Genome‐Wide Fitness and Genetic Interactions Determined by Tn‐seq, a High‐Throughput Massively Parallel Sequencing Method for Microorganisms: Emerging …

T van Opijnen, DW Lazinski… - Current protocols in …, 2015 - Wiley Online Library
The lagging annotation of bacterial genomes and the inherent genetic complexity of many
phenotypes is hindering the discovery of new drug targets and the development of new …

Escherichia coli as a model organism and its application in biotechnology

VMN Idalia, F Bernardo - … . Biotechnol. Appl. Tech Open Rij. Croat, 2017 - books.google.com
Without a doubt, in the past 20 or so years, we have achieved the power of biology in
different ways. In the present, we have many tools for developing novel technologies and …

[HTML][HTML] Synthetic control of plasmid replication enables target-and self-curing of vectors and expedites genome engineering of Pseudomonas putida

DC Volke, L Friis, NT Wirth, J Turlin, PI Nikel - Metabolic engineering …, 2020 - Elsevier
Genome engineering of non-conventional microorganisms calls for the development of
dedicated synthetic biology tools. Pseudomonas putida is a Gram-negative, non-pathogenic …

Genomic BLAST: custom-defined virtual databases for complete and unfinished genomes

L Cummings, L Riley, L Black… - FEMS Microbiology …, 2002 - academic.oup.com
Abstract BLAST (Basic Local Alignment Search Tool) searches against DNA and protein
sequence databases have become an indispensable tool for biomedical research. The …

VRprofile: gene-cluster-detection-based profiling of virulence and antibiotic resistance traits encoded within genome sequences of pathogenic bacteria

J Li, C Tai, Z Deng, W Zhong, Y He… - Briefings in …, 2018 - academic.oup.com
VRprofile is a Web server that facilitates rapid investigation of virulence and antibiotic
resistance genes, as well as extends these trait transfer-related genetic contexts, in newly …

[HTML][HTML] High quality 3C de novo assembly and annotation of a multidrug resistant ST-111 Pseudomonas aeruginosa genome: Benchmark of hybrid and non-hybrid …

JA Molina-Mora, R Campos-Sánchez, C Rodríguez… - Scientific Reports, 2020 - nature.com
Genotyping methods and genome sequencing are indispensable to reveal genomic
structure of bacterial species displaying high level of genome plasticity. However …

[HTML][HTML] PlasmidMaker is a versatile, automated, and high throughput end-to-end platform for plasmid construction

B Enghiad, P Xue, N Singh, AG Boob, C Shi… - Nature …, 2022 - nature.com
Plasmids are used extensively in basic and applied biology. However, design and
construction of plasmids, specifically the ones carrying complex genetic information, remains …

Engineering of bacterial strains and vectors for the production of plasmid DNA

DM Bower, KLJ Prather - Applied microbiology and biotechnology, 2009 - Springer
The demand for plasmid DNA (pDNA) is anticipated to increase significantly as DNA
vaccines and non-viral gene therapies enter phase 3 clinical trials and are approved for use …

[HTML][HTML] Reduced evolvability of Escherichia coli MDS42, an IS-less cellular chassis for molecular and synthetic biology applications

K Umenhoffer, T Fehér, G Balikó, F Ayaydin… - Microbial cell …, 2010 - Springer
Background Evolvability is an intrinsic feature of all living cells. However, newly emerging,
evolved features can be undesirable when genetic circuits, designed and fabricated by …

Alliance of Genome Resources Portal: unified model organism research platform

Nucleic acids research, 2020 - academic.oup.com
Abstract The Alliance of Genome Resources (Alliance) is a consortium of the major model
organism databases and the Gene Ontology that is guided by the vision of facilitating …