微生物学技术

Phylogenetic profiling involves the comparison of phylogenetic data across gene families. It is possible to construct phylogenetic trees, or related data structures, for specific gene families using a wide variety of tools and approaches. Phylogenetic profiling involves the com ...

Public online microarray databases contain tremendous amounts of expression data. Mining these data sources can provide a wealth of information on the underlying transcriptional networks. In this chapter, we illustrate how the web services COLOMBOS and DISTILLER can be used to ident ...

Various methods result in groups of functionally related genes obtained from genomes (operons, regulons, syntheny groups, and phylogenetic profiles), transcriptomes (co-expression groups) and proteomes (modules of interacting proteins). When such groups contain two or more ...

Enzymatic reactions form a hypergraph structure and their translation into a graph structure accompanies an information loss. This chapter introduces well-known topological transformations from metabolic reactions to a graph, and discusses their advantages and disadvan ...

The tree of life is the classical representation of the evolutionary relationships between existent species. A tree is appropriate to display the divergence of species through mutation, i.e., by vertical descent. However, lateral gene transfer (LGT) is excluded from such representati ...

The importance of horizontal/lateral gene transfer (LGT) in shaping the genomes of prokaryotic organisms has been recognized in recent years as a result of analysis of the increasing number of available genome sequences. LGT is largely due to the transfer and recombination activities of m ...

Metagenomics is revolutionizing the field of microbial ecology through techniques that eliminate the prerequisite of culturing. Metagenomic studies of microbial populations in different environments reveal the incredible diversity and adaptive capabilities of these ...

In order to ensure their function(s) in the cell, proteins are organized in machineries, underlaid by a complex network of interactions. Identifying protein interactions is thus crucial to our understanding of cell functioning. Technical advances in molecular biology and genomic tec ...

The BioCyc database collection at BioCyc.org integrates genome and cellular network information for more than 1,100 organisms. This method chapter describes Web-based tools for browsing metabolic and regulatory networks within BioCyc. These tools allow visualization of comp ...

RegulonDB contains the largest and currently best-known data set on transcriptional regulation in a single free-living organism, that of Escherichia coli K-12 (Gama-Castro et al. Nucleic Acids Res 36:D120–D124, 2008). This organized knowledge has been the gold standard for the impleme ...

This introductory review synthesizes the contents of the volume Bacterial Molecular Networks of the series Methods in Molecular Biology. This volume gathers 9 reviews and 16 method chapters describing computational protocols for the analysis of metabolic pathways, protein inte ...

Interactions between macromolecules are deciphered to gain information about biological processes and protein function. This information is hidden in large interaction networks, yet very complicated to dissect. In this context, the PRODISTIN Web site is dedicated to the cluster ...

In this chapter, we present and interpret some operations on biological networks that can easily performed with NeAT, a set of Web tools aimed at studying biological networks (or graphs) and classifications. These approaches are of particular interest for biologists and scientists who ne ...

R is a powerful language and widely used software tool for the analysis and visualization of data. Its core capabilities can be extended through many different add-on packages. Among the many packages are some which offer a broad range of facilities for analyzing statistical properties of gra ...

The detection and analysis of structural invariants in cellular reaction networks is of central importance to achieve a more comprehensive understanding of metabolism. In this work, we review different kinds of structural invariants in reaction networks and their Petri net-based r ...

Using the example of phosphate regulation in enteric bacteria, we demonstrate the particular suitability of stochastic Petri nets to model biochemical phenomena and their simulative exploration by various features of the software tool Snoopy.

Genetic Network Analyzer (GNA) is a tool for the qualitative modeling and simulation of gene regulatory networks, based on so-called piecewise-linear differential equation models. We describe the use of this tool in the context of the modeling of bacterial regulatory networks, notably t ...

Mutualistic microbial symbioses are one of the key innovations in the evolution of biological diversity, enabling the expansion of species’ niches and the production of sophisticated structures such as the eukaryotic cell. For some of the best-studied cases, we are beginning to have netw ...

Bacterial virulence is a multifactorial process. In this chapter, we review some known mechanisms used by bacteria to trigger their production of virulence factors. We develop the idea that although the onset of virulence shows up an abrupt transition, the modelling of this dynamics can be cla ...

This chapter describes how to use Smoldyn, which is a computer program for modeling cellular systems with spatial and stochastic detail. Smoldyn represents each molecule of interest as an individual point-like particle. These simulated molecules diffuse, interact with surfaces (e. ...