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  1. Research

    A systematic search for discriminating sites in the 16S ribosomal RNA gene

    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...

    Hilde Vinje, Trygve Almøy, Kristian Hovde Liland and Lars Snipen

    Microbial Informatics and Experimentation 2014 4:2

    Published on: 27 January 2014

  2. Research

    Sialic acid utilization by Cronobacter sakazakii

    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...

    Susan Joseph, Sumyya Hariri, Naqash Masood and Stephen Forsythe

    Microbial Informatics and Experimentation 2013 3:3

    Published on: 24 May 2013

  3. Research

    An efficient rRNA removal method for RNA sequencing in GC-rich bacteria

    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...

    Clelia Peano, Alessandro Pietrelli, Clarissa Consolandi, Elio Rossi, Luca Petiti, Letizia Tagliabue, Gianluca De Bellis and Paolo Landini

    Microbial Informatics and Experimentation 2013 3:1

    Published on: 7 January 2013

  4. Research

    Bioinformatic identification of Mycobacterium tuberculosis proteins likely to target host cell mitochondria: virulence factors?

    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.

    María Maximina Bertha Moreno-Altamirano, Iris Selene Paredes-González, Clara Espitia, Mauricio Santiago-Maldonado, Rogelio Hernández-Pando and Francisco Javier Sánchez-García

    Microbial Informatics and Experimentation 2012 2:9

    Published on: 22 December 2012

  5. Research

    Computational genomics-proteomics and Phylogeny analysis of twenty one mycobacterial genomes (Tuberculosis & non Tuberculosis strains)

    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...

    Fathiah Zakham, Othmane Aouane, David Ussery, Abdelaziz Benjouad and Moulay Mustapha Ennaji

    Microbial Informatics and Experimentation 2012 2:7

    Published on: 28 August 2012

  6. Research

    Analysis of evolutionary patterns of genes in Campylobacter jejuni and C. coli

    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...

    Lars Snipen, Trudy M Wassenaar, Eric Altermann, Jonathan Olson, Sophia Kathariou, Karin Lagesen, Monica Takamiya, Susanne Knøchel, David W Ussery and Richard J Meinersmann

    Microbial Informatics and Experimentation 2012 2:8

    Published on: 28 August 2012

  7. Research

    Growth comparison of several Escherichia coli strains exposed to various concentrations of lactoferrin using linear spline regression

    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)). ...

    Camilla Sekse, Jon Bohlin, Eystein Skjerve and Gerd E Vegarud

    Microbial Informatics and Experimentation 2012 2:5

    Published on: 16 April 2012

  8. Research

    Mycobacterium tuberculosis and Clostridium difficille interactomes: demonstration of rapid development of computational system for bacterial interactome prediction

    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 ...

    Seshan Ananthasubramanian, Rahul Metri, Ankur Khetan, Aman Gupta, Adam Handen, Nagasuma Chandra and Madhavi Ganapathiraju

    Microbial Informatics and Experimentation 2012 2:4

    Published on: 21 March 2012

  9. Review

    Metagenomics - a guide from sampling to data analysis

    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...

    Torsten Thomas, Jack Gilbert and Folker Meyer

    Microbial Informatics and Experimentation 2012 2:3

    Published on: 9 February 2012

  10. Research

    Linear normalised hash function for clustering gene sequences and identifying reference sequences from multiple sequence alignments

    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...

    Manal Helal, Fanrong Kong, Sharon CA Chen, Fei Zhou, Dominic E Dwyer, John Potter and Vitali Sintchenko

    Microbial Informatics and Experimentation 2012 2:2

    Published on: 26 January 2012

  11. Research

    Prediction of a novel RNA binding domain in crocodilepox Zimbabwe Gene 157

    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...

    Nicole S Little, Taylor Quon and Chris Upton

    Microbial Informatics and Experimentation 2011 1:12

    Published on: 21 November 2011

  12. Book report

    Natural genetic engineering: intelligence & design in evolution?

    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...

    David W Ussery

    Microbial Informatics and Experimentation 2011 1:11

    Published on: 31 October 2011

  13. Research

    Quantifying the effect of environment stability on the transcription factor repertoire of marine microbes

    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...

    Ivaylo Kostadinov, Renzo Kottmann, Alban Ramette, Jost Waldmann, Pier Luigi Buttigieg and Frank Oliver Glöckner

    Microbial Informatics and Experimentation 2011 1:9

    Published on: 7 September 2011

  14. Research

    The zinc-ribbon domain of Helicobacter pylori HP0958: requirement for RpoN accumulation and possible roles of homologs in other bacteria

    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...

    Lara E Pereira, Jennifer Tsang, Jan Mrázek and Timothy R Hoover

    Microbial Informatics and Experimentation 2011 1:8

    Published on: 23 August 2011

  15. Research

    Large-scale experimental studies show unexpected amino acid effects on protein expression and solubility in vivo in E. coli

    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...

    W Nicholson Price II, Samuel K Handelman, John K Everett, Saichiu N Tong, Ana Bracic, Jon D Luff, Victor Naumov, Thomas Acton, Philip Manor, Rong Xiao, Burkhard Rost, Gaetano T Montelione and John F Hunt

    Microbial Informatics and Experimentation 2011 1:6

    Published on: 27 June 2011

  16. Letter to the Editor

    The importance of metagenomic surveys to microbial ecology: or why Darwin would have been a metagenomic scientist

    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...

    Jack A Gilbert, Ronald O'Dor, Nicholas King and Timothy M Vogel

    Microbial Informatics and Experimentation 2011 1:5

    Published on: 14 June 2011

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