobile transposons and identify a novel Prevotella-lineage-specific repeat. (2016)
  • Author(s): Mariko Naito, Yoshitoshi Ogura, Takehiko Itoh, Mikio Shoji, Masaaki Okamoto, Tetsuya Hayashi, and Koji Nakayama.
  • Journal Title: DNA Research Volume: 23 (1) Pages: 11-19
  • DOI: 10.1093/dnares/dsv032
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] HTLV-1 bZIP Factor Impairs Anti-viral Immunity by Inducing Co-inhibitory Molecule, T Cell Immunoglobulin and ITIM Domain (TIGIT)． (2016)
  • Author(s): Keiko Yasuma, Jun-ichirou Yasunaga, Keiko Takemoto, Kenji Sugata, Norihiro Takenouchi, Masanori Nakagawa, Yutaka Suzuki, and Masao Matsuoka
  • Journal Title: PLoS Pathogens Volume: 12(1) Pages: e1005372
  • DOI: 10.1371/journal.ppat.1005372
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] The Genomic Basis of Parasitism in the Strongyloides Clade of Nematodes. (2016)
  • Author(s): Hunt, V., Tsai, I. J., Coghlan, A., Reid, A. J., Holroyd, N., Foth, B. J., Tracey, A., Cotton, J. A., Stanley, E. J., Beasley, H., Bennett, H., Brooks, K., Harsha, B., Kajitani, R., Kulkarni, A., Harbecke, D., Nagayasu, E., Nichol, S., Ogura, Y.(19番目), Hayashi, T.(26番目), Itoh, T(27番目)., et al.
  • Journal Title: Nature Genetics Volume: 48 Pages: 299-307
  • DOI: 10.1038/ng.3495
  • Open Access / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] Ethics of stem cell research - learning from human genome ELSI research (2016)
  • Author(s): Kazuto Kato.
  • Journal Title: Proceedings of Uehara Carnegie Oxford Conference Volume: - Pages: 117-124
• [Journal Article] MOCCS: clarifying DNA-binding motif ambiguity using ChIP-Seq data (2016)
  • Author(s): Ozaki H, Iwasaki W
  • Journal Title: Comput. Biol. Chem. Volume: in press Pages: in press
  • DOI: 10.1016/j.compbiolchem.2016.01.014
  • Peer Reviewed
• [Journal Article] Genomic and metagenomic analysis of microbes in a soil environment affected by the 2011 Great East Japan Earthquake Tsunami (2016)
  • Author(s): Hiraoka S, Machiyama A, Ijichi M, Inoue K, Oshima K, Hattori M, Yoshizawa S, Kogure K, and Iwasaki W
  • Journal Title: BMC Genomics Volume: 17 Pages: 53
  • DOI: 10.1186/s12864-016-2380-4
  • Peer Reviewed
• [Journal Article] Draft genome sequence of the pathogenic filamentous fungus Aspergillus lentulus IFM 54703T. (2016)
  • Author(s): Kusuya Y, Sakai K, Takahashi H, Yaguchi T
  • Journal Title: Genome Announc. Volume: 4 Pages: e01568-15
  • DOI: 10.1128/genomeA.01568-15
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Oncofetal protein IGF2BP3 facilitates the activity of proto-oncogene protein eIF4E through the destabilization of EIF4E-BP2 mRNA. (2015)
  • Author(s): Mizutani R., Imamachi N., Suzuki Y., Yoshida H., Tochigi N., Oonishi T., Suzuki Y., Akimitsu N.
  • Journal Title: Oncogene Volume: 2015 Nov 2 Pages: Epub
  • DOI: 10.1038/onc.2015.410
  • Peer Reviewed
• [Journal Article] Analysis of RNA decay factor mediated RNA stability contributions on RNA abundance. (2015)
  • Author(s): Maekawa S., Imamachi N., Irie T., Tani H., Matsumoto K., Mizutani R., Imamura K., Kakeda M., Yada T., Sugano S., Suzuki Y. and Akimitsu N.
  • Journal Title: BMC Genomics Volume: 16 Pages: 154
  • DOI: 10.1186/s12864-015-1358-y
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] A Novel Mutation in ELOVL4 Leading to Spinocerebellar Ataxia (SCA) With the Hot Cross Bun Sign but Lacking Erythrokeratodermia: A Broadened Spectrum of SCA34. (2015)
  • Author(s): Kokoro Ozaki , Hiroshi Doi, Jun Mitsui, Nozomu Sato, Yoichiro Iikuni, Takamasa Majima, Kiyomi Yamane, Takashi Irioka, Hiroyuki Ishiura, Koichiro Doi, Shinichi Morishita, Miwa Higashi, Teruhiko Sekiguchi, Kazuo Koyama, Naohisa Ueda, Yoshiharu Miura, Satoko Miyatake, Naomichi Matsumoto, Shoji Tsuji(21番目), et al.
