Contents

• Highlights
• Recent Publications
• Journal Papers
• Conference Papers I Presented
• Conference Papers/Presentations I Co-authored
• Book Chapters
• Japanese Language Publications
• Invited Lectures
• Meeting Reports
• PhD Thesis
• patents
• plus α

• Horton & Nakai, ISMB, 1997, Horton & Nakai, ISMB, 1996
  In this collaboration with Kenta Nakai, I applied several machine learning classifiers to the problem of predicted the subcellular localization site of proteins from their amino acid sequences. These papers had an impact on the academic literature and also lead to the practical tool PSORTII and its successor WoLF PSORT.

• Horton, JCB, 2001, Horton & Fujibuchi, JDA, 2007
  In the first paper I introduced an exact algorithm, TsukubaBB, for PWM (Position Weight Matrix, i.e. a fixed length Markov model) based motif discovery. In the second paper I improved TsukubaBB to be close to practical for some applications, and proved what I believe to be the only non-trivial upper bound regarding the complexity of this heavily studied -- but computationally not well understood problem.

(Somewhat) Highly Cited Papers

Recent Publications

2010 Journal Papers

• "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.

2010 Conference Papers

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

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:[html & pdf]

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]

2009 Conference Papers

• "RECOUNT: Next Generation Sequencing Error Correction Tool",
  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] [Paper (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] [pdf] [BibTeX]

2008 Conference Papers

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

• "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]

Journal Papers

2007

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

• "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] [BibTeX] [Google Scholar] [pdf] 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] [Google Scholar] [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] IAENG site: [IAENG site: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, 2007.
  [Abstract] [BibTeX] [Google Scholar] IPSJ site: [pdf] (their site suggests a different way to cite this article, not sure which is better)

• "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,... (73 authors), Paul Horton,... (62 authors), & Takashi Gojobori
  Nucleic Acids Research, doi:10.1093/nar/gkm999, 2007.
  [Abstract] [pdf] [BibTeX]

2006

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

2005

• "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] [Google Scholar]

1992-2001

• "Tsukuba BB: A Branch and Bound Algorithm for Local Multiple Alignment of DNA and Protein Sequences",
  Paul Horton,
  Journal of Computational Biology, 8(3):283-303, 2001.
  [Abstract] [Paper] [BibTeX] [google scholar] [Presented at CPM00]

• "Parallel Sequence Matching with TACO's Distributed Object Groups -- A Case Study from Molecular Biology",
  Jörg Nolte & Paul Horton,
  CLUSTER COMPUTING: The Journal of Networks Software and Applications, 4:71-77, 2001.
  Presented at The Ninth IEEE International Symposium on High Performance Distributed Computing, Pittsburgh, USA 2000.
  [Abstract] [BibTeX] [Citeseer]

• "PSORT: a Program for Detecting Sorting Signals in Proteins and Predicting their Subcellular Localization",
  Kenta Nakai & Paul Horton,
  Trends in Biochemical Sciences, 24(1):34-5, 1999.
  [Abstract] [Paper] [BibTeX] [google scholar]

• "An Assessment of Neural Network and Statistical Approaches for Prediction of E.coli Promoter Sites",,
  Paul Horton & Minoru Kanehisa,
  Nucleic Acid Research 20(16):4331-8, 1992.
  [Abstract] [Paper] [google scholar] [PubMed] [BibTeX]

Conference Papers I Presented (non-recent)

2006

• "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] [Google Scholar]

2005

• "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]

1994-2000

• "Tsukuba BB: A Branch and Bound Algorithm for Local Multiple Sequence Alignment",
  Paul Horton,
  Proceedings of Combinatorial Pattern Matching: 11th Annual Symposium, CPM 2000, Montréal, Canada, June 21-23, 2000.
  Published in Lecture Notes in Computer Science, 1848:84-98, 2000.
  [Abstract] [BibTeX] [JCB Journal Reference]

• "Alignment vs. Sum of All Alignments Scoring for Motif Extraction",
  Paul Horton,
  Proceedings of SIGMPS Symposium, Information Processing Society of Japan, 2006-MPS-5:231-8, 2000.
  [Abstract] [] [BibTeX] [Google Scholar] [Paper]

• "Better Prediction of Protein Cellular Localization Sites with the k Nearest Neighbors Classifier",
  Paul Horton & Kenta Nakai,
  Proceedings of Intelligent Systems in Molecular Biology, pp. 368-383. Halkidiki, Greece 1997.
  [Abstract] [Paper] [BibTeX] [PubMed] [google scholar] [Citeseer]

• "A Probabilistic Classification System for Predicting the Cellular Localization Sites of Proteins",
  Paul Horton & Kenta Nakai,
  Proceedings of Intelligent Systems in Molecular Biology, pp. 109-115. St. Louis, USA 1996.
  [Abstract] [Paper] [PubMed] [BibTeX] [google scholar] [Citeseer]

• "A Branch and Bound Algorithm for Local Multiple Alignment",
  Paul Horton,
  Proceedings of the Pacific Symposium on Biocomputing, pp. 368-383, Hawaii, USA 1996.
  [Abstract] [BibTeX] [Google Scholar] [Paper]

Conference Papers/Presentations I Co-authored (non-recent)

2007

• "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]

2004

• "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.
  Published in LNCS Lecture Notes in Bioinformatics, ISBN:3-540-24456-6, 3318:79-87. 2005.
  [Abstract] [BibTeX] [Google Scholar]

  1994

• "A Quantitative Analysis of Disk Drive Power Management in Portable Computers",
  Kester Li, Roger Kumpf, Paul Horton, & Thomas Anderson,
  Proceedings of the Winter 1994 USENIX Conference, San Francisco, USA, pp. 279-291, 1994.
  [Abstract] [Paper] [BibTeX] [google scholar] [Citeseer]

