Volume 4, 2003

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  Takako Takai-Igarashi, Toshihisa Takagi, Edgar Wingender: Preface.
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  Evelyn Camon, Daniel Barrell, Vivian Lee, Emily Dimmer, Rolf Apweiler: The Gene Ontology Annotation (GOA) Database - An integrated resource of GO annotations to the UniProt Knowledgebase.
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  Takeya Kasukawa, Hidemasa Bono, Yoshihide Hayashizaki, Yasushi Okazaki, Hideo Matsuda: MaXML: mouse annotation XML.
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  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, Gérard Lefranc: IMGT-ONTOLOGY for immunogenetics and immunoinformatics.
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  Teruyoshi Hishiki, Osamu Ogasawara, Yoshimasa Tsuruoka, Kousaku Okubo: Indexing anatomical concepts to OMIM Clinical Synopsis using UMLS Metathesaurus.
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  Edgar Wingender: TRANSPATH, TRANSFAC and CYTOMER as starting points for an ontology of regulatory networks.
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  Ken-ichiro Fukuda, Yuki Yamagata, Toshihisa Takagi: FREX: A query interface for biological processes with hierarchical and recursive structures.
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  Takako Takai-Igarashi, Riichiro Mizoguchi: Cell Signaling Networks Ontology.
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  Isabel Rojas, Esther Ratsch, Jasmin Saric, Ulrike Wittig: Notes on the use of ontologies in the biochemical domain.

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  Julio Vera, Néstor V. Torres: MetMAP: An integrated Matlab TM package for analysis and optimization of metabolic systems.
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  Vladimir B. Bajic, Vidhu Choudhary, Chuan Koh Hock: Content analysis of the core promoter region of human genes.

