Volume 3 2003   Special Issue: 3rd International Conference on Bioinformatics of Genome Regulation and Structure (BGRS 2002)    Editorial Nikolay A. Kolchanov and Ralf Hofestädt The 3rd International Conference on Bioinformatics of Genome Regulation and Structure (BGRS 2002) - Preface - 0001   Article Alexei E. Kazakov, Olga Vassieva, Mikhail S. Gelfand, Andrei Osterman, Ross Overbeek Bioinformatics classification and functional analysis of PhoH homologs 0002   Article Vassily A. Lyubetsky and Vladimir V. V'yugin Methods of horizontal gene transfer determination using phylogenetic data 0003   Article Ludmila V. Danilova, Vassily A. Lyubetsky and Mikhail S. Gelfand An algorithm for identification of regulatory signals in unaligned DNA sequences, its testing and parallel implementation 0004   Article Elena D. Stavrovskaya and Andrey A. Mironov Two genetic algorithms for identification of regulatory signals 0005   Article Christopher R. Lockwood and Timothy M. Frayling Combining genome and mouse knockout expression data to highlight binding sites for the transcription factor HNF1alpha 0006   Article                   Ekaterina Shelest, Alexander E. Kel, Ellen Gößling and Edgar Wingender Prediction of potential C/EBP/NF-kappaB composite elements using matrix-based search methods 0007   Article                   Victor G. Levitsky and Alexey V. Katokhin Recognition of eukaryotic promoters using a genetic algorithm based on iterative discriminant analysis 0008   Article Alexander V. Spirov and David M. Holloway Making the body plan: Precision in the genetic hierarchy of Drosophila embryo segmentation 0009   Article Rustem N. Tchuraev and Alexander V. Galimzyanov Parametric stability evaluation in computer experiments on the mathematical model of Drosophila control gene subnetwork 0010   Article Olga G. Smirnova and Irina L. Stepanenko Application of filter technology in Photomorphogenesis Gene Network 0011   Article Mathias Vandenbogaert and Vsevolod Makeev Analysis of bacterial RM-Systems through genome-scale analysis and related taxonomic issues 0012   Article Olga V. Kel-Margoulis, Dmitri Tchekmenev, Alexander E. Kel, Ellen Goessling, Klaus Hornischer, Birgit Lewicki-Potapov and Edgar Wingender Composition-sensitive analysis of the human genome for regulatory signals 0013   Article Yuri F. Bogdanov, Sergei Y. Dadashev and Tatiana M. Grishaeva In silico search for functionally similar proteins involved in meiosis and recombination in evolutionarily distant organisms 0015   Article Sonja M. Schwarzl, Danzhi Huang, Jeremy C. Smith and Stefan Fischer How well does charge reparametrisation account for solvent screening in molecular mechanics calculations? The example of myosin. 0016   Article Olga V. Kalinina, Vsevolod J. Makeev, Roman A. Sutormin, Mikhail S. Gelfand and Aleksandra B. Rakhmaninova The channel in transporters is formed by residues that are rare in transmembrane helices 0017   Article Lily P. Nizolenko, Alexander G. Bachinsky, Andrey N. Naumochkin, Andrey A. Yarigin and Dmitry A. Grigorovich Database of patterns PROF_PAT, used to detect local similarities 0018   Article                   Andreas Freier, Ralf Hofestädt and Matthias Lange IIUDB: An object-oriented system for modelling, integration and analysis of gene controlled metabolic networks 0019   Article Heike Pospisil, Alexander Herrmann, Harald Pankow and Jens G. Reich A database on alternative splice forms on the Integrated Genetic Map Service (IGMS) 0020          Further regular articles:        Article Daiya Takai and Peter A. Jones The CpG Island Searcher: A new WWW resource 0021   Article Boris Galitsky Revealing the set of mutually correlated positions for the protein families of immunoglobulin fold 0022   Article Hans-Peter Keck and Thomas Wetter Functional classification of proteins using a nearest neighbour algorithm 0023   Article Tannistha Nandi, Krishnamoorthy Kannan and Srinivasan Ramachandran The low complexity proteins from enteric pathogenic bacteria: Taxonomic parallels embedded in diversity 0024   Article Soumita Das and Keya Chaudhuri Identification of a unique IAHP (IcmF associated homologous proteins) cluster in Vibrio cholerae and other proteobacteria through in silico analysis 0025   Article Chad Creighton and Samir Hanash Expression of matrix metalloproteinase 9 (MMP-9/gelatinase B) in adenocarcinomas strongly correlated with expression of immune response genes 0026   Communication Georg Fuellen, Michael Spitzer, Paul Cullen and Stefan Lorkowski BLASTing proteomes, yielding phylogenies 0027     Special Issue: Petri Nets for Metabolic Networks    Editorial Ralf Hofestädt Petri nets and the simulation of metabolic networks 0028   Article Ionela Zevedei-Oancea and Stefan Schuster Topological analysis of metabolic networks based on Petri net theory 0029   Article Ming Chen and Ralf Hofestaedt Quantitative Petri net model of gene regulated metabolic networks in the cell 0030   Article Klaus Voss, Monika Heiner and Ina Koch Steady state analysis of metabolic pathways using Petri nets 0031   Article Hiroshi Matsuno, Yukiko Tanaka, Hitoshi Aoshima, Atsushi Doi, Mika Matsui and Satoru Miyano Biopathways representation and simulation on hybrid functional Petri net 0032          Further regular articles: Communication Arnim Wiezer and Rainer Merkl secureBLAST 0033   Report Nikolai Petrovsky, Christian Schönbach and Vladimir Brusic Bioinformatic strategies for better understanding of immune function 0034   Article Oliviero Carugo Prediction of protein polypeptide fragments exposed to the solvent 0035   Article Chintalapati Janaki and Rajendra R. Joshi Accelerating comparative genomics using parallel computing 0036   Article Maike Tech and Rainer Merkl YACOP: Enhanced gene prediction obtained by a combination of existing methods 0037   Article Miroslava Cuperlovic-Culf, Gilles A. Robichaud, Michel Nardini and Rodney J. Ouellette Investigation of interaction between Pax5 isoforms and thioredoxin using de novo modelling methods 0038   Article Alexander N. Gorban, Andrei Y. Zinovyev and Tatyana G. Popova Seven clusters in genomic triplet distributions 0039

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