先進ゲノム解析研究推進プラットフォーム

2016 Fiscal Year Annual Research Report

• Project/Area Number: 16H06279
• 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): 黒川 顕 国立遺伝学研究所, 生命情報研究センター, 教授 (20343246) ; 豊田 敦 国立遺伝学研究所, 生命情報研究センター, 特任教授 (10267495) ; 鈴木 穣 東京大学, 大学院新領域創成科学研究科, 教授 (40323646) ; 林 哲也 九州大学, 大学院医学研究院, 教授 (10173014) ; 伊藤 武彦 東京工業大学, 生命理工学院, 教授 (90501106)
• Project Period (FY): 2016 – 2021
• Keywords: 次世代DNAシーケンサー / 新規ゲノム配列決定 / リシーケンシング / エピゲノム / RNA-Seq / 1細胞解析 / メタゲノム解析 / スーパーコンピューター

Outline of Annual Research Achievements

①総括支援活動では、支援課題の公募を行い、領域外委員を多数とする審査委員会により選考し支援を行った。応募245件、採択95件(採択率38.8%)であった。
②大規模配列解析拠点ネットワーク支援活動においては、1)長鎖シーケンシングのためにSequel (PacBio)、2)ハプロタイプ解析・フィニッシングのためにクロミウム、GemCodeシステム(10XGenomics)、Irysテクノロジー(BidNano Genomics)、3) 1分子シーケンシングのためにMInION(Oxford Nanopore)、4) 1細胞解析のためにC1システム(Fluidigm)の試行や条件検討を行い、技術支援者の訓練も進めて、支援に使えるように努めた。
③高度情報解析支援ネットワーク活動においては、A) 基盤的解析パイプラインによる支援と高度化開発として、DDBJ解析ワークフロー「Pitagora-Galaxy」の実装、微生物ゲノムアノテーションパイプライン「DFAST」の開発、B) 総合的ゲノムアノテーションの支援と高度化開発として、真核生物ゲノムアセンブリ結果評価ツール「CEGMA」の開発、オーソログ遺伝子解析ツール「SonicParanoid」の開発、ミニアライメントツール「minialign」の開発、メタゲノムアセンブリツール「metaplatanus」の開発、Illumina+PacBioハイブリッドアセンブリツールの開発、アンプリコンメタゲノムクラスタリングツール「SaturnCluster」の開発、メニーコア超高速相同性検索ツール「PZLAST」の開発、C) 多層統合ゲノム情報解析技術を駆使した支援と高度化開発として、MiniIONでのRNA-seq解析技術の開発、TC conversionを考慮に入れた検索ツール「LAST」の拡張、3C解析技術の高度化、を進めた。成果論文欄には支援による成果と支援技術高度化等の関連成果論文を挙げた。

Current Status of Research Progress

2: Research has progressed on the whole more than it was originally planned.

Reason

・研究支援代表の下、研究支援分担者21名、連携研究支援者26名、総勢48名の班員が全国16の大学・研究機関(部局数は25)から参加して支援体制を構築した。また、国立遺伝学研究所を中核機関とし、参加する班員が所属する主な機関を連携機関とする連携ネットワークを形成して、機関の支援を受けられるように連携機関間で連携協定を締結した。
・以上の体制のもと、支援課題公募を行い、245件の応募があり、領域外委員を多数とする審査委員会において経費等の制限から95件を採択し、支援公募を行った。採択課題の支援技術分類は ; 新規ゲノム決定 : 14件、変異解析 : 25件、修飾解析 : 25件、RNA解析 : 58件、メタゲノム解析等 : 4件、超高感度解析 : 22件、情報解析のみ : 3件、合計151(採択1件あたり複数の技術支援がある)であり、多様な技術の提供ができた。初年度のため開始が少し遅れたが、一部試料準備ができないケースもあるが、データ産出はほぼすべて終了した。
・支援技術の高度化のための活動も大規模DNAシーケンシング支援、高度情報解析支援共に進めることができた。

Strategy for Future Research Activity

・できる限り多くの優れた課題の支援を行うべく、効率化と支援技術の高度化を進める。ゲノム解析は技術進展のスピードが特に速く、2-3年で解析手法が様変わりするからである。これに適切に対応し、最新の手法・技術を提供することが本プラットフォームに最重要であり、新たなDNAシーケンシング技術の導入・開発、目的に沿った情報解析技術の開発と整備が中心になる。
・現状は経費の制限から支援課題採択率は40%弱にとどまっており、より多い課題の支援やすそ野拡大への要望が高い。一方でゲノム解析においては一定規模以上で支援しないと意味のある結果が出ないことも多い。これらのバランスをとるためには様々な工夫が必要であり、利用料一部徴収も含めた検討を続ける。その場合、若手等の意欲をそがずに、最新の技術を提供できる機会を増やすことが最重要と考えている。
・大量データ解析の支援要望はますます増加していることから、解析パイプラインの整備とともに、情報解析講習会を開催していく。

Research Products

• [Int'l Joint Research] USDepartment of Energy Joint Genome Institute/University of California at Berkley/National Cancer Institute(米国)
  • Country Name: U.S.A.
