In Silico Biology, Volume 4

Volume 4, 2003

• Takako Takai-Igarashi, Toshihisa Takagi, Edgar Wingender:
  Preface.
  
• 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.
  
• Takeya Kasukawa, Hidemasa Bono, Yoshihide Hayashizaki, Yasushi Okazaki, Hideo Matsuda:
  MaXML: mouse annotation XML.
  
• 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.
  
• Teruyoshi Hishiki, Osamu Ogasawara, Yoshimasa Tsuruoka, Kousaku Okubo:
  Indexing anatomical concepts to OMIM Clinical Synopsis using UMLS Metathesaurus.
  
• Edgar Wingender:
  TRANSPATH, TRANSFAC and CYTOMER as starting points for an ontology of regulatory networks.
  
• Ken-ichiro Fukuda, Yuki Yamagata, Toshihisa Takagi:
  FREX: A query interface for biological processes with hierarchical and recursive structures.
  
• Takako Takai-Igarashi, Riichiro Mizoguchi:
  Cell Signaling Networks Ontology.
  
• Isabel Rojas, Esther Ratsch, Jasmin Saric, Ulrike Wittig:
  Notes on the use of ontologies in the biochemical domain.
  

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

Volume 4, 2004

• Evanthia E. Pashou, Zoi I. Litou, Theodore Liakopoulos, Stavros J. Hamodrakas:
  waveTM: Wavelet-based transmembrane segment prediction.
  
• Arun Krishnan, Kuo-Bin Li, Praveen Issac:
  Rapid detection of conserved regions in protein sequences using wavelets.
  
• Chintalapati Janaki, Rajendra R. Joshi:
  Motif detection in Arabidopsis: Correlation with gene expression data.
  
• Daniel V. Guebel:
  Canonical sensitivities: A useful tool to deal with large perturbations in metabolic network modeling.
  
• Lance W. Hahn, Jason H. Moore:
  Ideal discrimination of discrete clinical endpoints using multilocus genotypes.
  
• Michael Hiller, Rolf Backofen, Stephan Heymann, Anke Busch, Timo Mika Gläßer, Johann Christoph Freytag:
  Efficient prediction of alternative splice forms using protein domain homology.
  
• Hans B. Sieburg, Christa E. Müller-Sieburg:
  Classification of short kinetics by shape.
  
• Kishore R. Sakharkar, Vincent T. K. Chow:
  PPD - Proteome Profile Database.
  
• Adam Ameur, Erik Aurell, Mats Carlsson, Jakub Orzechowski Westholm:
  Global gene expression analysis by combinatorial optimization.
  
• Katja Wegner, Stephan Jansen, Stefan Wuchty, Ralph Gauges, Ursula Kummer:
  combAlign: A protein sequence comparison algorithm considering recombinations.
  
• Huiqing Liu, Hao Han, Jinyan Li, Limsoon Wong:
  Using amino acid patterns to accurately predict translation initiation sites.
  
• Atsushi Doi, Sachie Fujita, Hiroshi Matsuno, Masao Nagasaki, Satoru Miyano:
  Constructing biological pathway models with hybrid functional Petri net.
  
• Tan Chee Meng, Sandeep Somani, Pawan Dhar:
  Modeling and simulation of biological systems with stochasticity.
  
• 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.
  
• Mi Zhou, Yan Cui:
  GeneInfoViz: Constructing and visualizing gene relation networks.
  
• Phillip P. Le, Amit Bahl, Lyle H. Ungar:
  Using prior knowledge to improve genetic network reconstruction from microarray data.
  
• 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.
  
• Limor Kozobay-Avraham, Sergey Hosid, Alexander Bolshoy:
  Curvature distribution in prokaryotic genomes.
  
• 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.
  
• Alexandre G. de Brevern, Cristina Benros, Romain Gautier, Hélène Valadié, Serge A. Hazout, Catherine Etchebest:
  Local backbone structure prediction of proteins.
  
• Meena K. Sakharkar, Vincent T. K. Chow, Pandjassarame Kangueane:
  Distributions of exons and introns in the human genome.
  
• 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.
  
• 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.
  
• 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.
  
• 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.
  
• Seema Namboori, Narayanaswamy Srinivasan, Shashi B. Pandit:
  Recognition of remotely related structural homologues using sequence profiles of aligned homologous protein structures.
  
• Jobst Landgrebe, Frank Bretz, Edgar Brunner:
  Efficient two-sample designs for microarray experiments with biological replications.
  
• 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.
  
• Katja Rateitschak, Tobias Müller, Martin Vingron:
  Annotating significant pairs of transcription factor binding sites in regulatory DNA.
  
• 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.
  
• 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.
  
• Lorenz Bülow, Martin Schindler, Claudia Choi, Reinhard Hehl:
  PathoPlant: a database on plant-pathogen interactions.
  
• 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.
  
• 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.
  
• Tannistha Nandi, Samir K. Brahmachari, Krishnamoorthy Kannan, Srinivasan Ramachandran:
  Clusters of proteins in archaeal and bacterial proteomes using compositional analysis.
  
• Oriel Bergig, Danny Barash, Evgeny Nudler, Klara Kedem:
  STR2: A structure to string approach for locating G-box riboswitch shapes in pre-selected genes.
  
• Vignesh Muthuvijayan, Mark R. Marten:
  In silico reconstruction of nutrient-sensing signal transduction pathways in Aspergillus nidulans.
  

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