Publication List, Sequence Analysis Team

Contents

• Recent Publications
• Journal Papers
• Selected Conference Papers
• Technical Reports
• Book Chapters
• Meeting Reports
• Other
• Selected Posters

Recent Publications

2013 Journal Papers

• "Finding protein-coding genes through human polymorphisms"
  PLoS One, 8(1):e54210, 2013. doi:10.1371/journal.pone.0054210>, Epub 2013 Jan 22.
  [Abstract] [BibTeX] [PLoS ONE site]

2012 Journal Papers

• "Identification of cargo proteins specific for the nucleocytoplasmic transport carrier transportin by combination of an in vitro transport system and SILAC-based quantitative proteomics",
  Makoto Kimura, Shingo Kose, Nobuaki Okumura, Kenichiro Imai, Maiko Furuta, Noriyuki Sakiyama, Kentaro Tomii, Paul Horton, Toshifumi Takao & Naoko Imamoto
  Molecular & Cellular Proteomics, Jan;12(1):145-57, 2013. doi:10.1074/mcp.M112.019414, Epub 2012 Oct 19.
  [Abstract] [BibTeX] [PubMed]

• "Mammalian NUMT insertion is non-random",
  Junko Tsuji, Martin C. Frith, Kentaro Tomii & Paul Horton
  Nucleic Acids Research, Oct;40(18):9073-88, 2012. doi:10.1093/nar/gks424, Epub 2013 July 3.
  [Abstract] [BibTeX] [NAR site]
  

• "A mostly traditional approach improves alignment of bisulfite-converted DNA",
  Martin C. Frith, Ryota Mori & Kiyoshi Asai
  Nucleic Acids Research, Jul;40(13):e100, 2012. doi:10.1093/nar/gks275. Epub 2012 Mar 28.
  

• "ValidNESs: a database of validated leucine-rich nuclear export signals",
  Szu-Chen Fu, Hsuan-Cheng Huang, Paul Horton & Hsueh-Fen Juan
  Nucleic Acids Research Jan;41(Database issue):D338-43, 2013. doi:10.1093/nar/gks936. Epub 2012 Oct 22.
  [Abstract] [pdf]
  

• "EST and transcriptome analysis of cephalochordate amphioxus — past, present and future",
  Yu-Bin Wang, Shu-Hwa Chen, Chun-Yen Lin & Jr-Kai Yu
  Briefings in Functional Genomics, Feb. 2012.
  [Oxford site]

2011 Journal Papers

• "RecountDB: a database of mapped and count corrected transcribed sequences",
  Edward Wijaya, Martin C. Frith, Kiyoshi Asai & Paul Horton
  Nucleic Acids Research, (2012 NAR Database Issue) doi:10.1093/nar/gkr1172, (4 pages), published online December 1, 2011.
  [Abstract] [BibTeX] [pdf] [NAR site]

• "Probabilistic alignments with quality scores: an application to short-read mapping toward accurate SNP/indel detection",
  Michiaki Hamada, Edward Wijaya, Martin C. Frith & Kiyoshi Asai
  Bioinformatics, 27:3085-92, 2011.
  

• "Prediction of leucine-rich nuclear export signal containing proteins with NESsential",
  Szu-Chin Fu, Kenichiro Imai & Paul Horton
  Nucleic Acids Research, doi:10.1093/nar/gkr493 (12 pages), published online June 24, 2011.
  [Abstract] [BibTeX] [pdf] [Supplementary] [NAR site] [F1000 "must read"]

• "Eukaryotic-wide sequence analysis of mitochondrial β-barrel outer membrane proteins",
  Kenichiro Imai, Naoya Fujita, M. Micheal Gromiha & Paul Horton
  BMC Genomics, 12:79, 2011.
  [Abstract] [BibTeX] [pdf] [BMC site]

• "Adaptive seeds tame genomic sequence comparison",
  S.M. Kiełbasa, Raymond Wan, Kengo Sato, Paul Horton & Martin C. Frith
  Genome Research, 21:487-93, 2011.
  [Abstract] [BibTeX] [pdf] [Supplementary] [GR site]

• "Gentle Masking of Low-Complexity Sequences Improves Homology Search",
  Martin C. Frith
  PLoS ONE 6(12):e28819, 2011.
  

2010 Journal Papers

• "A new repeat-masking method enables specific detection of homologous sequences",
  Martin C. Frith
  Nucleic Acids Research, 39:e23, 2010.
  [NAR site]

• "Incorporating sequence quality data into alignment improves DNA read mapping",
  Martin C. Frith, Raymond Wan & Paul Horton
  Nucleic Acids Research, 38(7):e100, 2010.
  [abstract] [BibTeX] [pdf]

• "Parameters for accurate genome alignment",
  Martin C. Frith, Michiaki Hamada & Paul Horton
  BMC Bioinformatics 11:80, Feb 9 2010.
  [Abstract] [BibTeX] [pdf] [BMC site] highly accessed.