Volume 4, 2004

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  Evanthia E. Pashou, Zoi I. Litou, Theodore Liakopoulos, Stavros J. Hamodrakas: waveTM: Wavelet-based transmembrane segment prediction.
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  Arun Krishnan, Kuo-Bin Li, Praveen Issac: Rapid detection of conserved regions in protein sequences using wavelets.
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  Chintalapati Janaki, Rajendra R. Joshi: Motif detection in Arabidopsis: Correlation with gene expression data.
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  Daniel V. Guebel: Canonical sensitivities: A useful tool to deal with large perturbations in metabolic network modeling.
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  Lance W. Hahn, Jason H. Moore: Ideal discrimination of discrete clinical endpoints using multilocus genotypes.
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  Michael Hiller, Rolf Backofen, Stephan Heymann, Anke Busch, Timo Mika Gläßer, Johann Christoph Freytag: Efficient prediction of alternative splice forms using protein domain homology.
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  Hans B. Sieburg, Christa E. Müller-Sieburg: Classification of short kinetics by shape.
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  Kishore R. Sakharkar, Vincent T. K. Chow: PPD - Proteome Profile Database.
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  Adam Ameur, Erik Aurell, Mats Carlsson, Jakub Orzechowski Westholm: Global gene expression analysis by combinatorial optimization.
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  Katja Wegner, Stephan Jansen, Stefan Wuchty, Ralph Gauges, Ursula Kummer: combAlign: A protein sequence comparison algorithm considering recombinations.
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  Huiqing Liu, Hao Han, Jinyan Li, Limsoon Wong: Using amino acid patterns to accurately predict translation initiation sites.
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  Atsushi Doi, Sachie Fujita, Hiroshi Matsuno, Masao Nagasaki, Satoru Miyano: Constructing biological pathway models with hybrid functional Petri net.
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  Tan Chee Meng, Sandeep Somani, Pawan Dhar: Modeling and simulation of biological systems with stochasticity.
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  Haïtham Sghaier, Thuy Le Huyen Ai, Tokumasa Horiike, Takao Shinozawa: Molecular chaperones: proposal of a systematic computer-oriented nomenclature and construction of a centralized database.
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  Mi Zhou, Yan Cui: GeneInfoViz: Constructing and visualizing gene relation networks.
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  Phillip P. Le, Amit Bahl, Lyle H. Ungar: Using prior knowledge to improve genetic network reconstruction from microarray data.
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  Kishore R. Sakharkar, Meena K. Sakharkar, Vincent T. K. Chow: A novel genomics approach for the identification of drug targets in pathogens, with special reference to Pseudomonas aeruginosa.
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  Limor Kozobay-Avraham, Sergey Hosid, Alexander Bolshoy: Curvature distribution in prokaryotic genomes.
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  Sávio T. Farias, Marx G. van der Linden, Thais G. Rêgo, Demétrius A. M. Araújo, Maria Christina M. Bonato: Thermo-search: lifestyle and thermostability analysis.
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  Alexandre G. de Brevern, Cristina Benros, Romain Gautier, Hélène Valadié, Serge A. Hazout, Catherine Etchebest: Local backbone structure prediction of proteins.
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  Meena K. Sakharkar, Vincent T. K. Chow, Pandjassarame Kangueane: Distributions of exons and introns in the human genome.
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  Fan Long, Hong Liu, Chang S. Hahn, Pavel Sumazin, Michael Q. Zhang, Asher Zilberstein: Genome-wide prediction and analysis of function-specific transcription factor binding sites.
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  Davinder K. Kohli, Chittur V. Srikanth, Anand K. Bachhawat: A search tool for identification and analysis of conserved sequence patterns in Saccharomyces spp. orthologous promoters.
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  Steffen Möller, Dirk Koczan, Pablo Serrano-Fernández, Uwe K. Zettl, Hans-Jürgen Thiesen, Saleh M. Ibrahim: Selecting SNPs for association studies based on population frequencies: a novel interactive tool and its application to polygenic diseases.
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  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, Sumio Sugano: Large-scale collection and characterization of promoters of human and mouse genes.
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  Seema Namboori, Narayanaswamy Srinivasan, Shashi B. Pandit: Recognition of remotely related structural homologues using sequence profiles of aligned homologous protein structures.
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  Jobst Landgrebe, Frank Bretz, Edgar Brunner: Efficient two-sample designs for microarray experiments with biological replications.
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  Betsey D. Dyer, Mark D. LeBlanc, Stephen Benz, Peter Cahalan, Brian Donorfio, Patrick Sagui, Adam Villa, Gregory Williams: A DNA motif lexicon: cataloguing, annotating sequences.
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  Katja Rateitschak, Tobias Müller, Martin Vingron: Annotating significant pairs of transcription factor binding sites in regulatory DNA.
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  Hong Liu, Nanxiang Ge, Kin-Tak Yu, David Krolikowski, Asher Zilberstein, Chang S. Hahn: Prediction of IFN-gamma regulated gene transcription.
• 
  Nestor Sosa, Andreas Kremling, Esther Ratsch, Isabel Rojas: Web-based visualisation of the transcriptional control network of Escherichia coli.
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  Guillaume Meurice, Catherine Deborde, Daniel Jacob, Hélène Falentin, Patrick Boyaval, 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.
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  Lorenz Bülow, Martin Schindler, Claudia Choi, Reinhard Hehl: PathoPlant: a database on plant-pathogen interactions.
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  Mack E. Crayton III, Carll E. Ladd, Martin Sommer, Gregory Hampikian, Linda D. Strausbaugh: An organizational model of transcription factor binding sites for a histone promoter in D. melanogaster.
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  A. V. S. K. Mohan Katta, Rajeshwari Marikkannu, Rajiv V. Basaiawmoit, Sankaran Krishnaswamy: Consensus based validation of membrane porins.
• 
  Shashi B. Pandit, Narayanaswamy Srinivasan: Identification and analysis of a new family of bacterial serine proteinases.
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  Tannistha Nandi, Samir K. Brahmachari, Krishnamoorthy Kannan, Srinivasan Ramachandran: Clusters of proteins in archaeal and bacterial proteomes using compositional analysis.
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  Oriel Bergig, Danny Barash, Evgeny Nudler, Klara Kedem: STR2: A structure to string approach for locating G-box riboswitch shapes in pre-selected genes.
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  Vignesh Muthuvijayan, Mark R. Marten: In silico reconstruction of nutrient-sensing signal transduction pathways in Aspergillus nidulans.

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