  • Counterpart Institution: USDepartment of Energy Joint Genome Institute/University of California at Berkley/National Cancer Institute
  • # of Other Institutions: 18
• [Int'l Joint Research] University of Calgary/University of Western Ontario(Canada)
  • Country Name: Canada
  • Counterpart Institution: University of Calgary/University of Western Ontario
• [Int'l Joint Research] Sam Ratulangi University(Indonesia)
  • Country Name: Indonesia
  • Counterpart Institution: Sam Ratulangi University
• [Int'l Joint Research] Mahidol University(Thailand)
  • Country Name: Thailand
  • Counterpart Institution: Mahidol University
• [Int'l Joint Research] Radboud University(オランダ)
  • Country Name: NETHERLANDS
  • Counterpart Institution: Radboud University
• [Int'l Joint Research]
  • # of Other Countries: 9
• [Journal Article] Evolutionary acquisition of promoter-associated non-coding RNA (pancRNA) repertoires diversifies species-dependent gene activation mechanisms in mammals. (2017)
  • Author(s): Masahiro Uesaka, Kiyokazu Agata, Takao Oishi, Kinichi Nakashima, Takuya Imamura
  • Journal Title: BMC Genomics Volume: 18 Pages: 285
  • DOI: 10.1186/s12864-017-3662-1
  • Peer Reviewed / Open Access
• [Journal Article] Function and evolution of a Lotus japonicus AP2/ERF family transcription factor that is required for development of infection threads. (2017)
  • Author(s): Koji Yano, Seishiro Aoki, Meng Liu, Yosuke Umehara, Norio Suganuma, Wataru Iwasaki, Shusei Sato, Takashi Soyano, Hiroshi Kouchi and Masayoshi Kawaguchi.
  • Journal Title: DNA Research Volume: 24 Pages: 193-203
  • DOI: 10.1093/dnares/dsw052
  • Peer Reviewed / Open Access
• [Journal Article] Constitutive centromere-associated network controls centromere drift in vertebrate cells. (2017)
  • Author(s): Hori T, Kagawa N, Toyoda A, Fujiyama A, Misu S, Monma N, Makino F, Ikeo K, Fukagawa T.
  • Journal Title: J Cell Biol. Volume: 216 Pages: 101-113
  • DOI: 10.1083/jcb.201605001
  • Peer Reviewed / Open Access
• [Journal Article] Multiple Independent Changes in Mitochondrial Genome Conformation in Chlamydomonadalean Algae. (2017)
  • Author(s): Takashi Hamaji, Hiroko Kawai Toyooka, Atsushi Toyoda, Yohei Minakuchi, Masahiro Suzuki, Asao Fujiyama, Hisayoshi Nozaki and David Roy Smith.
  • Journal Title: Genome Biol Evol. Volume: 9 Issue: 4 Pages: 993-999
  • DOI: 10.1093/gbe/evx060
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Differential Binding of Three Major Human ADAR Isoforms to Coding and Long Non-Coding Transcripts. (2017)
  • Author(s): Josephine Galipon, Rintaro Ishii, Yutaka Suzuki, Masaru Tomita, and Kumiko Ui-Tei.
