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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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