This paper presents two approaches to the individual-based modelling of bacterial
ecologies and evolution using computational tools. The first approach is a fine-grained
model that is based on networks of interactivity between computational objects
representing genes and proteins. The second approach is a coarser-grained, agent-based
model, which is designed to explore the evolvability of adaptive behavioural
strategies in artificial bacteria represented by learning classifier systems. The
structure and implementation of these computational models is discussed, and some
results from simulation experiments are presented. Finally, the potential applications
of the proposed models to the solution of real-world computational problems, and
their use in improving our understanding of the mechanisms of evolution, are briefly
outlined.

C. Vlachos

R. Gregory

R. C. Paton

J. R. Saunders

Q. H. Wu

Individual-Based Modelling of Bacterial Ecologies and Evolution

This paper gives a brief survey of the use of algebraic rewriting systems for modellingand simulating various biological processes, particularly at the cellular level.

Jean-Louis  Giavitto

Grant  Malcolm

Olivier  Michel

Rewriting Systems and the Modelling of Biological Systems

This paper presents an overview of computational biology approaches and surveys
some of the natural computing models using, in both cases, a formal language-based
approach.

Marian Gheorghe

Victor Mitrana

A Formal Language-Based Approach in Biology

The purpose of this short article is to examine certain aspects of protein functionalitywith relation to some key organizing ideas. This is important from a computationalviewpoint in order to take account of modelling both biological systems andknowledge of these systems. We look at some of the lexical dimensions of thefunction and how certain constructs can be related to underlying ideas. The pervasivecomputational metaphor is then discussed in relation to protein multifunctionality,and the specific case of von Willebrand factor as a &#8216;smart&#8217; multifunctional proteinis briefly considered. Some diagrammatic techniques are then introduced to betterarticulate protein function.

C.-H.  Toh

Computational Aspects of Protein Functionality

Interactions between proteins are essential for intracellular communication. They
form complex networks which have become an important source for functional
analysis of proteins. Combining phylogenies with network analysis, we investigate
the evolutionary history of interaction networks from the bHLH, NR and bZIP
transcription-factor families. The bHLH and NR networks show a hub-like structure
with varying γ values. Mutation and gene duplication play an important role
in adding and removing interactions. We conclude that in several of the protein
families that we have studied, networks have primarily arisen by the development of
heterodimerizing transcription factors, from an ancestral gene which interacts with
any of the newly emerging proteins but also homodimerizes.

Gregory D. Amoutzias

David L. Robertson

Erich Bornberg-Bauer

The Evolution of Protein Interaction Networks in Regulatory Proteins

We have identified four novel repeats and two domains in cell surface proteins
encoded by the Methanosarcina acetivorans genome and in some archaeal and
bacterial genomes. The repeats correspond to a certain number of amino acid residues
present in tandem in a protein sequence and each repeat is characterized by conserved
sequence motifs. These correspond to: (a) a 42 amino acid (aa) residue RIVW repeat;
(b) a 45 aa residue LGxL repeat; (c) a 42 aa residue LVIVD repeat; and (d) a 54 aa
residue LGFP repeat. The domains correspond to a certain number of aa residues in
a protein sequence that do not comprise internal repeats. These correspond to: (a) a
200 aa residue DNRLRE domain; and (b) a 70 aa residue PEGA domain. We discuss
the occurrence of these repeats and domains in the different proteins and genomes
analysed in this work.

S. Adindla

K.  K. Inampudi

K. Guruprasad

L. Guruprasad

Identification and Analysis of Novel Tandem Repeats in the Cell Surface Proteins of Archaeal and Bacterial Genomes Using Computational Tools

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International Journal of Genomics publishes papers in all areas of genome-scale analysis, including bioinformatics, clinical and disease genomics, epigenomics, evolutionary and functional genomics, genome engineering, and synthetic genomics.

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International Journal of Genomics - Table of contents 2004

International Journal of Genomics | Hindawi

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International Journal of Genomics publishes papers in all areas of genome-scale analysis, including bioinformatics, clinical and disease genomics, epigenomics, evolutionary and functional genomics, genome engineering, and synthetic genomics.

International Journal of Genomics