• "Computational Prediction of Subcellular Localization",
  Kenta Nakai & Paul Horton,
  In: Protein Targeting Protocols, 2nd ed. M. van der Giezen. (Ed.) Humana Press, USA, pp. 429-466, 2007.
  Also cited as: Methods Mol Biol., 390:429-66,2007.
  [Abstract] [BibTeX] [google scholar] [PubMed]

• "Protein Localization Prediction",
  Paul Horton, Yuri Mukai & Kenta Nakai,
  In: The Practical Bioinformatician, Limsoon Wong (Ed.), World Scientific Publishing Company, pp. 193-215, 2004.
  [Abstract] [BibTeX]

Poster Abstracts That Somebody Cited

• "Module Discovery in Gene Expression Data Using Closed Itemset Mining Algorithm",
  Yoshifumi Okada, Wataru Fujibuchi & Paul Horton
  Abstract of Poster in the 17th International Conference on Genome Informatics (GIW2006), Tokyo, Japan, December 2006.
  [Google Scholar]

• "Searching for similar gene expression profiles across platforms",
  Wataru Fujibuchi, Larisa Kiseleva & Paul Horton
  Abstract of Poster in the 16th International Conference on Genome Informatics (GIW2005), Tokyo, Japan, December 2005.
  [Google Scholar]

• 総説
• 解説
• 研究報告

• 「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]

• 「アミノ酸配列に基づくタンパク質の細胞内局在予測」,
  (Prediction of subcellular localization sites of proteins from their amino acid sequences)
  中井謙太・Paul Horton 実験医学増刊号、「バイオインフォマティクスツール の開発と生命研究への応用の最前線」、羊土社、26(7):140-6, 2008.
  [Abstract]

• 「PSORT」,
  Paul Horton・中井謙太,
  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]

• 「共通モチーフ抽出問題とギブスサンプリング」,
  Paul Horton,
  日本バイオインフォマティクス学会(編)、"バイオインフォマティクス事典"、共立出版、2006.

• 「極大２部クリーク列挙法による遺伝子発現モジュールの抽出」
  (A biclustering method for finding gene expression modules based on a maximal biclique enumeration)
  岡田吉史、藤渕　航、Paul Horton
  (Yoshifumi Okada, Fujibuchi Wataru and Paul Horton)
  IPSJ SIG Technical Report, 2006-BIO-6:17-23. 2006.
  [Abstract] [BibTeX] [pdf]

• 「恣意的判断基準を排除した時系列データの周期性判定法」
  (Periodicity judgment for time series data without arbitrary criterion)
  富永大介、Paul Horton
  (Daisuka Tominaga & Paul Horton)
  IPSJ SIG Technical Report, 2006-BIO-4:17-24 2006.
  [Abstract] [BibTeX]

• 「細胞の知識ベース開発と遺伝子発現プロファイルによる細胞種と特徴予測」
  (Development of Cell Knowledge Base and Prediction of Cell Types and Characteristics by Gene Expression Profiles)
  藤渕　航, Larisa Kiseleva, 谷口丈晃、Paul Horton
  (Wataru Fujibuchi, Larisa Kiseleva, Takeaki Taniguchi & Paul Horton)
  IPSJ SIG Technical Report, 2005-BIO-2:33-7. 2005.
  [Abstract] [BibTeX]

This is on old list from before I started putting my slides up on the internet. Newer invited lectures and other presentations are available here.

• "Mitochondrial β-barrel Outer Membrane Proteins, All Accounted For?",
  Westlake International Conference on Personalized Medicine, Hángzhōu, China, May 2009.
• "Proteome-Wide Sequence Analysis of Mitochondrial β-barrel Membrane Proteins",
  ATI International Forum, J-PARC, Toukaimura, Japan, March 2009.
• "Computational and Biological Insights from Database Mining of Human Microarray Data",
  Systems Biology and Bioinformatics Symposium SBBS07, Taiwan University, Taipei, Taiwan, March 2007.
• "The bioinformatics of protein subcellular localization",
  Winter School in Mathematical and Computational Biology, University of Queensland, Brisbane, Australia, June 2006.
• "Post-genomic Computational Biology Challenge: A Life Sciences Data Explosion in the Twilight of Moore's Law",
  Proceedings of the Computational Science Symposium, ISPJ Symposium Series 2005(11):9-12., Nagoya Japan, October 2005.

Meeting Reports

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

String algorithms and Machine Learning Applications for Computational Biology,
Paul Horton, PhD Thesis, Computer Science, the University of California at Berkeley, 1997.
[BibTeX] [Google Scholar]

Patents

It was mostly the first author's (Wataru Fujibuchi) idea, but in any case it was interesting going through the application process. I must say the patent attorneys were very smart!

Plus α

• I gave a highlights track presentation entitled "Mitochondrial beta-barrel Outer Membrane Proteins, All Accounted For?" at ISMB ECCB 2009. The talk basically covered results described in Imai et al., Cell 2008..

• I made a presention on how to train neural networks to effectively recognize promoters sequences in E. coli, at a historic conference which was retroactively defined to be the first Genome Informatics Workshop (after switching the conference language from Japanese to English), and later again renamed to be the GIW International Conference on Genome Informatics. The Japanese reference is:
  

  大腸菌のプロモータ部位を予測するニューラル・ネットの構成最適化、
  ホートン・ポール & 金久　實、
  知識情報処理技術とヒトゲノム計画、講演要旨集、A-2, 芝公園、機会振興会館、12月、1990.