  • Journal Title: JAMA Neurol. Volume: 72(7) Pages: 797-805
  • DOI: 10.1001/jamaneurol.2015.0610.
  • Peer Reviewed
• [Journal Article] The tRNA Splicing Endonuclease Complex Cleaves the Mitochondria-localized CBP1 mRNA. (2015)
  • Author(s): Tsuboi, T., Yamazaki, R., Nobuta, R., Ikecuhi, K., Makino, S., Ohtaki, Y., Suzuki, Y., Yoshihisa, T., Trotta, C. and Inada, T.
  • Journal Title: J Biol. Chem. Volume: 290 Pages: 16021-16030
  • DOI: 10.1074/jbc.M114.634592
  • Peer Reviewed / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] New Susceptibility Gene, IKZF1, for Cold Medicine-Related Stevens-Johnson Syndrome/Toxic Epidermal Necrolysis with Severe Mucosal Involvements. (2015)
  • Author(s): Ueta M, Sawai H, Sotozono C, Hitomi Y, Kaniwa N, Kim MK, Seo KY, Yoon KC, Joo CK, Kannabiran C, Wakamatsu TH, Sangwan V, Rathi V, Basu S, Ozeki T, Mushiroda T, Sugiyama E, Maekawa K, Nakamura R, Aihara M, Matsunaga K, Sekine A, Gomes JAP, Hamuro J, Saito Y, Kubo M, Kinoshita S, Tokunaga K
  • Journal Title: J Allergy Clin Immunol. Volume: 135(6) Pages: 1538-1545.e17.
  • DOI: 10.1016/j.jaci.2014.12.1916.
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Domestication and cereal feeding developed domestic pig-type intestinal microbiota in animals of suidae. (2015)
  • Author(s): Ushida K, Tsuchida S, Ogura Y, Toyoda A, Maruyama F.
  • Journal Title: Anim Sci J. Volume: Aug 27 Pages: 12492
  • DOI: 10.1111/asj.12492
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Draft Genome Sequence of Lactobacillus gorillae strain KZ01T, isolated from a western lowland gorilla. (2015)
  • Author(s): Tsuchida S, Nezuo M, Tsukahara M, Ogura Y, Hayashi T, Ushida K.
  • Journal Title: Genome Announc. Volume: Oct 15;3(5) Pages: e01196-15
  • DOI: 10.1128/genomeA.01196-15
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Comparative genome and transcriptome analyses of the social amoeba Acytostelium subglobosum that accomplishes multicellular development without germ-soma differentiation. (2015)
  • Author(s): Urushihara H, Kuwayama H, Fukuhara K, Itoh T, Kagoshima H, Shin-I T, Toyoda A, Ohishi K, Taniguchi T, Noguchi H, Kuroki Y, Hata T, Uchi K, Mohri K, King JS, Insall RH, Kohara Y, Fujiyama A.
  • Journal Title: BMC Genomics Volume: 16 Pages: 80
  • DOI: 10.1186/s12864-015-1278-x.
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Dynamic transition of transcription and chromatin landscape during fission yeast adaptation to glucose starvation. (2015)
  • Author(s): Oda A., Takemata N., Hirata Y., Miyoshi T., Suzuki Y., Sugano S., Ohta K.
  • Journal Title: Genes to Cells Volume: 20 Pages: 392-407
  • DOI: 10.1111/gtc.12229
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Genome analysis of a novel Bradyrhizobium sp. DOA9 carrying a symbiotic plasmid. (2015)
  • Author(s): Okazaki S, Noisangiam R, Okubo T, Kaneko T, Oshima K, Hattori M, Teamtisong K, Songwattana P, Tittabutr P, Boonkerd N, Saeki K, Sato S, Uchiumi T, Minamisawa K, *Teaumroong N.
  • Journal Title: PLOS ONE Volume: 10(2) Pages: e0117392
  • DOI: 10.1371/journal.pone.0117392
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Spatial Interplay between Polycomb and Trithorax Complexes Controls Transcriptional Activity in T Lymphocytes. (2015)
  • Author(s): Onodera A, Tumes DJ, Watanabe Y, Hirahara K, Kaneda A, Sugiyama F, Suzuki Y, Nakayama T.
  • Journal Title: Mol Cell Biol. Volume: 35(22) Pages: 3841-53
  • DOI: 10.1128/MCB.00677-15
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Tepidicaulis marinum gen. nov., sp. nov., a novel marine bacterium denitrifying nitrate to nitrous oxide strictly under microaerobic conditions. (2015)
  • Author(s): Takeuchi M., Yamagishi T., Kamagata Y., Oshima K., Hattori M., Katayama T., Hanada S., Tamaki H., Marumo K., Maeda H., Nedachi M., Iwasaki W., Suwa Y., Sakata S.
