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Beginner’s guide to comparative bacterial genome analysis using next-generation sequence data
Tập 3 Số 1 - 2013
Growth comparison of several Escherichia coli strains exposed to various concentrations of lactoferrin using linear spline regression
- 2012
Abstract Background 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)). To carry this out, we present a simple statistical procedure that
separates microbial growth curves that are due to natural random perturbations
and growth curves that ...
Linear normalised hash function for clustering gene sequences and identifying reference sequences from multiple sequence alignments
Tập 2 - Trang 1-11 - 2012
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 density and boundaries for sets
of potentially related sequences of genes with variable degrees of polymorphism
remains a significant challenge. The aim of this study was to develop a method
tha...
Natural genetic engineering: intelligence & design in evolution?
Tập 1 - Trang 1-4 - 2011
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 selection, that is important
in the history of life. In the presence of heritable traits that vary, selection
results in the evolution of a population towards an optimal composition of those
tra...
The Regulatory Network of Pseudomonas aeruginosa
Tập 1 - Trang 1-11 - 2011
Pseudomonas aeruginosa is an important bacterial model due to its metabolic and
pathogenic abilities, which allow it to interact and colonize a wide range of
hosts, including plants and animals. In this work we compile and analyze the
structure and organization of an experimentally supported regulatory network in
this bacterium. The regulatory network consists of 690 genes and 1020 regulatory
inte...
Bioinformatic identification of Mycobacterium tuberculosis proteins likely to target host cell mitochondria: virulence factors?
Tập 2 - Trang 1-10 - 2012
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. On the other hand, it has
been shown that several bacterial proteins are able to target mitochondria,
playing a critical role in bacterial pathogenesis and modulation of cell death.
However, m...
Deep sequencing of evolving pathogen populations: applications, errors, and bioinformatic solutions
Tập 4 - Trang 1-14 - 2014
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 applications of
deep sequencing to pathogen evolution. Pioneering deep sequencing studies from
the virology literature are discussed, such as whole genome Roche-454 sequencing
analyses of th...
Where the bugs are: analyzing distributions of bacterial phyla by descriptor keyword search in the nucleotide database
Tập 1 - Trang 1-8 - 2011
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 bacterial taxa in relation to
defined habitats and contexts. In the present report the NCBI nucleotide
sequence database is used as dataset to extract information relative to the
distribution ...