2011 Conference Papers

• "Evolutionary sequence divergence predicts protein sub-cellular localization signals",
  Yoshinori Fukasawa, Ross KK Leung, Stephen KW Tsui & Paul Horton
  Proceedings 5th IEEE International Conference on Systems Biology, 307-312.
  Zhuhai, China, September 2011.
  [Abstract] [BibTeX] [pdf]

2010 Conference Papers

• "In Search of True Reads: A Classification Approach to Next Generation Sequencing Data Selection",
  Edward Wijaya, Jean-François Pessiot, Martin C. Frith, Wataru Fujibuchi, Kiyoshi Asai & Paul Horton
  Proceedings of the Workshop on data-mining of Next Generation Sequencing Data, BIBM 2010, 561-566.
  Hong Kong, December 2010.
  [Abstract] [BibTeX] [pdf]

• "Improved Prediction of Transcription Binding Sites from Chromatin Modification Data",
  Kengo Sato, Tom Whitington, Timothy L. Bailey & Paul Horton
  Proceedings of the 2010 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB2010), 1-7.
  Montreal, Canada, May 2010
  [Abstract] [BibTeX] [pdf]

Journal Papers -2009

2009 Journal Papers

• "HAMSTER: Visualizing microarray experiments as a set of minimum spanning trees",
  Raymond Wan, Larisa Kiseleva, Hajime Harada, Hiroshi Mamitsuka & Paul Horton
  Source Code for Biology and Medicine, 4:8, 2009.
  [Abstract] [BibTeX] [pdf] [Source Code Biol Med site] highly accessed

• "Universal partitioning of the hierarchical fold network of 50-residue segments in proteins",
  J. Ito,Y. Sonobe, K. Ikeda, K. Tomii & J. Higo
  BMC Structural Biology, 9:(34), 2009.
  [Abstract] [BibTeX] BMC Struct Biol site:[html & pdf]

• "MEME SUITE: tools for motif discovery and searching",
  TL Bailey, M Boden, FA Buske, MC Frith, CE Grant, L Clementi, J Ren,WW Li & WS Noble
  Nucleic Acids Research, 37(Web Server issue):W202-8, 2009.
  [Abstract] [BibTeX]

2008 Journal Papers

• "Mitochondrial β-Barrel Proteins, an Exclusive Club?"(Correspondence),
  Kenichiro Imai, M. Michael Gromiha & Paul Horton
  Cell, 135(7):1158-9, 2008.
  [Abstract] [pdf] [BibTeX]

• "Protein-segement universe exhibiting transitions at intermediate segment length in conformational subspaces",
  K. Ikeda, T. Hirokawa, J. Higo, & K. Tomii
  BMC Structural Biology, 8:37, 2008.
  

• "The whole alignment and nothing but the alignment: the problem of spurious alignment flanks",
  Martin C. Frith, Yonil Park, Sergey L. Sheetlin & John L. Spouge,
  Nucleic Acids Research, 36:5863-71, 2008.
  [Abstract] [pdf] [BibTeX]

• "Discovering Sequence Motifs with Arbitrary Insertions and Deletions",
  Martin Frith, Neil Saunders, Bostjan Kobe, & Timothy L. Bailey,
  PLoS Comput Biol, 4(5):e1000071, 2008.
  [Abstract] [pdf] [BibTeX] PLoS Comput Biol site:[html & pdf]

2007 Journal Papers

• "CellMontage: Similar Expression Profile Search Server",
  Wataru Fujibuchi, Larisa Kiseleva, Takeaki Taniguchi, Hajime Harada, & Paul Horton,
  23(22):3103-4, Bioinformatics 2007.
  [Abstract] [pdf] [BibTeX]

• "WoLF PSORT: Protein Localization Predictor",
  Paul Horton, Keun-Joon Park, Takeshi Obayashi, Naoya Fujita, Hajime Harada, C.J. Adams-Collier, & Kenta Nakai,
  Nucleic Acids Research, 35:W585-7, 2007.
  [Abstract] [pdf] [BibTeX] NAR site:[Abstract] [html] [pdf]

• "An Upper Bound on the Hardness of Exact Matrix Based Motif Discovery",
  Paul Horton & Wataru Fujibuchi,
  Journal of Discrete Algorithms, 5:4, 706-13, 2007.
  [Abstract] [BibTeX] [Presented at CPM05] JDA site:[html,pdf]