  • Journal Title: Int. J. Syst. Evol. Microbiol. Volume: 65 Pages: 1749-1754
  • DOI: 10.1099/ijs.0.000167
  • Peer Reviewed
• [Journal Article] RNA-seq transcriptional profiling of an arbuscular mycorrhiza provides insights into regulated and coordinated gene expression in Lotus japonicus and Rhizophagus irregularis. (2015)
  • Author(s): Handa, Y., Nishide, H., Takeda, N., Suzuki, Y., Kawaguchi, M., Saito, K.
  • Journal Title: Plant and Cell Physiology Volume: 56 Pages: 1490-1511
  • DOI: 10.1093/pcp/pcv07
  • Peer Reviewed
• [Journal Article] Mapping the genetic diversity of HLA haplotypes in the Japanese populations. (2015)
  • Author(s): Saw, W.Y., X. Liu, C.C. Khor, F. Takeuchi, T. Katsuya, R. Kimura, T. Nabika, T. Ohkubo, Y. Tabara, K. Yamamoto, M. Yokota, Japanese Genome Variation Consortium, Y.Y. Teo, and N. Kato
  • Journal Title: Scientific Reports Volume: 5 Pages: 17855
  • DOI: 10.1038/srep17855.
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] From the laboratory to the field: assaying histone methylation at FLOWERING LOCUS C in naturally growing Arabidopsis halleri. (2015)
  • Author(s): Nishio H, Buzas DM, Nagano AJ, Suzuki Y, Sugano S, Ito M, Morinaga S, Kudoh H.
  • Journal Title: Genes & Genetic Systems Volume: 2016 May 2 Pages: Epub
  • DOI: 10.1266/ggs.15-00071
  • Peer Reviewed / Open Access
• [Journal Article] Novel mitochondria-targeted heat-soluble proteins identified in the anhydrobiotic tardigrade improve osmotic tolerance of human cells. (2015)
  • Author(s): Tanaka, S., Tanaka, J., Miwa, Y., Horikawa, D., D., Katayama, T., Arakawa, K., Toyoda, A., Kubo, T., and, Kunieda, T.
  • Journal Title: PLoS ONE Volume: 10 Pages: e0118272
  • DOI: 10.1371/journal.pone.0118272
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Resequencing of the common marmoset genome improves genome assemblies and gene-coding sequence analysis (2015)
  • Author(s): Sato K, Kuroki Y, Kumita W, Fujiyama A, Toyoda A, Kawai J, Iriki A, Sasaki E, Okano H, Sakakibara Y.
  • Journal Title: Scientific Reports Volume: 5 Pages: 16894
  • DOI: 10.1038/srep16894
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Identification of a gene cluster responsible for hydrogen evolution in Vibrio tritonius strain AM2 with transcriptional analyses. (2015)
  • Author(s): Yuta Matsumura, Hidayu Al-saari, Sayaka Mino, Satoshi Nakagawa, Fumito Maruyama, Yoshitoshi Ogura, Tetsuya Hayashi, Ken Kurokawa, Toko Sawabe, Tomoo Sawabe.
  • Journal Title: Int. J. Hydrogen Energy Volume: 40 Pages: 9137-9146
  • Peer Reviewed
• [Journal Article] Regnase-1 and Roquin Regulate a Common Element in Inflammatory mRNAs by Spatiotemporally Distinct Mechanisms. (2015)
  • Author(s): Mino T, Murakawa Y, Fukao A, Vandenbon A, Wessels HH, Ori D, Uehata T, Tartey S, Akira S, Suzuki Y, Vinuesa CG, Ohler U, Standley DM, Landthaler M, Fujiwara T, Takeuchi O.
  • Journal Title: Cell Volume: 161 Pages: 1058-73
  • DOI: 10.1016/j.cell.2015.04.029.
  • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] Next-generation sequencing of 28 ALS-related genes in a Japanese ALS cohort. (2015)
  • Author(s): Nakamura R, Sone J, Atsuta N, Tohnai G, Watanabe H, Yokoi D, Nakatochi M, Watanabe H, Ito M, Senda J, Katsuno M, Tanaka F, Li Y, Izumi Y, Morita M, Taniguchi A, Kano O, Oda M, Kuwabara S, Abe K, Aiba I, Okamoto K, Mizoguchi K, Hasegawa K, Aoki M, Hattori N, Tsuji S, Nakashima K, Kaji R, Sobue G
  • Journal Title: Neurobiol Aging Volume: 2015 Dec 7 Pages: Epub
  • DOI: 10.1016/j.neurobiolaging.2015.11.030.
  • Peer Reviewed
• [Journal Article] Complete genome sequence of Methylobacterium aquaticum strain 22A, isolated from Racomitrium japonicum moss. (2015)
  • Author(s): Tani A, Ogura Y, Hayashi T, Kimbara K
  • Journal Title: Genome Announc Volume: 3 Pages: e00266-15
  • DOI: 10.1128/genomeA.00266-15.
