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Research
The 16S rRNA is by far the most common genomic marker used for prokaryotic classification, and has been used extensively in metagenomic studies over recent years. Along the 16S gene there are regions with more...
Microbial Informatics and Experimentation 2014 4:2
Published on: 27 January 2014
Review
Deep sequencing harnesses the high throughput nature of next generation sequencing technologies to generate population samples, treating information contained in individual reads as meaningful. Here, we review...
Microbial Informatics and Experimentation 2014 4:1
Published on: 15 January 2014
Research
The Cronobacter genus is composed of seven species, and can cause infections in all age groups. Of particular concern is C. sakazakii, as this species is strongly associated with severe and often fatal cases of n...
Microbial Informatics and Experimentation 2013 3:3
Published on: 24 May 2013
Review
High throughput sequencing is now fast and cheap enough to be considered part of the toolbox for investigating bacteria, and there are thousands of bacterial genome sequences available for comparison in the pu...
Microbial Informatics and Experimentation 2013 3:2
Published on: 10 April 2013
Research
Next generation sequencing (NGS) technologies have revolutionized gene expression studies and functional genomics analysis. However, further improvement of RNA sequencing protocols is still desirable, in order...
Microbial Informatics and Experimentation 2013 3:1
Published on: 7 January 2013
Research
M. tuberculosis infection either induces or inhibits host cell death, depending on the bacterial strain and the cell microenvironment. There is evidence suggesting a role for mitochondria in these processes.
Microbial Informatics and Experimentation 2012 2:9
Published on: 22 December 2012
Research
The genus Mycobacterium comprises different species, among them the most contagious and infectious bacteria. The members of the complex Mycobacterium tuberculosis are the most virulent microorganisms that have ki...
Microbial Informatics and Experimentation 2012 2:7
Published on: 28 August 2012
Research
The thermophilic Campylobacter jejuni and Campylobacter coli are considered weakly clonal populations where incongruences between genetic markers are assumed to be due to random horizontal transfer of genomic DNA...
Microbial Informatics and Experimentation 2012 2:8
Published on: 28 August 2012
Research
The efficiencies of the stop codons TAA, TAG, and TGA in protein synthesis termination are not the same. These variations could allow many genes to be regulated. There are many similar nucleotide trimers found...
Microbial Informatics and Experimentation 2012 2:6
Published on: 31 May 2012
Research
We wanted to compare growth differences between 13 Escherichia coli strains exposed to various concentrations of the growth inhibitor lactoferrin in two different types of broth (Syncase and Luria-Bertani (LB)). ...
Microbial Informatics and Experimentation 2012 2:5
Published on: 16 April 2012
Research
Protein-protein interaction (PPI) networks (interactomes) of most organisms, except for some model organisms, are largely unknown. Experimental methods including high-throughput techniques are highly resource ...
Microbial Informatics and Experimentation 2012 2:4
Published on: 21 March 2012
Review
Metagenomics applies a suite of genomic technologies and bioinformatics tools to directly access the genetic content of entire communities of organisms. The field of metagenomics has been responsible for subst...
Microbial Informatics and Experimentation 2012 2:3
Published on: 9 February 2012
Research
Comparative genomics has put additional demands on the assessment of similarity between sequences and their clustering as means for classification. However, defining the optimal number of clusters, cluster den...
Microbial Informatics and Experimentation 2012 2:2
Published on: 26 January 2012
Review
Microorganisms are ubiquitous on earth and have diverse metabolic transformative capabilities important for environmental biodegradation of chemicals that helps maintain ecosystem and human health. Microbial b...
Microbial Informatics and Experimentation 2012 2:1
Published on: 4 January 2012
Research
Understanding the mechanisms responsible for cellular responses depends on the systematic collection and analysis of information on the main biological concepts involved. Indeed, the identification of biologic...
Microbial Informatics and Experimentation 2011 1:14
Published on: 30 December 2011
Software
Periodic spacing of short adenine or thymine runs phased with DNA helical period of ~10.5 bp is associated with intrinsic DNA curvature and deformability, which play important roles in DNA-protein interactions...
Microbial Informatics and Experimentation 2011 1:13
Published on: 28 November 2011
Research
Although the crocodilepox virus (CRV) is currently unclassified, phylogenetic analyses suggest that its closest known relatives are molluscum contagiosum virus (MCV) and the avipox viruses. The CRV genome is a...
Microbial Informatics and Experimentation 2011 1:12
Published on: 21 November 2011
Book report
There are many things that I like about James Shapiro's new book "Evolution: A View from the 21st Century" (FT Press Science, 2011). He begins the book by saying that it is the creation of novelty, and not sel...
Microbial Informatics and Experimentation 2011 1:11
Published on: 31 October 2011
Letter to the Editor
Microbial Informatics and Experimentation 2011 1:10
Published on: 31 October 2011
Research
DNA-binding transcription factors (TFs) regulate cellular functions in prokaryotes, often in response to environmental stimuli. Thus, the environment exerts constant selective pressure on the TF gene content o...
Microbial Informatics and Experimentation 2011 1:9
Published on: 7 September 2011
Research
Helicobacter pylori HP0958 protein (FlgZ) prevents the rapid turnover of RpoN (σ54), a transcription factor required for expression of several flagellar genes in H. pylori. FlgZ possesses a zinc-ribbon domain (DU...
Microbial Informatics and Experimentation 2011 1:8
Published on: 23 August 2011
Research
The associations between bacteria and environment underlie their preferential interactions with given physical or chemical conditions. Microbial ecology aims at extracting conserved patterns of occurrence of b...
Microbial Informatics and Experimentation 2011 1:7
Published on: 26 July 2011
Research
The biochemical and physical factors controlling protein expression level and solubility in vivo remain incompletely characterized. To gain insight into the primary sequence features influencing these outcomes, w...
Microbial Informatics and Experimentation 2011 1:6
Published on: 27 June 2011
Letter to the Editor
Scientific discovery is incremental. The Merriam-Webster definition of 'Scientific Method' is "principles and procedures for the systematic pursuit of knowledge involving the recognition and formulation of a p...
Microbial Informatics and Experimentation 2011 1:5
Published on: 14 June 2011
Editorial
Microbial Informatics and Experimentation 2011 1:1
Published on: 14 June 2011