• "Exhaustive Search Method of Gene Expression Modules and Its Application to Human Tissue Data",
  Yoshifumi Okada, Kosaku Okubo, Paul Horton, & Wataru Fujibuchi,
  IAENG International Journal of Computer Science, 34(1):16, IJCS_34_1_16 2007.
  [Abstract] [BibTeX] [pdf] [Presented at IAENG-ICCS2007]

• "A Biclustering Method for Gene Expression Module Discovery Using Closed Itemset Enumeration Algorithm",
  Yoshifumi Okada, Wataru Fujibuchi & Paul Horton,
  IPSJ Transactions on Bioinformatics, 48(SIG5):39-48, 2007.
  [Abstract] [BibTeX]

• "The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts.",
  Genome Information Integration Project and H-Invitational 2
  Chisato Yamasaki,...(135 authors)..., Tadashi Imanishi, & Takashi Gojobori
  Naoki Osato, Paul Horton and Mitsuteru Nakao are middle authors.
  Nucleic Acids Research, doi:10.1093/nar/gkm999, 2007.
  [Abstract] [pdf] [BibTeX]

2006 Journal Papers

• "RaPiDS: An Algorithm for Rapid Expression Profile Database Search",
  Paul Horton, Larisa Kiseleva & Wataru Fujibuchi,
  Genome Informatics, 17(2):67-76, 2006.
  [Abstract] [Paper] [BibTeX] [Presented at GIW06]

• "Inference of Scale-free Networks From Gene Expression Time Series",
  Daisuke Tominaga & Paul Horton,
  Journal of Bioinformatics and Computational Biology, 4(2):503-14, 2006.
  [Abstract] [BibTeX] [Presented at MCCMB05]

• "Comparative Genomic Analysis of Transcription Regulation Elements Involved In Human Map Kinase G-Protein Coupling Pathway",
  Natalia Polouliakh, Tohru Natsume, Hajime Harada, Wataru Fujibuchi, & Paul Horton,
  Journal of Bioinformatics and Computational Biology, 4(2):469-82, 2006.
  [Abstract] [BibTeX] [Presented at MCCMB05]

• "Network-based de-noising improves prediction from microarray data",
  Tsuyoshi Kato, Yukio Murata, Koh Miura, Kiyoshi Asai, Paul B. Horton, Koji Tsuda & Wataru Fujibuchi,
  BMC Bioinformatics, 7(Suppl 1)S4:20 March, 2006.
  [Abstract] [Paper] [BibTeX] [BMC Bioinf]

2005 Journal Papers

• "Discrimination of Outer Membrane Proteins Using Support Vector Machines",
  Keun-Joon Park, Michael Gromiha, Paul Horton & Makiko Suwa, Bioinformatics, 21(23):4223-9, 2005.
  [Abstract] [BibTeX]

• "Automatic Gene Collection System for Genome-scale Overview of G-protein Coupled Receptors in Eukaryotes",
  Y. Ono, W. Fujibuchi & M. Suwa,
  Gene, 364:63-73, 2005.
  [Abstract] [BibTeX]

Selected Conference Papers (Presentations) -2009

2009 Conference Papers

• "RECOUNT: Expectation Maximization Based Error Correction Tool for Next Generation Sequencing Data",
  Edward Wijaya, Martin C. Frith, Yutaka Suzuki & Paul Horton
  Proceedings of 20th International Conference on Genome Informatics (GIW2009), Tokyo, Japan, December 2009.
  also as: Genome Informatics, 23(1):189-201, 2009.
  [Abstract] [pdf (with minor corrections)] [Supplementary] [BibTeX] [GIW site pdf]

• "Introduction and application of CellExpress, a new database for studying human tissue specific gene expression",
  Larisa Kiseleva, Raymond Wan & Paul Horton
  Proceedings of the Moscow Conference on Computational Molecular Biology (MCCMB'09), Moscow, Russia, July 2009.
  [Abstract]

• "Database Development and Discrimination Algorithms for Membrane Protein Functions",
  M. Michael Gromiha, Y. Yabuki, K. Imai, P. Horton & K. Fukui
  Proceedings of World Academy of Science, Engineering and Technology (PWASET), Dubai, UAE, January, pp. 358-361, 2009.
  [Abstract] [BibTeX]

2008 Conference Papers

• "DisLex: a Transformation for Discontiguous Suffix Array Construction",
  Paul Horton, Szymon M. Kiełbasa and Martin C. Frith
  Proceedings of the workshop on Knowledge, Language, and Learning in Bioinformatics (KLLBI), Hanoi, Vietnam, pp. 1-11, December 2008.
  [Abstract] [pdf] [BibTeX]