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Variants associated with Gaucher disease in multiple system atrophy. (2015)
  • Author(s): Mitsui J, Matsukawa T, Sasaki H, Yabe I, Matsushima M, Durr A, Brice A, Takashima H, Kikuchi A, Aoki M, Ishiura H, Yasuda T, Date H, Ahsan B, Iwata A, Goto J, Ichikawa Y, Nakahara Y, Momose Y, Takahashi Y, Hara K, Kakita A, Yamada M, Takahashi H, Onodera O, Nishizawa M, Tsuji S(71番目), et al.
  • Journal Title: Ann Clin Transl Neurol. Volume: 2 Pages: 417-426
  • DOI: 10.1002/acn3.185
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Complete genome sequence of a phenanthrene degrader, Mycobacterium sp. strain EPa45 (NBRC 110737), isolated from a phenanthrene-degrading consortium. (2015)
  • Author(s): Kato H, Ogawa N, Ohtsubo Y, Oshima K, Toyoda A, Mori H, Nagata Y, Kurokawa K, Hattori M, Fujiyama A, Tsuda M
  • Journal Title: Genome Announcements Volume: 3 Pages: e00782-15
  • DOI: 10.1128/genomeA.00782-15
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Time-series metagenomic analysis reveals robustness of soil microbiome against chemical disturbance. (2015)
  • Author(s): Kato H, Mori H, Maruyama F, Toyoda A, Oshima K, Endo R, Fuchu G, Miyakoshi M, Dozono A, Ohtsubo Y, Nagata Y, Hattori M, Fujiyama A, Kurokawa K, Tsuda M
  • Journal Title: DNA Research Volume: 22 Pages: 413-424
  • DOI: 10.1093/dnares/dsv023
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Draft genome sequence of the archiascomycetous yeast Saitoella complicata. (2015)
  • Author(s): Yamauchi K, Kondo S, Hamamoto M, Takahashi Y, Ogura Y, Hayashi T, Nishida H
  • Journal Title: Genome Announcements Volume: 3 Pages: e00220-15
  • DOI: 10.1128/genomeA.00220-15
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Defining the genome features of Escherichia albertii, an emerging enteropathogen closely related to Escherichia coli. (2015)
  • Author(s): Tadasuke Ooka, Yoshitoshi Ogura, Keisuke Katsura, Kazuko Seto, Hideki Kobayashi, Kimiko Kawano, Eisuke Tokuoka, Masato Furukawa, Seiya Harada, Shuji Yoshino, Junji Seto, Tetsuya Ikeda, Keiji Yamaguchi, Kazunori Murase, Yasuhiro Gotoh, Naoko Imuta, Junichiro Nishi, Tania A. Gomes,Lothar Beutin, and Tetsuya Hayashi
  • Journal Title: Genome Biol Evol Volume: 7(12) Pages: 3170-3179
  • DOI: 10.1093/gbe/evv211
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Ecophysiology of Thioploca ingrica as revealed by the complete genome sequence supplemented with proteomic evidence. (2015)
  • Author(s): Hisaya Kojima, Yoshitoshi Ogura, Nozomi Yamamoto, Tomoaki Togashi, Hiroshi Mori, Tomohiro Watanabe, Fumiko Nemoto, Ken Kurokawa, Tetsuya Hayashi and Manabu Fukui
  • Journal Title: The ISME Journal Volume: 9 Pages: 1166-1176
  • DOI: 10.1038/ismej.2014.209
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] A genetic mechanism for female-limited Batsian mimicry in Pupilio butterfly. (2015)
  • Author(s): Nishikawa H., Iijima T., Kajitani R., Yamaguchi J., Ando T., Suzuki Y., Sugano S., Fujiyama A., Kosugi S., Hirakawa H., Tabata S., Ozaki K., Morimoto H., Ihara, K. Obara M., Hori H., Itoh T. and Fujiwara H.
  • Journal Title: Nature Genetics Volume: 47 Pages: 405-409
  • DOI: 10.1038/ng.3241
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Genome-wide association study of clinically defined gout identifies multiple risk loci and its association with clinical subtypes. (2015)
  • Author(s): H. Matsuo, K. Yamamoto, H. Nakaoka, A. Nakayama, M. Sakiyama, T. Chiba, A. Takahashi, T. Nakamura, H. Nakashima, Y. Takada, I. Danjoh, S. Shimizu, J. Abe, Y. Kawamura, S. Terashige, H. Ogata, S. Tatsukawa, G. Yin, R. Okada, E. Morita, M. Naito, A. Tokumasu, H. Onoue, K. Iwaya, I. Inoue(35番目), et al.
  • Journal Title: Ann. Rheum. Dis. Volume: 72 Pages: 652-659
  • DOI: 10.1136/annrheumdis-2014-206191
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Aggregation of rare/low-frequency variants of the mitochondria respiratory chain-related proteins in rheumatoid arthritis patients. (2015)
  • Author(s): Mitsunaga S, Hosomichi K, Okudaira Y, Nakaoka H, Suzuki Y, Kuwana M, Sato S, Kaneko Y, Homma Y, Oka A, Shiina T, Inoko H, Inoue I.
