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Microbial Informatics and Experimentation

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  1. Content type: 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...

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

    Citation: Microbial Informatics and Experimentation 2014 4:2

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  2. Content type: 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...

    Authors: Kerensa McElroy, Torsten Thomas and Fabio Luciani

    Citation: Microbial Informatics and Experimentation 2014 4:1

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  3. Content type: 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...

    Authors: Susan Joseph, Sumyya Hariri, Naqash Masood and Stephen Forsythe

    Citation: Microbial Informatics and Experimentation 2013 3:3

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  4. Content type: 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...

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

    Citation: Microbial Informatics and Experimentation 2013 3:1

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  5. Content type: 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.

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

    Citation: Microbial Informatics and Experimentation 2012 2:9

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  6. Content type: 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...

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

    Citation: Microbial Informatics and Experimentation 2012 2:7

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  7. Content type: 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...

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

    Citation: Microbial Informatics and Experimentation 2012 2:8

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  8. Content type: 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)). ...

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

    Citation: Microbial Informatics and Experimentation 2012 2:5

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  9. Content type: 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 ...

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

    Citation: Microbial Informatics and Experimentation 2012 2:4

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  10. Content type: 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...

    Authors: Torsten Thomas, Jack Gilbert and Folker Meyer

    Citation: Microbial Informatics and Experimentation 2012 2:3

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  11. Content type: 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...

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

    Citation: Microbial Informatics and Experimentation 2012 2:2

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  12. Content type: 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...

    Authors: Lynda BM Ellis and Lawrence P Wackett

    Citation: Microbial Informatics and Experimentation 2012 2:1

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  13. Content type: 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...

    Authors: Sónia Carneiro, Anália Lourenço, Eugénio C Ferreira and Isabel Rocha

    Citation: Microbial Informatics and Experimentation 2011 1:14

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  14. Content type: 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...

    Authors: Jan Mrázek, Tejas Chaudhari and Aryabrata Basu

    Citation: Microbial Informatics and Experimentation 2011 1:13

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  15. Content type: 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...

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

    Citation: Microbial Informatics and Experimentation 2011 1:9

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  16. Content type: 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...

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

    Citation: Microbial Informatics and Experimentation 2011 1:8

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  17. Content type: 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...

    Authors: 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

    Citation: Microbial Informatics and Experimentation 2011 1:6

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  18. Content type: 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...

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

    Citation: Microbial Informatics and Experimentation 2011 1:5

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