Transposon-based and plasmid-based genetic tools for editing genomes of gram-negative bacteria
E Martínez-García, V de Lorenzo - Synthetic gene networks: methods and …, 2012 - Springer
A good part of the contemporary synthetic biology agenda aims at reprogramming
microorganisms to enhance existing functions and/or perform new tasks. Moreover, the …
microorganisms to enhance existing functions and/or perform new tasks. Moreover, the …
Searching for drug targets in microbial genomes
MY Galperin, EV Koonin - Current opinion in biotechnology, 1999 - Elsevier
Comparative analysis of the complete genome sequences of 10 bacterial pathogens
available in the public databases offers the first insights into the drug discovery approaches …
available in the public databases offers the first insights into the drug discovery approaches …
Prokaryotic gene clusters: a rich toolbox for synthetic biology
M Fischbach, CA Voigt - Biotechnology journal, 2010 - Wiley Online Library
Bacteria construct elaborate nanostructures, obtain nutrients and energy from diverse
sources, synthesize complex molecules, and implement signal processing to react to their …
sources, synthesize complex molecules, and implement signal processing to react to their …
Targeted development of registries of biological parts
Background The design and construction of novel biological systems by combining basic
building blocks represents a dominant paradigm in synthetic biology. Creating and …
building blocks represents a dominant paradigm in synthetic biology. Creating and …
[HTML][HTML] The limitations of draft assemblies for understanding prokaryotic adaptation and evolution
N Ricker, H Qian, RR Fulthorpe - Genomics, 2012 - Elsevier
The de novo assembly of next generation sequencing data is a daunting task made more
difficult by the presence of genomic repeats or transposable elements, resulting in an …
difficult by the presence of genomic repeats or transposable elements, resulting in an …
MOB-suite: software tools for clustering, reconstruction and typing of plasmids from draft assemblies
J Robertson, JHE Nash - Microbial genomics, 2018 - microbiologyresearch.org
Large-scale bacterial population genetics studies are now routine due to cost-effective
Illumina short-read sequencing. However, analysing plasmid content remains difficult due to …
Illumina short-read sequencing. However, analysing plasmid content remains difficult due to …
Scaffolding and validation of bacterial genome assemblies using optical restriction maps
Motivation: New, high-throughput sequencing technologies have made it feasible to cheaply
generate vast amounts of sequence information from a genome of interest. The …
generate vast amounts of sequence information from a genome of interest. The …
Alternative hosts for functional (meta) genome analysis
Microorganisms are ubiquitous on earth, often forming complex microbial communities in
numerous different habitats. Most of these organisms cannot be readily cultivated in the …
numerous different habitats. Most of these organisms cannot be readily cultivated in the …
Rational design of a plasmid origin that replicates efficiently in both gram-positive and gram-negative bacteria
AV Bryksin, I Matsumura - PloS one, 2010 - journals.plos.org
Background Most plasmids replicate only within a particular genus or family.
Methodology/Principal Findings Here we describe an engineered high copy number …
Methodology/Principal Findings Here we describe an engineered high copy number …
plasmidSPAdes: assembling plasmids from whole genome sequencing data
Motivation: Plasmids are stably maintained extra-chromosomal genetic elements that
replicate independently from the host cell's chromosomes. Although plasmids harbor …
replicate independently from the host cell's chromosomes. Although plasmids harbor …