Hideki NAGASAKI, Ph.D.
Genome Informatics Laboratory,
Center for Information Biology and DDBJ,
National Institute of Genetics, ROIS
1111 Yata, Mishima, Shizuoka 411-08540, JAPAN
Phone: +81-55-981-6836
FAX: +81-55-981-6889
e-mail: hnagasak-at-nig-dot-ac-dot-jp
#Publication list
Nagasaki H, Mochizuki T, Kodama Y, Saruhashi S, Morizaki S, Sugawara H, Ohyanagi H, Kurata N, Okubo K, Takagi T, Kaminuma E, Nakamura Y.
DDBJ Read Annotation Pipeline: A Cloud Computing-Based Pipeline for High-Throughput Analysis of Next-Generation Sequencing Data.
DNA Res. 2013;20(4):383-90. PMID: 23657089
Nagasaki H, Ebana K, Shibaya T, Yonemaru J, Yano M.
Core single-nucleotide polymorphisms – a tool for genetic analysis of the Japanese rice population.
Breed. Sci. 2010 60:648-55. PMID: 23641177
Nagasaki H, Arita M, Nishizawa T, Suwa M, Gotoh O.
Automated classification of alternative splicing and transcriptional initiation and construction of visual database of classified patterns.
Bioinformatics. 2006 May 15;22(10):1211-6. PMID: 16500940
Nagasaki H, Arita M, Nishizawa T, Suwa M, Gotoh O.
Species-specific variation of alternative splicing and transcriptional initiation in six eukaryotes.
Gene. 2005 Dec 30;364:53-62. PMID: 16219431
Nagasaki H, Yamamoto K, Shomura A, Koga-ban Y, Takasuga A, Yano M, Minobe Y, Sasaki T.
Rice class III chitinase homologues isolated by random cloning of rice cDNAs.
DNA Res. 1997 Dec 31; 4(6): 379-85. PMID: 9501993
Hori K, Nonoue Y, Ono N, Shibaya T, Ebana K, Matsubara K, Ogiso-Tanaka E, Tanabata T, Sugimoto K, Taguchi-Shiobara F, Yonemaru J, Mizobuchi R, Uga Y, Fukuda A, Ueda T, Yamamoto S, Yamanouchi U, Takai T, Ikka T, Kondo K, Hoshino T, Yamamoto E, Adachi S, Nagasaki H, Shomura A, Shimizu T, Kono I, Ito S, Mizubayashi T, Kitazawa N, Nagata K, Ando T, Fukuoka S, Yamamoto T, Yano M.
Genetic architecture of variation in heading date among Asian rice accessions.
BMC Plant Biology 05/2015; 15(1):115. PMID: 25953146
Kobayashi M, Nagasaki H, Garcia V, Just D, Bres C, Mauxion JP, Le Paslier MC, Brunel D, Suda K, Minakuchi Y, Toyoda A, Fujiyama A, Toyoshima H, Suzuki T, Igarashi K, Rothan C, Kaminuma E, Nakamura Y, Yano K, Aoki K.
Genome-Wide Analysis of Intraspecific DNA Polymorphism in ‘Micro-Tom’, a Model Cultivar of Tomato (Solanum lycopersicum).
Plant Cell Physiol. 2014 Feb;55(2):445-54. PMID: 24319074
Hosomichi K, Mitsunaga S, Nagasaki H, Inoue Ituro.
A Bead-based Normalization for Uniform Sequencing depth (BeNUS) protocol for multi-samples sequencing exemplified by HLA-B.
BMC Genomics 2014, 15:645. PMID: 25087472
Aoki K, Ogata Y, Igarashi K, Yano K, Nagasaki H, Kaminuma E, Toyoda A.
Functional genomics of tomato in a post-genome-sequencing phase.
Breeding Sci. 2013 Mar;63(1):14-20. doi: 10.1270/jsbbs.63.14. Epub 2013 Mar 1.
Yonemaru J, Yamamoto T, Ebana K, Yamamoto E, Nagasaki H, Shibaya T, Yano M.
Genome-wide haplotype changes produced by artificial selection during modern rice breeding in Japan.
PLoS One. 2012;7(3):e32982. PMID: 22427922
Arai-Kichise Y, Shiwa Y, Nagasaki H, Ebana K, Yoshikawa H, Yano M, Wakasa K.
Discovery of Genome-wide DNA Polymorphisms in a Landrace Cultivar of Japonica Rice by Whole-genome Sequencing. Plant Cell Physiol. 2011 Jan 21. PMID: 21258067. doi: 10.1093/pcp/pcr003
Ebana K, Yonemaru J, Fukuoka S, Iwata H, Kanamori H, Namiki N, Nagasaki H, Yano M.