  • Journal Title: J Hum Genet Volume: 60 Pages: 449-454
  • DOI: 10.1038/jhg.2015.50
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Germline mutation rates and the long-term phenotypic effects of mutation accumulation in wild-type laboratory mice and mutator mice (2015)
  • Author(s): Arikuni Uchimura, Mayumi Higuchi, Yohei Minakuchi, Mizuki Ohno, Atsushi Toyoda, Asao Fujiyama, Ikuo Miura, Shigeharu Wakana, Jo Nishino, Takeshi Yagi
  • Journal Title: Genome Research Volume: 25 Pages: 1125-1134
  • DOI: 10.1101/gr.186148.114
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] How should the legal framework for the protection of human genomic data be formulated?―Implications from the revision processes of the Act on the Protection of Personal Information (PPI Act). (2015)
  • Author(s): Natsuko Yamamoto, Minae Kawashima, Takanori Fujita, Masatomo Suzuki and Kazuto Kato.
  • Journal Title: Journal of Human Genetics Volume: 60 Pages: 225-226
  • DOI: 10.1038/jhg.2014.121
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Epigenome-wide association study suggests that SNPs in the promoter region of RETN influence plasma resistin level via effects on DNA methylation at neighboring sites. (2015)
  • Author(s): Nakatochi M, Ichihara S, Yamamoto K, Ohnaka K, Kato Y, Yokota S, Hirashiki A, Naruse K, Asano H, Izawa H, Matsubara T, Yokota M
  • Journal Title: Diabetologia Volume: 58 Pages: 2781-2790
  • DOI: 10.1007/s00125-015-3763-9
  • Peer Reviewed / Open Access
• [Journal Article] Trans-ancestry genome-wide association study identifies 12 genetic loci influencing blood pressure and implicates a role for DNA methylation. (2015)
  • Author(s): Kato N, Loh M, Takeuchi F, Verweij N, Wang X, Zhang W, Kelly TN, Saleheen D, Lehne B, Leach IM, Drong AW, Abbott J, Wahl S, Tan ST, Scott WR, Campanella G, Chadeau-Hyam M, Afzal U, Ahluwalia TS, Bonder MJ, Chen P, Dehghan A, Edwards TL, Esko T, Go MJ, Harris SE, Hartiala J, Yamamoto K(63番目), et al.
  • Journal Title: Nat Genet Volume: 47 Pages: 1282-1293
  • DOI: 10.1038/ng.3405
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Submicroscopic deletions at 13q32.1 cause congenital microcoria. (2015)
  • Author(s): Fares-Taie L, Gerber S, Tawara A, Ramirez-Miranda A, Douet JY, Verdin H, Guilloux A, Zenteno JC, Kondo H, Moisset H, Passet B, Yamamoto K, Iwai M, Tanaka T, Nakamura Y, et al.
  • Journal Title: Am J Hum Genet. Volume: 96 Pages: 631-639
  • DOI: 10.1016/j.ajhg.2015.01.014
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Meta-analysis of genome-wide association studies of adult height in East Asians identifies 17 novel loci. (2015)
  • Author(s): He M, Xu M, Zhang B, Liang J, Chen P, Lee JY, Johnson TA, Li H, Yang X, Dai J, Liang L, Gui L, Qi Q, Huang J, Li Y, Adair LS, Aung T, Cai Q, Cheng CY, Cho MC, Cho YS, Chu M, Cui B, Gao YT, Go MJ, Gu D, Gu W, Guo H, Hao Y, Hong J, Hu Z, Hu Y, Huang J, Hwang JY, Ikram MK, Yamamoto K(67番目), et al.
  • Journal Title: Hum Mol Genet. Volume: 24 Pages: 1791-1800
  • DOI: 10.1093/hmg/ddu583
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] DomSign: a top-down annotation pipeline to enlarge enzyme space in the protein universe. (2015)
  • Author(s): Wang T, Mori H, Zhang C, Kurokawa K, Xing XH, Yamada T
  • Journal Title: BMC Bioinfo. Volume: 16 Pages: 96
  • DOI: 10.1186/s12859-015-0499-y
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] FuncTree: Functional analysis and visualization for large-scale omics data. (2015)
  • Author(s): Uchiyama T, Irie M, Mori H, Kurokawa K, Yamada T
  • Journal Title: PLoS One Volume: 10(5) Pages: e0126967
  • DOI: 10.1371/journal.pone.0126967
  • Peer Reviewed / Open Access
• [Journal Article] The naming of names: guidelines for gene nomenclature in Marchantia. (2015)
  • Author(s): Bowman JL, Araki T, Arteaga-Vazquez MA, Berger F, Dolan L, Haseloff J, Ishizaki K, Kyozuka J, Lin SS, Nagasaki H, Nakagami H, Nakajima K, Nakamura Y, Ohashi-Ito K, Sawa S, Shimamura M, Solano R, Tsukaya H, Ueda T, Watanabe Y, Yamato KT, Zachgo S, Kohchi T.