  • Journal Title: Genes(Basel). Volume: 8 Issue: 2 Pages: 68
  • DOI: 10.3390/genes8020068
  • Peer Reviewed / Open Access
• [Journal Article] Comprehensive genetic exploration of selective tooth agenesis of mandibular incisors by exome sequencing. (2017)
  • Author(s): Yamaguchi T, Hosomichi K, Yano K, Kim YI, Nakaoka H, Kimura R, Otsuka H, Nonaka N, Haga S, Takahashi M, Shirota T, Kikkawa Y, Yamada A, Kamijo R, Park SB, Nakamura M, Maki K, Inoue I.
  • Journal Title: Hum Genome Var. Volume: 4 Pages: 17005
  • DOI: 10.1038/hgv.2017.5.
  • Peer Reviewed / Open Access
• [Journal Article] GWAS of clinically defined gout and subtypes identifies multiple susceptibility loci that include urate transparter genes. (2017)
  • Author(s): Nakayama A, Nakaoka H, Ito T, Inoue I, Matsuo H, et al.
  • Journal Title: Ann Rheum Dis Volume: 76 Pages: 869-877
  • DOI: 10.1136/annrheumdis-2016-209632
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Clinical implications of SCN1A missense and truncation variants in a large Japanese cohort with Dravet syndrome. (2017)
  • Author(s): Ishii A, Watkins JC, Chen D, Hirose S, Hammer MF.
  • Journal Title: Epilepsia. Volume: 58 Issue: 2 Pages: 282-290
  • DOI: 10.1111/epi.13639.
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] A de novo missense mutation of GABRB2 causes early myoclonic encephalopathy. (2017)
  • Author(s): Ishii A, Kang JQ, Schornak CC, Hernandez CC, Shen W, Watkins JC, Macdonald RL, Hirose S.
  • Journal Title: J Med Genet. Volume: 54 Issue: 3 Pages: 202-211
  • DOI: 10.1136/jmedgenet-2016-104083.
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] ADARB1 catalyzes circadian A-to-I editing and regulates RNA rhythm. (2017)
  • Author(s): Hideki Terajima, Hikari Yoshitane, Haruka Ozaki, Yutaka Suzuki, Shigeki Shimba, Shinya Kuroda, Wataru Iwasaki, and Yoshitaka Fukada.
  • Journal Title: Nature Genetics Volume: 49 Pages: 146-151
  • DOI: 10.1038/ng.3731
  • Peer Reviewed
• [Journal Article] Rapid and cost effective high-throughput sequencing for identification of germline mutation of BRCA1 and BRCA2 (2017)
  • Author(s): Ahmadloo S, Nakaoka H, Hayano T, Hosomichi K, You H, Utsuno E, Sangai T, Nishimura M, Matsushita K, Hata A, Nomura F, Inoue I.
  • Journal Title: J Hum Genet Volume: 62 Pages: 561-567
  • DOI: 10.1038/jhg.2017.5
  • Peer Reviewed / Open Access
• [Journal Article] Training alignment parameters for arbitrary sequencers with LAST-TRAIN. (2017)
  • Author(s): Michiaki Hamada, Yukiteru Ono, Kiyoshi Asai, Martin CFrith.
  • Journal Title: Bioinformatics Volume: 33 Issue: 6 Pages: 926-928
  • DOI: 10.1093/bioinformatics/btw742
  • Peer Reviewed / Open Access
• [Journal Article] Genetic polymorphisms in Plasmodium falciparum chloroquine resistance genes, pfcrt and pfmdr1, in North Sulawesi, Indonesia (2017)
  • Author(s): Patrick Reteng, Visia Vrisca, Inka Sukarno, Ilham Habib Djarkoni, Jane Angela Kalangi, George Eduardo Jacobs, Lucky Ronald Runtuwene, Yuki Eshita, Ryuichiro Maeda, Yutaka Suzuki, Arthur Elia Mongan, Sarah Maria Warouw, Junya Yamagishi and Josef Tuda.
  • Journal Title: BMC Res Notes Volume: 10 Pages: 147
  • DOI: 10.1186/s13104-017-2468-1
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] 改正個人情報保護法でゲノム研究はどう変わるか? (2017)
  • Author(s): 清水佳奈, 山本奈津子, 川嶋実苗, 片山俊明, 荻島創一
  • Journal Title: 実験医学 Volume: 35 Issue: 4 Pages: 600-605
• [Journal Article] Genome evolution in the allotetraploid frog Xenopus laevis. (2016)
  • Author(s): Session AM, Toyoda A, Suzuki Y, Fujiyama A, Taira M, et al.
