Volume 4 2003   Special Issue: Ontology Workshop Tokyo 2003    Editorial Takako Takai-Igarashi, Toshihisa Takagi and Edgar Wingender Ontology Workshop Tokyo 2003 - Preface - 0001   Communication Evelyn Camon, Daniel Barrell, Vivian Lee, Emily Dimmer and Rolf Apweiler The Gene Ontology Annotation (GOA) Database - An integrated resource of GO annotations to the UniProt Knowledgebase 0002   Article Takeya Kasukawa, Hidemasa Bono, Yoshihide Hayashizaki, Yasushi Okazaki and Hideo Matsuda MaXML: mouse annotation XML 0003   Article                   Marie-Paule Lefranc, Véronique Giudicelli, Chantal Ginestoux, Nathalie Bosc, Géraldine Folch, Delphine Guiraudou, Joumana Jabado-Michaloud, Séverine Magris, Dominique Scaviner, Valérie Thouvenin, Kora Combres, David Girod, Stéphanie Jeanjean, Céline Protat, Mehdi Yousfi-Monod, Elodie Duprat, Quentin Kaas, Christelle Pommié, Denys Chaume and Gérard Lefranc IMGT-ONTOLOGY for immunogenetics and immunoinformatics, http://imgt.cines.fr 0004   Article Teruyoshi Hishiki, Osamu Ogasawara, Yoshimasa Tsuruoka and Kousaku Okubo Indexing anatomical concepts to OMIM Clinical Synopsis using UMLS Metathesaurus 0005   Communication Edgar Wingender TRANSPATH, TRANSFAC and CYTOMER as starting points for an ontology of regulatory networks 0006   Article Ken Ichiro Fukuda, Yuki Yamagata and Toshihisa Takagi FREX: A query interface for biological processes with hierarchical and recursive structures 0007   Article Takako Takai-Igarashi and Riichiro Mizoguchi Cell Signaling Networks Ontology 0008   Review Isabel Rojas, Esther Ratsch, Jasmin Saric and Ulrike Wittig Notes on the use of ontologies in the biochemical domain 0009          Further regular articles:        Article Julio Vera and Néstor V. Torres MetMAP: An integrated MatlabTM package for analysis and optimization of metabolic systems 0010   Article Vladimir B. Bajic, Vidhu Choudhary and Chuan Koh Hock Content analysis of the core promoter region of human genes 0011       2004   Communication Evanthia E. Pashou, Zoi I. Litou, Theodore D. Liakopoulos and Stavros J. Hamodrakas waveTM: Wavelet-based transmembrane segment prediction 0012   Article Arun Krishnan, Kuo-Bin Li and Praveen Issac Rapid detection of conserved regions in protein sequences using wavelets 0013   Article Chintalapati Janaki and Rajendra R. Joshi Motif detection in Arabidopsis: Correlation with gene expression data 0014   Article Daniel V. Guebel Canonical sensitivities: A useful tool to deal with large perturbations in metabolic network modeling 0015   Article Lance W. Hahn and Jason H. Moore Ideal discrimination of discrete clinical endpoints using multilocus genotypes 0016   Article Michael Hiller, Rolf Backofen, Stephan Heymann, Anke Busch, Timo Mika Gläßer and Johann-Christoph Freytag Efficient prediction of alternative splice forms using protein domain homology 0017   Article Hans B. Sieburg and Christa E. Müller-Sieburg Classification of short kinetics by shape 0018   Communication Kishore R. Sakharkar and Vincent T. K. Chow PPD - Proteome Profile Database 0019   Article Adam Ameur, Erik Aurell, Mats Carlsson and Jakub Orzechowski Westholm Global gene expression analysis by combinatorial optimization 0020   Article Katja Wegner, Stephan Jansen, Stefan Wuchty, Ralph Gauges and Ursula Kummer combAlign: A protein sequence comparison algorithm considering recombinations 0021   Article Huiqing Liu, Hao Han, Jinyan Li and Limsoon Wong Using amino acid patterns to accurately predict translation initiation sites 0022   Article Atsushi Doi, Sachie Fujita, Hiroshi Matsuno, Masao Nagasaki and Satoru Miyano Constructing biological pathway models with hybrid functional Petri net 0023   Review Tan Chee Meng, Sandeep Somani and Pawan Dhar Modeling and simulation of biological systems with stochasticity 0024   Article Haïtham Sghaier, Thuy Le Huyen Ai, Tokumasa Horiike and Takao Shinozawa Molecular chaperones: proposal of a systematic computer-oriented nomenclature and construction of a centralized database 0025   Article Mi Zhou and Yan Cui GeneInfoViz: Constructing and visualizing gene relation networks 0026   Article Phillip P. Le, Amit Bahl and Lyle H. Ungar Using prior knowledge to improve genetic network reconstruction from microarray data 0027   Communication Kishore R. Sakharkar, Meena K. Sakharkar and Vincent T. K. Chow