• "Characterizing Genes by Marginal Expression Distribution",
  Edward Wijaya, Hajime Harada & Paul Horton
  Proceedings of Bioscience and BioTechnology (BSBT2008), Sānyà, China, December 2008.
  Post-proceedings published as: CCIS, 28:164-175, 2009.
  [Abstract] [pdf] [BibTeX]

• "A Tiling Bound for Pairwise Global Sequence Alignment",
  Paul Horton & Martin Frith
  Proceedings of Bioscience and BioTechnology (BSBT2008), Sānyà, China, December 2008.
  Post-proceedings published as: CCIS, 30:93-98, 2009.
  [Abstract] [pdf] [BibTeX]

2007 Conference Papers

• "Exhaustive Search of Maximal Biclusters in Gene Expression Data",
  Yoshifumi Okada, Wataru Fujibuchi & Paul Horton,
  Proceedings of IAENG International Conference on Computer Science (ICCS'07), Hong Kong, China, March 2007.
  Published in Lecture Notes in Engineering and Computer Science, 2(1):307-312, 2007.
  [Abstract] [BibTeX] [Journal Reference]

• "Graphical Representation of Cell/tissue Type Relationships",
  Larisa Kiseleva, Raymond Wan & Paul Horton,
  Proceedings of Moscow Conference on Computational Molecular Biology (MCCMB'07), Moscow, Russia, July 2007.
  [Abstract]

2006 Conference Papers

• "RaPiDS: An Algorithm for Rapid Expression Profile Database Search",
  Paul Horton, Larisa Kiseleva & Wataru Fujibuchi,
  Proceedings of the 17th International Conference on Genome Informatics GIW06, Yokohama, Japan, pp. 67-76, December 2006.
  [Abstract] [Paper] [BibTeX] [Genome Informatics Journal Reference]

• "Protein Subcellular Localization Prediction with WoLF PSORT",
  Paul Horton, Keun-Joon Park, Takeshi Obayashi & Kenta Nakai,
  Proceedings of the 4th Annual Asia Pacific Bioinformatics Conference APBC06, Taipei, Taiwan. pp. 39-48, 2006.
  [Abstract] [Paper] [BibTeX]

2005 Conference Papers

• "An Upper Bound on the Hardness of Exact Matrix Based Motif Discovery",
  Paul Horton & Wataru Fujibuchi,
  Proceedings of Combinatorial Pattern Matching: 16th Annual Symposium, CPM 2005, Jeju, Korea, June 19-22, 2005. Published in Lecture Notes in Computer Science, 3537:219-228, 2005.
  [Abstract] [BibTeX] [JDA Journal Reference]

• "Comparative Genomic Analysis of Transcription Regulation Elements Involved in the Human MAP Kinase G-Protein Coupling Pathway",
  Natalia Polouliakh, Tohru Natsume & Paul Horton,
  Proceedings of Moscow Conference on Computational Molecular Biology MCCMB05, pp. 301-303. 2005.
  [Abstract] [BibTeX] [JBCB Journal Reference]

• "Optimization of S-sytem Models for Quantitative Time-Developing Gene Networks",
  Daisuke Tominaga & Paul Horton,
  Proceedings of Moscow Conference on Computational Molecular Biology MCCMB05, pp. 82-83. 2005.
  [Abstract] [BibTeX] [JBCB Journal Reference]

2004 Conference Papers

• "Parameter Landscape Analysis for Common Motif Discovery Programs",
  Natalia Poluliakh, Michiko Konno, Paul Horton & Kenta Nakai,
  Selected Papers from The First Annual RECOMB Satellite Workshop on Regulatory Genomics, 2004. LNCS Lecture Notes in Bioinformatics, ISBN:3-540-24456-6, 3318:79-87. 2005.
  [Abstract] [BibTeX]

Technical Reports

• "A biclustering method for finding gene expression modules based on a maximal biclique enumeration",(in Japanese),
  Yoshifumi Okada, Fujibuchi Wataru & Paul Horton,
  IPSJ SIG Technical Report 2006-BIO-6:17-23, 2006.
  [Abstract] [BibTeX]

• "Periodicity judgment for time series data without arbitrary criterion"(in Japanese),
  Daisuke Tominaga & Paul Horton,
  IPSJ SIG Technical Report 2006-BIO-4, 2006.
  [Abstract] [BibTeX]

• "Development of Cell Knowledge Base and Prediction of Cell Types and Characteristics by Gene Expression Profiles"(in Japanese),
  Wataru Fujibuchi, Larisa Kiseleva, Takeaki Taniguchi & Paul Horton,
  IPSJ SIG Technical Report 2005-BIO-2:33-7, 2005.
  [Abstract] [BibTeX]