  • Journal Title: Nature Volume: 538 Pages: 336-343
  • DOI: 10.1038/nature19840
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] A case of succinic semialdehyde dehydrogenase deficiency with status epilepticus and rapid regression. (2016)
  • Author(s): Horino A, Kawawaki H, Fukuoka M, Tsuji H, Hattori Y, Inoue T, Nukui M, Kuki I, Okazaki S, Tomiwa K, Hirose S.
  • Journal Title: Brain Dev. Volume: 38 Issue: 9 Pages: 866-70
  • DOI: 10.1016/j.braindev.2016.03.010.
  • Peer Reviewed
• [Journal Article] Mitochondrial Genome Sequences of Four Strains of the Bloom-Forming Raphidophyte Heterosigma akashiw (2016)
  • Author(s): Ogura Y, Nakayama N, Hayashi T, Ueki S.
  • Journal Title: Genome Announc. Volume: 4 Issue: 6 Pages: e01288-16
  • DOI: 10.1128/genomeA.01288-16.
  • Peer Reviewed / Open Access
• [Journal Article] Complete Genome Sequence of a Phycodnavirus, Heterosigma akashiwo Virus Strain 53. (2016)
  • Author(s): Ogura Y, Hayashi T, Ueki S.
  • Journal Title: Genome Announc. Volume: 4 Issue: 6 Pages: e01279-16
  • DOI: 10.1128/genomeA.01279-16.
  • Peer Reviewed / Open Access
• [Journal Article] Complete Genome Sequence of Klebsiella oxytoca Strain JKo3. (2016)
  • Author(s): Iwase T, Ogura Y, Hayashi T, Mizunoe Y.
  • Journal Title: Genome Announc. Volume: 4 Issue: 6 Pages: e01221-16
  • DOI: 10.1128/genomeA.01221-16.
  • Peer Reviewed / Open Access
• [Journal Article] Phylogenetic Analysis of Enteroaggregative Escherichia coli Sequence Type 131. (2016)
  • Author(s): Imuta N, Ooka T, Seto K, Kawahara R, Koriyama T, Kojyo T, Iguchi A, Tokuda K, Kawamura H, Yoshiie K, Ogura Y, Hayashi T, Nishi J.
  • Journal Title: J Chin Microbiol. Volume: 54 Issue: 8 Pages: 2128-34
  • DOI: 10.1128/JCM.00711-16.
  • Peer Reviewed / Open Access
• [Journal Article] Complete Genome Sequence of Klebsiella pneumoniae YH43. (2016)
  • Author(s): Iwase T, Ogura Y, Hayashi T, Mizunce Y.
  • Journal Title: Genome Announc. Volume: 4 Issue: 2 Pages: e00242-16
  • DOI: 10.1128/genomeA.00242-16.
  • Peer Reviewed / Open Access
• [Journal Article] Genome sequence and analysis of the Japanese morning glory, Ipomoea nil. (2016)
  • Author(s): Hoshino A, Jayakumar V, Toyoda A, Noguchi H, Itoh T, Seki M, Kohara Y, Suzuki Y, Sugano S, Fujiyama A, Sakakibara Y, et al.
  • Journal Title: Nat Commun, Volume: 7 Pages: 13295
  • DOI: 10.1038/ncomms13295
  • Peer Reviewed / Open Access
• [Journal Article] Comprehensive microbiome analysis of tonsillar crypts in IgA nephropathy. (2016)
  • Author(s): Watanabe H, Goto S, Mori H, Higashi K, Hosomichi K, Takanashi N, Aizawa N, Yamada T, Inoue I, Kurokawa K, Narita I.
  • Journal Title: Nephrol Dial Transplant. Pages: pii:gfw343
  • DOI: 10.1093/ndt/gfw343
  • Peer Reviewed
• [Journal Article] Phylogenomics and Morphology of Extinct Paleognaths Reveal the Origin and Evolution of the Ratites. (2016)
  • Author(s): Yonezawa T, Segawa T, Mori H, Campos PF, Hongoh Y, Endo H, Akiyoshi A, Manabe M, Kohno N, Nishida S, Wu J, Jin H, Kishino H, Kurokawa K, Yoshifumi N, Tanabe H, Mukoyama H, Yoshida K, Rasoamiaramanana A, Yamagishi S, Hayashi Y, Yoshida A, Koike H, Akishinonomiya F, Willerslev E, Hasegawa M.