A novel genomics approach for the identification of drug targets in pathogens, with special reference to Pseudomonas aeruginosa 0028   Article Limor Kozobay-Avraham, Sergey Hosid and Alexander Bolshoy Curvature distribution in prokaryotic genomes 0029   Communication Sávio T. Farias, Marx G. van der Linden, Thais G. Rêgo, Demétrius A. M. Araújo and Maria Christina M. Bonato Thermo-search: lifestyle and thermostability analysis 0030   Communication Alexandre G. de Brevern, Cristina Benros, Romain Gautier, Hélène Valadié, Serge Hazout and Catherine Etchebest Local backbone structure prediction of proteins 0031   Communication Meena Kishore Sakharkar, Vincent T. K. Chow and Pandjassarame Kangueane Distributions of exons and introns in the human genome 0032   Article Fan Long, Hong Liu, Chang Hahn, Pavel Sumazin, Michael Q. Zhang and Asher Zilberstein Genome-wide prediction and analysis of function-specific transcription factor binding sites 0033   Communication Davinder K. Kohli, Chittur V. Srikanth and Anand K. Bachhawat A search tool for identification and analysis of conserved sequence patterns in Saccharomyces spp. orthologous promoters 0034   Article Steffen Möller, Dirk Koczan, Pablo Serrano-Fernandez, Uwe K. Zettl, Hans-Jürgen Thiesen and Saleh M. Ibrahim Selecting SNPs for association studies based on population frequencies: a novel interactive tool and its application to polygenic diseases 0035   Article Yutaka Suzuki, Riu Yamashita, Matsuyuki Shirota, Yuta Sakakibara, Joe Chiba, Junko Mizushima-Sugano, Alexander E. Kel, Takahiro Arakawa, Piero Carninci, Jun Kawai, Yoshihide Hayashizaki, Toshihisa Takagi, Kenta Nakai and Sumio Sugano Large-scale collection and characterization of promoters of human and mouse genes 0036   Article Seema Namboori, Narayanaswamy Srinivasan and Shashi B. Pandit Recognition of remotely related structural homologues using sequence profiles of aligned homologous protein structures 0037   Article Jobst Landgrebe, Frank Bretz and Edgar Brunner Efficient two-sample designs for microarray experiments with biological replications 0038   Article Betsey D. Dyer, Mark D. LeBlanc, Stephen Benz, Peter Cahalan, Brian Donorfio, Patrick Sagui, Adam Villa and Gregory Williams A DNA motif lexicon: cataloguing and annotating sequences 0039   Article Katja Rateitschak, Tobias Müller and Martin Vingron Annotating significant pairs of transcription factor binding sites in regulatory DNA 0040   Article Hong Liu, Nanxiang Ge, Kin-Tak Yu, David Krolikowski, Asher Zilberstein and Chang S. Hahn Prediction of IFN-gamma regulated gene transcription 0041   Article Nestor Sosa, Andreas Kremling, Esther Ratsch and Isabel Rojas Web-based visualisation of the transcriptional control network of Escherichia coli 0042   Article Guillaume Meurice, Catherine Deborde, Daniel Jacob, Hélène Falentin, Patrick Boyaval and Diliana Dimova In silico exploration of the fructose-6-phosphate phosphorylation step in glycolysis: genomic evidence of the coexistence of an atypical ATP-dependent along with a PPi-dependent phosphofructokinase in Propionibacterium freudenreichii subsp. shermanii. 0043   Article Lorenz Bülow, Martin Schindler, Claudia Choi and Reinhard Hehl PathoPlant®: a database on plant-pathogen interactions. 0044   Article Mack E. Crayton III, Carll E. Ladd, Martin Sommer, Gregory Hampikian and Linda D. Strausbaugh An organizational model of transcription factor binding sites for a histone promoter in D. melanogaster 0045   Article A.V.S.K. Mohan Katta, Rajeshwari Marikkannu, Rajiv V. Basaiawmoit and Sankaran Krishnaswamy Consensus based validation of membrane porins 0046   Article Shashi B. Pandit and Narayanaswamy Srinivasan Identification and analysis of a new family of bacterial serine proteinases 0047   Article Tannistha Nandi, Samir K. Brahmachari, Krishnamoorthy Kannan and Srinivasan Ramachandran Clusters of proteins in archaeal and bacterial proteomes using compositional analysis 0048   Article Oriel Bergig, Danny Barash, Evgeny Nudler and Klara Kedem STR2: A structure to string approach for locating G-box riboswitch shapes in pre-selected genes 0049   Article Vignesh Muthuvijayan and Mark R. Marten In silico reconstruction of nutrient-sensing signal transduction pathways in Aspergillus nidulans 0050

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