Book Chapters

• "Localization prediction and structure-based in silico analysis of bacterial proteins - with emphasis on outer membrane proteins",
  Kenichiro Imai, Sikander Hayat, Noriyuki Sakiyama Naoya Fujita, Kentaro Tomii , Arne Elofsson & Paul Horton
  To appear in Data Mining for Systems Biology. Will also be citable as Methods Mol Biol.
  [Abstract] [BibTeX] [pdf]

• "Computational Prediction of Subcellular Localization",
  Kenta Nakai & Paul Horton
  In: Protein Targeting Protocols, 2nd ed. M. van der Giezen. (Ed.) Humana Press, USA. 2007.
  Also cited as: Methods Mol Biol., 390:429-66,2007.
  [Abstract] [BibTeX] [PubMed]

• "Protein Localization Prediction",
  Paul Horton, Yuri Mukai & Kenta Nakai,
  In: The Practical Bioinformatician, Limsoon Wong (Ed.), World Scientific Publishing Company, 2004.
  [Abstract] [BibTeX] [pdf]

Japanese Book Chapters・日本語の解説等

• 「タンパク質の構造・機能ドメイン、相互作用データベース」,
  崎山則征、富井健太郎、ポール・ホートン (Noriyuki SAKIYAMA, Kentaro TOMII & Paul HORTON)
  有田正規(編)、"使えるデータベース・ウェブツール"、羊土社、2011.
  (Short chapter introducing some online resources for protein sequence analysis)
  [Abstract] [BibTeX]

• 「ヌクレオソーム位置とその配列解析」,
  Paul Horton
  ファルマシア, 44(4):352-3, 2008.
  (Minireview on recent advances regarding nucleosome positioning)
  [Abstract] [BibTeX]

• 「アミノ酸配列に基づくタンパク質の細胞内局在予測」,
  中井謙太・Paul Horton (Kenta NAKAI & Paul HORTON)
  実験医学(増刊), 26(7):140-146, 2008.
  (Prediction of subcellular localization sites of proteins from their amino acid sequences)
  [Abstract] [BibTeX]

• 「PSORT」,
  Paul Horton、中井謙太 (Paul HORTON & Kenta NAKAI)
  中村・礒合・石川・平川・坊農(編)、"バイオデータベースとウェブツールの手とり足とり活用法 改訂第２版"、羊土社、2007.
  (Book chapter in book on bioinformatics tools and databases)
  [Abstract] [BibTeX]

• 「遺伝子発現プロファイルデータベースGEOデータベース」,
  ポリュリャーフ ナターリヤ、藤渕 航 (Natalia Poluliakh & Wataru Fujibuchi),
  ゲノム研究実験ハンドブック、第２章、101-108頁、 辻本豪三、田中利男（編集）、羊土社、 2004.
  [BibTeX]

Meeting Reports

• "Summary of talks and papers at ISCB-Asia/SCCG 2012",
  Konstantin Tretyakov, Tatyana Goldberg, Victor X Jin & Paul Horton
  A report on ISCB-Asia/SCCG 2012, Shenzhen, China, 14–17 December 2012.
  BMC Genomics, 14(Suppl 2):I1 doi:10.1186/1471-2164-14-S2-I1, 2013.
  [Abstract] [BibTeX] [BMC Genomics site]

• "Genome informatics: advances in theory and practice",
  Szu-Chin Fu & Paul Horton
  A report on the 20th International Conference on Genome Informatics, Yokohama, Japan, 14-16 December 2009.
  Genome Medicine, 2:7 doi:10.1186/gm128, 2010.
  [Abstract] [BibTeX] [pdf] [Genome Medicine site]

Other

• "Paving the future: finding suitable ISMB venues",
  Burkhard Rost, Terry Gaasterland, Thomas Lengauer, Michal Linial, Scott Markel, BJ McKay Morrison, Reinhard Schneider, Paul Horton & Janet Kelso
  Bioinformatics, 28(19):2556–9, 2012. doi:10.1093/bioinformatics/bts420,Epub 2012 Jul 13.
  [Abstract] [BibTeX] [PubMed] [Bioinformatics site]

Selected Posters

• "Patterns of Mitochondrial DNA Insertion in Mammalian Nuclear Genomes",
  Junko Tsuji, Martin Frith, Kentaro Tomii & Paul Horton
  Best Poster Award, Cold Spring Harbor Asia Conference, Bioinformatics of Human and Animal Genomics, Suzhou, China, November 2011.
  [conference site]

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