  • Journal Title: Current Biology Volume: 27 Issue: 1 Pages: 66-77
  • DOI: 10.1016/j.cub.2016.10.029.
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Control of transcriptional pausing by biased thermal fluctuations on repetitive genomic sequences. (2016)
  • Author(s): Imashimizu M, Afek A, Takahashi H, Lubkowska L, Lukatsky DB.
  • Journal Title: Proc Natl Acad Sci USA Volume: 113 Issue: 47 Pages: E7409-E7417
  • DOI: 10.1073/pnas.1607760113
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] AgIn : measuring the landscape of CpG methylation ofindividual repetitive elements. (2016)
  • Author(s): Suzuki Y, Korlach J, Turner SW, Tsukahara T, Taniguchi J, Qu W, Ichikawa K, Yoshimura J, Yurino H, Takahashi Y, Mitsui J, Ishiura H, Tsuji S, Takeda H, Morishita S.
  • Journal Title: Bioinformatics Volume: 32 Issue: 19 Pages: 2911-2919
  • DOI: 10.1093/bioinformatics/btw360
  • Peer Reviewed / Open Access
• [Journal Article] Assessing Cell-to-Cell DNA Methylation Variability on Individual Long Reads. (2016)
  • Author(s): Qu W, Tsukahara T, Nakamura R, Yurino H, Hashimoto S, Tsuji S, Takeda H, Morishita S.
  • Journal Title: Sci Rep. Volume: 6 Pages: 21317
  • DOI: 10.1038/srep21317
  • Peer Reviewed / Open Access
• [Journal Article] Parallel mitogenome sequencing alleviates random rooting effect in phylogeography. (2016)
  • Author(s): Shotaro Hirase, Hirohiko Takeshima, Mutsumi Nishida, and Wataru Iwasaki.
  • Journal Title: Genome Biology and Evolution Volume: 8 Pages: 1267-1278
  • DOI: 10.1093/gbe/evw063
  • Peer Reviewed / Open Access
• [Journal Article] Structural mechanism for light-driven transport by a new type of chloride ion pump, Nonlabens marinus rhodopsin-3. (2016)
  • Author(s): Toshiaki Hosaka, Susumu Yoshizawa, Yu Nakajima, Noboru Ohsawa, Masakatsu Hato, Edward F, DeLong, Kazuhiro Kogure, Shigeyuki Yokoyama, Tomomi Kimura-Someya, Wataru Iwasaki, and Mikako Shirouzu.
  • Journal Title: Journal of Biological Chemistry Volume: 291 Pages: 17488-17495
  • DOI: 10.1074/jbc.M116.728220
  • Peer Reviewed / Open Access
• [Journal Article] Metagenomics and bioinformatics in microbial ecology : Current status and beyond. (2016)
  • Author(s): Satoshi Hiraoka, Ching-chia Yang, and Wataru Iwasaki.
  • Journal Title: Microbes and Environments Volume: 31 Pages: 204-212
  • DOI: 10.1264/jsme2ME16024
  • Peer Reviewed / Open Access
• [Journal Article] Flexible selection of diversified Na+/K+ATPase α-subunit isoforms for osmoregulation in teleosts. (2016)
  • Author(s): Marty Kwok-Shing Wong, Supriya Pipil, Haruka Ozaki, Yutaka Suzuki, Wataru Iwasaki, and Yoshio Takei.
  • Journal Title: Zoological Letters Volume: 2 Pages: 15
  • DOI: 10.1186/s40851-016-0050-7
  • Peer Reviewed / Open Access
• [Journal Article] Global deceleration of gene evolution following recent genome hybridizations in fungi. (2016)
  • Author(s): Sira Sriswasdi, Masako Takashima, Ri-ichiroh Manabe, Moriya Ohkuma, Takashi Sugita, and Wataru Iwasaki.
  • Journal Title: Genome Research Volume: 26 Pages: 1081-1090
  • DOI: 10.1101/gr.205948.116
  • Peer Reviewed / Open Access
• [Journal Article] Germline variants of prostate cancer in Japanese families. (2016)
  • Author(s): Hayano T, Matsui H, Ohtake N, Hosomichi K, Suzuki K, Inoue I.
