Using genome-scale models to predict biological capabilities
Constraint-based reconstruction and analysis (COBRA) methods at the genome scale have
been under development since the first whole-genome sequences appeared in the mid …
been under development since the first whole-genome sequences appeared in the mid …
[HTML][HTML] Automating the design-build-test-learn cycle towards next-generation bacterial cell factories
Automation is playing an increasingly significant role in synthetic biology. Groundbreaking
technologies, developed over the past 20 years, have enormously accelerated the …
technologies, developed over the past 20 years, have enormously accelerated the …
Mutant phenotypes for thousands of bacterial genes of unknown function
MN Price, KM Wetmore, RJ Waters, M Callaghan… - Nature, 2018 - nature.com
One-third of all protein-coding genes from bacterial genomes cannot be annotated with a
function. Here, to investigate the functions of these genes, we present genome-wide mutant …
function. Here, to investigate the functions of these genes, we present genome-wide mutant …
iML1515, a knowledgebase that computes Escherichia coli traits
Figure 1 iML1515 genome-scale reconstruction.(a) The iML1515 model contains 1,515
open reading frames that encode enzymes that catalyze 2,719 reactions involving 1,192 …
open reading frames that encode enzymes that catalyze 2,719 reactions involving 1,192 …
Construction and analysis of two genome-scale deletion libraries for Bacillus subtilis
A systems-level understanding of Gram-positive bacteria is important from both an
environmental and health perspective and is most easily obtained when high-quality …
environmental and health perspective and is most easily obtained when high-quality …
The Essential Genome of Escherichia coli K-12
Transposon-directed insertion site sequencing (TraDIS) is a high-throughput method
coupling transposon mutagenesis with short-fragment DNA sequencing. It is commonly used …
coupling transposon mutagenesis with short-fragment DNA sequencing. It is commonly used …
Pooled CRISPR interference screening enables genome-scale functional genomics study in bacteria with superior performance
To fully exploit the microbial genome resources, a high-throughput experimental platform is
needed to associate genes with phenotypes at the genome level. We present here a novel …
needed to associate genes with phenotypes at the genome level. We present here a novel …
[HTML][HTML] Phenotypic landscape of a bacterial cell
The explosion of sequence information in bacteria makes developing high-throughput, cost-
effective approaches to matching genes with phenotypes imperative. Using E. coli as proof …
effective approaches to matching genes with phenotypes imperative. Using E. coli as proof …
Genome-wide CRISPR-dCas9 screens in E. coli identify essential genes and phage host factors
High-throughput genetic screens are powerful methods to identify genes linked to a given
phenotype. The catalytic null mutant of the Cas9 RNA-guided nuclease (dCas9) can be …
phenotype. The catalytic null mutant of the Cas9 RNA-guided nuclease (dCas9) can be …
A comprehensive genome‐scale reconstruction of Escherichia coli metabolism—2011
The initial genome‐scale reconstruction of the metabolic network of Escherichia coli K‐12
MG1655 was assembled in 2000. It has been updated and periodically released since then …
MG1655 was assembled in 2000. It has been updated and periodically released since then …