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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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