  • Journal Title: PLOS ONE Volume: 11 Pages: e0164233
  • DOI: 10.1371/journal.pone.0164233.
  • Peer Reviewed / Open Access
• [Journal Article] Allelic imbalance in regulation of ANRIL through chromatin interaction at 9p21 endometriosis risk locus. (2016)
  • Author(s): Nakaoka H, Gurumurthy A, Hayano T, Ahmadloo S, Omer WH, Yoshihara K, Yamamoto A, Kurose K, Enomoto T, Akira S, Hosomichi K, Inoue I.
  • Journal Title: PLOS Genet Volume: 12 Issue: 4 Pages: e1005893
  • DOI: 10.1371/journal.pgen.1005893.
  • Peer Reviewed / Open Access
• [Journal Article] Rtools : a web server for various secondary structural analyses on single RNA sequences. (2016)
  • Author(s): Michiaki Hamada, Yukiteru Ono, Hisanori Kiryu, Kengo Sato, Yuki Kato, Tsukasa Fukunaga, Ryota Mori, Kiyoshi Asai.
  • Journal Title: Nucleic Acids Res Volume: 44(W1) Pages: W302-W307
  • DOI: 10.1093/nar/gkw337
  • Peer Reviewed / Open Access
• [Journal Article] Improved Aocuracy in RNA-Protein Rigid Body Docking by Incorporating Force Field for Molecular Dynamics Simulation into the Scoring Function. (2016)
  • Author(s): Junichi Iwakiri, Michiaki Hamada, Kiyoshi Asai, Tomoshi Kameda.
  • Journal Title: J. Chem Theory Comput. Volume: 12 Issue: 9 Pages: 4688-4697
  • DOI: 10.1021/acs.jctc.6b00254
  • Peer Reviewed
• [Journal Article] DFAST and DAGA : web-based integrated genome annotation tools and resources (2016)
  • Author(s): Tanizawa Y, Fujisawa T, Kamimuma E, Nakamura Y, Arita M.
  • Journal Title: Bioscience of Microbiota, Food and Health Volume: 35 Issue: 4 Pages: 173-184
  • DOI: 10.12938/bmfh.16-003
  • Peer Reviewed / Open Access
• [Journal Article] An algorithm for aligning and clustering read mapping profiles of deep sequencing in non-coding RNA processing. (2016)
  • Author(s): Tsuchiya M, Amano K, Abe M, Seki M, Hase S, Sato K, Sakakibara Y.
  • Journal Title: Bioinformatics Volume: 32 Issue: 12 Pages: i369-i377
  • DOI: 10.1093/bioinformatics/btw273
  • Peer Reviewed / Open Access
• [Journal Article] Challenges raised by gene editing. (2016)
  • Author(s): Kazuto Kato.
  • Journal Title: Issues in Science and Technoogy, Volume: XXXⅡ Issue: 4
• [Journal Article] ヒトゲノムデータの保護と利用に向けた仕組みづくり (2016)
  • Author(s): 加藤和人, 山本奈津子
  • Journal Title: 実験医学 Volume: 34 Issue: 16 Pages: 2670-2671
• [Journal Article] 次世代シーケンサーデータの解析手法 第6回ゲノムアセンブリ (2016)
  • Author(s): 谷澤 靖洋、神沼 英里、中村 保一、清水 謙多郎、門田 幸二
  • Journal Title: Japanese Journal of Lactic Acid Bacteria Volume: 27 Issue: 1 Pages: 41-52
  • DOI: 10.4109/jslab.27.41
  • Open Access
• [Presentation] Towards Better Genome Annotation. (2017)
  • Author(s): Yasuhiro Tanizawa and Yasukazu Nakamura
  • Organizer: Symposium on "Genome Evolution at Mishima"(GEM)
  • Place of Presentation: 三島
  • Year and Date: 2017-03-27 – 2017-03-29
  • Int'l Joint Research / Invited
• [Presentation] Nanopore sequencing for convenient RNA Seq analysis (2017)
  • Author(s): Masahide Seki, Eri Katsumata, Yutaka Suzuki
  • Organizer: Advances in Genome Biology and Technology 2017 General Meeting
  • Place of Presentation: Florida, USA
  • Year and Date: 2017-02-13 – 2017-02-16