  • Journal Title: Plant Cell Physiol. Volume: pcv193 Pages: pcv193
  • DOI: 10.1093/pcp/pcv19
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] DNA data bank of Japan (DDBJ) progress report. (2015)
  • Author(s): Mashima J, Kodama Y, Kosuge T, Fujisawa T, Katayama T, Nagasaki H, Okuda Y, Kaminuma E, Ogasawara O, Okubo K, Nakamura Y, Takagi T.
  • Journal Title: Nucleic Acids Res. Volume: gkv1105 Pages: gkv1105
  • DOI: 10.1093/nar/gkv1105
  • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] GMcloser: closing gaps in assemblies accurately with a likelihood-based selection of contig or long-read alignments. (2015)
  • Author(s): Kosugi S, Hirakawa H, Tabata S.
  • Journal Title: Bioinformatics Volume: 31(23) Pages: 3733-41
  • DOI: 10.1093/bioinformatics/btv465
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Somatic primary piRNA biogenesis driven by cis-acting RNA elements and trans-acting Yb (2015)
  • Author(s): Ishizu H, Iwasaki YW, Hirakata S, Ozaki H, Iwasaki W, Siomi H, Siomi MC
  • Journal Title: Cell Rep. Volume: 12 Pages: 429-40
  • DOI: 10.1016/j.celrep.2015.06.035
  • Peer Reviewed / Open Access
• [Journal Article] MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes (2015)
  • Author(s): Miya M, Sato Y, Fukunaga T, Sado T, Poulsen JY, Sato K, Minamoto T, Yamamoto S, Yamanaka H, Araki H, Kondoh M, Iwasaki W
  • Journal Title: Roy. Soc. Open Sci. Volume: 2 Pages: 150088
  • DOI: 10.1098/rsos.150088
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Selection of orthologous genes for construction of a highly resolved phylogenetic tree and clarification of the phylogeny of Trichosporonales species (2015)
  • Author(s): Takashima M, Manabe R, Iwasaki W, Ohyama A, Ohkuma M, Sugita T
  • Journal Title: PLOS ONE Volume: 10 Pages: e0131217
  • DOI: 10.1371/journal.pone.0131217
  • Peer Reviewed / Open Access
• [Journal Article] Associations between nucleosome phasing, sequence asymmetry, and tissue-specific expression in a set of inbred Medaka species. (2015)
  • Author(s): Nakatani Y, Mello CC, Hashimoto S, Shimada A, Nakamura R, Tsukahara T, Qu W, Yoshimura J, Suzuki Y, Sugano S, Takeda H, Fire A, Morishita S.
  • Journal Title: BMC Genomics Volume: 16(1) Pages: 978
  • DOI: 10.1186/s12864-015-2198-5
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] A linear time algorithm for detecting long genomic regions enriched with a specific combination of epigenetic states. (2015)
  • Author(s): Ichikawa, K., Morishita, S.
  • Journal Title: BMC Genomics Volume: 16 Pages: S8
  • DOI: 10.1186/1471-2164-16-S2-S8
  • Peer Reviewed / Open Access
• [Journal Article] Clinicopathological features of the first Asian family having vocal cord and pharyngeal weakness with distal myopathy due to a MATR3 mutation. (2015)
  • Author(s): Yamashita S, Mori A, Nishida Y, Kurisaki R, Tawara N, Nishikami T, Misumi Y, Ueyama H, Imamura S, Higuchi Y, Hashiguchi A, Higuchi I, Morishita S, Yoshimura J, Uchino M, Takashima H, Tsuji S, Ando Y.