Genetic structure revealed by a whole-genome single-nucleotide polymorphism survey of diverse accessions of cultivated Asian rice (Oryza sativa L.). Breed. Sci. 2010 60:390-7. doi:10.1270/jsbbs.60.390
Yamamoto T, Nagasaki H, Yonemaru J, Ebana K, Nakajima M, Shibaya T, Yano M.
Fine definition of the pedigree haplotypes of closely related rice cultivars by means of genome-wide discovery of single-nucleotide polymorphisms.
BMC Genomics 2010, 11:267. PMID: 20423466
Ohnuma S, Miura K, Horii A, Fujibuchi W, Kaneko N, Gotoh O, Nagasaki H, Mizoi T, Tsukamoto N, Kobayashi T, Kinouchi M, Okabe M, Sasaki H, Shiiba K, Miyagawa K, Sasaki I.
Cancer-associated splicing variants of the CDCA1 and MSMB genes expressed in cancer cell lines and surgically resected gastric cancer tissues.
Surgery. 2009 Jan;145(1):57-68. PMID: 19081476
Genome Information Integration Project And H-Invitational 2
The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts.
Nucleic Acids Res. 2008 Jan;36(Database issue):D793-9. Epub 2007 Dec 18. PMID: 18089548
Machida et al.
Genome sequencing and analysis of Aspergillus oryzae.
Nature. 2005 Dec 22;438(7071):1157-61. PMID: 16372010
International Rice Genome Sequencing Project.
The map-based sequence of the rice genome.
Nature. 2005 Aug 11;436(7052):793-800. PMID: 16100779
Imanishi et al.
Integrative annotation of 21,037 human genes validated by full-length cDNA clones.
PLoS Biol. 2004 Jun;2(6):e162. PMID: 15103394
Sasaki et al.
The genome sequence and structure of rice chromosome 1.
Nature. 2002 Nov 21; 420(6913): 312-6. PMID: 12447438
Sakata K, Nagamura Y, Numa H, Antonio BA, Nagasaki H, Idonuma A, Watanabe W, Shimizu Y, Horiuchi I, Matsumoto T, Sasaki T, Higo K.
RiceGAAS: an automated annotation system and database for rice genome sequence.
Nucleic Acids Res. 2002 Jan 1; 30(1): 98-102. PMID: 11752265
Sakata K, Antonio BA, Mukai Y, Nagasaki H, Sakai Y, Makino K, Sasaki T.
INE: a rice genome database with an integrated map view.
Nucleic Acids Res. 2000 Jan 1; 28(1): 97-101. PMID: 10592192
Sasaki T, Song J, Koga-Ban Y, Matsui E, Fang F, Higo H, Nagasaki H, Hori M, Miya M, Murayama-Kayano E, et al.
Toward cataloguing all rice genes: large-scale sequencing of randomly chosen rice cDNAs from a callus cDNA library.
Plant J. 1994 Oct; 6(4): 615-24. PMID: 7987417
長崎英樹
実験医学増刊Vol.32 No.20 「今日から使える! データベース・ウェブツール 達人になるための実践ガイド100」 pp.176-179
長崎英樹、望月孝子、谷沢靖洋、神沼英里、中村保一
実験医学別冊 「次世代シークエンス解析スタンダード」pp.352-360
長崎 英樹、神沼 英里
実験医学増刊号 「使えるデータベース・ウェブツール」pp.203-209
Gotoh O., Nagasaki H.
Analysis of alternative splicing and alternative transcriptional initiation.
Journal of Animal Genetics 2005 32(2): 39-46. Japanese.
#Recent presentations
Plant and Animal Genome XXI Conference (Jan. 2013)
Liverwort Genome Analysis using DDBJ Pipeline and Construction of the Genome Annotation Database
Plant and Animal Genome XX Conference (Jan. 2012)
DDBJ Sequence Read Archive and a cloud-computing based annotation tool for new-generation sequencing data
Plant and Animal Genome XIX Conference (Jan. 2011)
DDBJ Read Annotation Pipeline: A Cloud Computing Based Pipeline For High-Throughput Analysis Of Next Generation Sequencing Data (poster).
BMB2011 workshop (Dec. 2011)
NGSアーカイブ配列のクラウド型解析パイプラインDDBJ Pipeline進捗: de novoアセンブル配列注釈ワークフロー
BMB2010 workshop (Dec. 2010)
Detection and application of genome-wide SNPs between rice cultivars using high throughput sequencer.