  • Int'l Joint Research
• [Presentation] 個人情報保護法の改正について(パネリストとして話題提供) (2017)
  • Author(s): 山本奈津子
  • Organizer: 文部科学省新学術領域 市民公開シンポジウム「生命科学研究の最前線～いのちのしくみに迫り、健康を守る～
  • Place of Presentation: 東京
  • Year and Date: 2017-01-15
  • Invited
• [Presentation] Recent Iegislative efforts to balance the use of large-scale personal genomic data and the protection of privacy in Japan. (2017)
  • Author(s): Natsuko Yamamoto
  • Organizer: Advanced Genome Science International Symposium “The start of new genomics”
  • Place of Presentation: 東京
  • Year and Date: 2017-01-11
  • Int'l Joint Research / Invited
• [Presentation] Bacterial genome annotation web-platform DFAST-Toward faster genome publication. (2017)
  • Author(s): Yasuhiro Tanizawa and Yasukazu Nakamura
  • Organizer: Advanced Genome Science International Symposium “The Start of New Genomics”
  • Place of Presentation: 東京
  • Year and Date: 2017-01-10 – 2017-01-11
  • Int'l Joint Research / Invited
• [Presentation] Nanopore sequencing for genotyping pathogens of tropical diseases (2016)
  • Author(s): Yutaka Suzuki
  • Organizer: Joint International Tropical Medicine Meeting 2016
  • Place of Presentation: Bangkok, Thailand
  • Year and Date: 2016-12-07 – 2016-12-09
  • Int'l Joint Research / Invited
• [Presentation] ゲノム情報の改正個人情報保護法上の位置づけに関する考察 (2016)
  • Author(s): 山本奈津子, 川嶋実苗, 藤田卓仙
  • Organizer: 第36回医療情報学連合大会(第17回日本医療情報学会学術大会)
  • Place of Presentation: 横浜
  • Year and Date: 2016-11-21 – 2016-11-24
• [Presentation] 個人情報保護法改正の影響を考える(ワークショップのオーガナイザーとして。学会論文集は以下の著者で執筆) (2016)
  • Author(s): 藤田卓仙, 荻島創一, 三井純, 鈴木穣, 上原哲太郎, 山本奈津子, 川嶋実苗, 鈴木正朝
  • Organizer: 第36回医療情報学連合大会(第17回日本医療情報学会学術大会)
  • Place of Presentation: 横浜
  • Year and Date: 2016-11-21 – 2016-11-24
• [Presentation] EUデータ保護の動向(パネリストとして話題提供) (2016)
  • Author(s): 山本奈津子
  • Organizer: 第5回生命医薬情報学連合大会
  • Place of Presentation: 東京
  • Year and Date: 2016-09-29
  • Invited
• [Presentation] Genomic data sharing in East Asia-Current status in Japan- (2016)
  • Author(s): Kazuto Kato
  • Organizer: 12th ICGC meeting
  • Place of Presentation: Boston, USA
  • Year and Date: 2016-09-20
  • Int'l Joint Research / Invited
• [Presentation] Algorithms on Marginal Distributions of RNA Secondary Structures, (2016)
  • Author(s): Kiyoshi Asai
  • Organizer: ALGO2016
  • Place of Presentation: Aarhus University, Denmark
  • Year and Date: 2016-08-23
  • Int'l Joint Research / Invited
• [Presentation] Rtools : a web server for various secondary structural analyses on single RNA sequences, (2016)
  • Author(s): Michiaki Hamada, Yukiteru Ono, Hisanori Kiryu, Kengo Sato, Yuki Kato, Tsukasa Fukunaga, Ryota Mori, Kiyoshi Asai,
  • Organizer: RNA2016
  • Place of Presentation: 京都
  • Year and Date: 2016-06-29 – 2016-06-30
  • Int'l Joint Research
• [Presentation] シングルセル解析～トランスクリプトームから多層オミクス解析へ (2016)
  • Author(s): 鈴木穣
  • Organizer: アジレントゲノミクスフォーラム
  • Place of Presentation: 東京
  • Year and Date: 2016-06-10
  • Invited
• [Presentation] Genomic Medicine in Japan : Recent Changes in the Government Policy, and New Ethical and Legal Challenges (2016)
  • Author(s): Kazuto Kato.