  • Journal Title: Neuropathology and Applied Neurobiology Volume: 41(3) Pages: 391-398
  • DOI: 10.1111/nan.12179
  • Peer Reviewed / Open Access
• [Journal Article] Bioinformatics tools for lncRNA research. (2015)
  • Author(s): Junichi Iwakiri, Michiaki Hamada, Kiyoshi Asai
  • Journal Title: Biochimica et biophysica acta (BBA) Gene Regulatory Mechanisms Volume: 1859(1) Pages: 23-30
  • DOI: 10.1016/j.bbagrm.2015.07.014
  • Peer Reviewed
• [Journal Article] Hybrid De Novo Genome Assembly Using MiSeq and SOLiD Short Read Data. (2015)
  • Author(s): Tsutomu Ikegami, Toyohiro Inatsugi, Isao Kojima, Myco Umemura, Hiroko Hagiwara, Masayuki Machida, Kiyoshi Asai
  • Journal Title: PLoS ONE Volume: 10(4) Pages: e0126289
  • DOI: 10.1371/journal.pone.0126289
  • Peer Reviewed / Open Access
• [Journal Article] Learning chromatin states with factorized information criteria. (2015)
  • Author(s): Michiaki Hamada, Yukiteru Ono, Ryohei Fujimaki, Kiyoshi Asai
  • Journal Title: Bioinformatics Volume: 31(15) Pages: 2426-2433
  • DOI: 10.1093/bioinformatics/btv163
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] A semi-supervised learning approach for RNA secondary structure prediction. (2015)
  • Author(s): Haruka Yonemoto, Kiyoshi Asai, Michiaki Hamada
  • Journal Title: Computational biology and chemistry Volume: 57 Pages: 72-79
  • DOI: 10.1016/j.compbiolchem.2015.02.002
  • Peer Reviewed
• [Journal Article] Visualizing translocation dynamics and nascent transcript errors in paused RNA polymerases in vivo. (2015)
  • Author(s): Imashimizu M, Takahashi H, Oshima T, McIntosh C, Bubunenko M, Court DL, Kashlev M
  • Journal Title: Genome Biol. Volume: 16(1) Pages: 98
  • DOI: 10.1186/s13059-015-0666-5
  • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] Draft genome sequence of the pathogenic filamentous fungus Aspergillus udagawae strain IFM 46973T (2015)
  • Author(s): Kusuya Y, Takahashi-Nakaguchi A, Takahashi H, Yaguchi T
  • Journal Title: Genome Announc. Volume: 3(4) Pages: e00834-15
  • DOI: 10.1128/genomeA.00834-15
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] High-speed Westfall-Young permutation procedure for genome-wide association studies. (2015)
  • Author(s): Terada A, Kim H, Sese J.
  • Journal Title: In Proc. of ACM BCB 2015. Volume: 1 Pages: 17-26
  • DOI: 10.1145/2808719.2808721
  • Peer Reviewed
• [Presentation] Enhancer landscape dynamics and the role of IRF8 in mononuclear phagocyte development. (2015)
  • Author(s): Kurotaki D, Nakabayashi J, Nishiyama A, Sasaki H, Kaneko N, Koizumi S, Ozato K, Suzuki Y, Tamura T
  • Organizer: 55th American Society of Hematology Annual Meeting and Exposition
  • Place of Presentation: Orlando, USA
  • Year and Date: 2015-12-06 – 2015-12-06
• [Presentation] R-Spondin1 promotes Paneth cell growth, maintains intestinal microbial ecology, and ameliorates graft-versus-host disease (2015)
  • Author(s): Hayase E, Hashimoto D, Nakamura K, Ogura Y, Hayashi T, Kurokawa K, Ayabe T, and Teshima T.
  • Organizer: 57th ASH Annual Meeting
  • Place of Presentation: Orlando, FL, USA
  • Year and Date: 2015-12-06 – 2015-12-06
• [Presentation] The identification of pistil-specific genes by global transcriptome analyses in tomato (Solanum lycopersicum). (2015)
  • Author(s): Ezura K, Ji-Seong K, Mori K, Kuhara S, Suzuki Y, Ariizumi T and Ezura H.
  • Organizer: The 12th Solanaceae Conference
  • Place of Presentation: Bordeaux, France
  • Year and Date: 2015-10-25 – 2015-10-29
• [Presentation] LAMPLINK: An additional function for PLINK to detect statistically significant genetic interactions (2015)
  • Author(s): Terada A, Tsuda K, Sese J
  • Organizer: American Society of Human Genetics
  • Place of Presentation: 米国ボルチモア
  • Year and Date: 2015-10-06 – 2015-10-10
• [Presentation] A novel causative gene for permanent tooth agenesis. (2015)
  • Author(s): Yamaguchi T, Hosomichim K, Kim YI, Yano K, Haga S, Katayama K, Park SB, Inoue I, Maki K.
  • Organizer: 8th International Orthodontic Congress
  • Place of Presentation: London, UK
  • Year and Date: 2015-09-27 – 2015-09-30
  • Int'l Joint Research
• [Presentation] A highly resolved phylogenetic tree of Trichosporonales species based on multiple gene sequence analysis. (2015)
  • Author(s): Masako Takashima, Ri-ichiroh Manabe, Wataru Iwasaki, Akira Ohyama, Moriya Ohkuma, and Takashi Sugita.
  • Organizer: 32nd International Specialized Symposium on Yeasts
  • Place of Presentation: Hotel Gio Centro Congressi, Perugia, Italy
  • Year and Date: 2015-09-13 – 2015-09-17
  • Int'l Joint Research
• [Presentation] The CpMinus1 gene, specifically localized on the mating-type minus genome, is responsible for the sex determination of heterothallic Closterium peracerosum-strigosum-littorale complex (2015)
  • Author(s): Komiya, A., Abe, J., Kawai, J., Suzuki, Y., Ootsuki, R., Tsuchikane, Y., Nishiyama, T., Sekimoto, H.