  • Organizer: Precision Medicine : Legal and Ethical Challenges
  • Place of Presentation: 香港
  • Year and Date: 2016-04-08
  • Int'l Joint Research / Invited
• [Presentation] Revisions of Japanese Personal Data Protection Laws and Challenges in Promoting Biomedical Research Using Human Genetic/Genomic Data (2016)
  • Author(s): Natsuko Yamamoto
  • Organizer: The 13th International Congress of Human Genetics (ICGC2016)
  • Place of Presentation: 京都
  • Year and Date: 2016-04-06
  • Int'l Joint Research
• [Presentation] ELSI practices and regulations for collaboration and public participation in personal genome research. (2016)
  • Author(s): Kazuto Kato.
  • Organizer: The 13th International Congress of Human Genetics (ICGC2016)
  • Place of Presentation: 京都
  • Year and Date: 2016-04-05
  • Int'l Joint Research
• [Book] 実験医学別冊NGSアプリケーションRNA-Seq実験ハンドブック (2016)
  • Author(s): 鈴木穣 編
  • Total Pages: 282
  • Publisher: 羊土社
• [Book] 実験医学増刊 「RNA-Seq実験ハンドブック」 (2016)
  • Author(s): 森下真一
  • Pages: 236-241
  • Total Pages: 282
  • Publisher: 羊土社
• [Book] 遺伝子医学MOOK別冊「最新精神・神経遺伝医学研究と遺伝カウンセリング」 (2016)
  • Author(s): 森下真一
  • Pages: 51-60
  • Total Pages: 308
  • Publisher: 株式会メディカル ドゥ
• [Book] 実験医学別冊「メタゲノム解析実験ハンドブック」 (2016)
  • Author(s): 鈴木慶彦、森下真一
  • Pages: 149-155
  • Total Pages: 231
  • Publisher: 羊土社
• [Remarks] minialign
  • URL: https://github.com/ocxtal/minialign
• [Remarks] EAGLE
  • URL: https://github.com/tony-kuo/eagle
• [Remarks] LAST-TRAIN
  • URL: http://last.cbrc.jp/
• [Remarks] Rtools
  • URL: http://rtools.cbrc.jp
• [Remarks] SHARAKU
  • URL: http://www.dna.bio.keio.ac.jp/sharaku/
• [Remarks] DFAST
  • URL: https://dfast.nig.ac.jp
• [Remarks] DNApod
  • URL: http://tga.nig.ac.jp/dnapod/
• [Remarks] libgaga
  • URL: https://github.com/ocxtal/libgaba
• [Remarks] taw(Tiny Amazon Wrapper)
  • URL: https://github.com/mkasa/taw/
• [Remarks] Mudi
  • URL: http://naoii.nig.ac.jp/mudi_top.html
• [Remarks] DDBJ pipeline
  • URL: https://p.ddbj.nig.ac.jp/
• [Remarks] Local Package Manager
  • URL: https://lpm.bio/
• [Remarks] DBTSS
  • URL: http://dbtss.hgc.jp/
• [Remarks]
• [Remarks]
• [Patent(Industrial Property Rights)] 次世代シーケンサーを用いた迅速な遺伝子検索方法 (2017)
  • Inventor(s): 中岡博史、井ノ上逸朗
  • Industrial Property Rights Holder: 大学共同利用機関法人 情報・システム研究機構
  • Industrial Property Rights Type: 特願
  • Industrial Property Number: 特願2017-6314
  • Filing Date: 2017-01-17
• [Patent(Industrial Property Rights)] 情報処理システム、情報処理方法、及びプログラム (2017)
  • Inventor(s): 黒川顕、東光一、森宙史
  • Industrial Property Rights Holder: 大学共同利用機関法人情報・システム研究機構
  • Industrial Property Rights Type: 特願
  • Industrial Property Number: 特願2017-12340
  • Filing Date: 2017-01-26
• [Funded Workshop] 国際シンポジウム"The Start of New Genomics" (2017)
  • Place of Presentation: 東京大学伊藤謝恩ホール(東京)
  • Year and Date: 2017-01-10 – 2017-01-11