  • Organizer: 6th European Phycological Congress
  • Place of Presentation: London, England
  • Year and Date: 2015-08-25 – 2015-08-25
• [Presentation] Adaptive evolution and ever metamorphosing DNA methylation systems (2015)
  • Author(s): Hirokazu Yano, Yoshikazu Furuta, Zobaidul M. Alam, Emiko Rimbara, Hiroe Namba-Fukuyo, Tomoko Shibata, Tomoaki Nishiyama, Shuji Shigenobu, Mitsuyasu Hasebe, Yutaka Suzuki, Sumio Sugano, Keigo Shibayama, Ichizo Kobayashi
  • Organizer: 7th NEB Meeting on DNA Restriction and Modification
  • Place of Presentation: グダンスク、ポーランド
  • Year and Date: 2015-08-24 – 2015-08-29
• [Presentation] MiFish, a set of universal primers for metabarcoding environmental DNA from fishes: Detection of >230 species from aquarium tanks and coral reefs in the subtropical western North Pacific. (2015)
  • Author(s): Masaki Miya, Yukuto Sato, Tsukasa Fukunaga, Tetsuya Sado, Jan Yde Poulsen, Keiichi Sato, Toshifumi Minamoto, Satoshi Yamamoto, Hiroki Yamanaka, Hitoshi Araki, Michio Kondoh, and Wataru Iwasaki.
  • Organizer: 6th International Barcode of Life Conference
  • Place of Presentation: University of Guelph, Canada
  • Year and Date: 2015-08-19 – 2015-08-19
  • Int'l Joint Research
• [Presentation] Network of DNA methyltransferase behind the adaptive phenotype in Helicobacteri pylori. (2015)
  • Author(s): Hirokazu Yano, Zobaidul M. Alam, Emiko Rimbara, Yoshikazu Furuta, Yutaka Suzuki, Sumio Sugano, Keigo Shibayama, Ichizo Kobayashi
  • Organizer: Gordon Research Conference, Microbial Population Biology
  • Place of Presentation: Andover, NH, USA
  • Year and Date: 2015-07-19 – 2015-07-24
• [Presentation] Genetic analysis of natural variations for cold habituation in C. elegans (2015)
  • Author(s): Misaki Okahata, Akane Ohta, Yohei Minakuchi, Atsushi Toyoda, Atsushi Kuhara
  • Organizer: 20th C. elegans International meeting
  • Place of Presentation: Los Angels, USA
  • Year and Date: 2015-06-24 – 2015-06-28
  • Int'l Joint Research
• [Presentation] The mechanisms of Copper acquisition and detoxification in Aspergillus fumigatus. (2015)
  • Author(s): Kusuya Y, Kurokawa K, Takahashi H.
  • Organizer: ISHAM 2015
  • Place of Presentation: Melbourne, Australia
  • Year and Date: 2015-05-04 – 2015-05-08
  • Int'l Joint Research
• [Presentation] Methylome analysis of the 14q32.2 imprinted region in patients with imprinting defects on human chromosome 14. (2015)
  • Author(s): Masayo Kagami, Takahide Hayano, Kazuyoshi Hosomichi, Kazuhiko Nakabayashi, Maki Fukami, Tsutomu Ogata, Ituro Inoue.
  • Organizer: 2nd EUROPEAN IMPRINTING DISORDER SCHOOL COST Action BM1208
  • Place of Presentation: Paris, France
  • Year and Date: 2015-05-04 – 2015-05-04
• [Presentation] Visualizing translocation dynamics and nascent 1 transcript errors in paused RNA polymerases in vivo. (2015)
  • Author(s): Imashimizu M, Takahashi H, Oshima T, McIntosh C, Bubunenko M, Court DL, Kashlev M.
  • Organizer: NCI Symposium on Chromosome Biology
  • Place of Presentation: Bethesda, USA
  • Year and Date: 2015-04-16 – 2015-04-17
• [Book] 微生物統合データベースによる微生物と環境の研究への貢献, 難培養微生物研究の最新技術 III―微生物の生き様に迫り課題解決へ― (2015)
  • Author(s): 森宙史、東光一、山田拓司、黒川顕
  • Total Pages: 216(10-19)
  • Publisher: シーエムシー出版
• [Book] 次世代シーケンサー活用術「１分子シーケンサーを用いた非モデル生物の de novo ゲノム解読」 (2015)
  • Author(s): 柴田朋子、笠原雅弘、重信秀治、西山智明、長谷部光泰
  • Total Pages: 212(115-126)
  • Publisher: 化学同人
• [Book] 生命情報処理における機械学習～多重検定と推定量設計～ (2015)
  • Author(s): 瀬々潤、浜田道昭
  • Total Pages: 192
  • Publisher: 講談社サイエンティフィック
• [Remarks] 領域ホームページ
  • URL: http://www.genome-sci.jp/old2010-2015/
• [Remarks] シーラカンスゲノム公開サーバ
  • URL: http://coelacanth.nig.ac.jp
• [Remarks] アフリカツメガエルゲノム公開サーバ
  • URL: http://xenopus.lab.nig.ac.jp
• [Remarks] カイコゲノムフィニッシング公開サーバ
  • URL: http://kaiko.nig.ac.jp/