Causal mutations from adaptive laboratory evolution are outlined by multiple scales of genome annotations and condition-specificity

Enzyme promiscuity shapes adaptation to novel growth substrates

(2019) Gabriela I Guzmán et al.   Molecular Systems Biology

OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states

(2019) Amitesh Anand et al.   MOLECULAR BIOLOGY AND EVOLUTION

The emergence of adaptive laboratory evolution as an efficient tool for biological discovery and industrial biotechnology

(2019) Troy E. Sandberg et al.   METABOLIC ENGINEERING

Adaptation to the coupling of glycolysis to toxic methylglyoxal production in tpiA deletion strains of Escherichia coli requires synchronized and counterintuitive genetic changes

(2018) Douglas McCloskey et al.   METABOLIC ENGINEERING

Adaptive laboratory evolution resolves energy depletion to maintain high aromatic metabolite phenotypes in Escherichia coli strains lacking the Phosphotransferase System

(2018) Douglas McCloskey et al.   METABOLIC ENGINEERING

Multiple Optimal Phenotypes Overcome Redox and Glycolytic Intermediate Metabolite Imbalances in Escherichia coli pgi Knockout Evolutions

(2018) Douglas McCloskey et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Experimental Design, Population Dynamics, and Diversity in Microbial Experimental Evolution

(2018) Bram Van den Bergh et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Growth Adaptation of gnd and sdhCB Escherichia coli Deletion Strains Diverges From a Similar Initial Perturbation of the Transcriptome

(2018) Douglas McCloskey et al.   Frontiers in Microbiology

A resource of variant effect predictions of single nucleotide variants in model organisms

(2018) Omar Wagih et al.   Molecular Systems Biology

RegulonDB v 10.5: tackling challenges to unify classic and high throughput knowledge of gene regulation in E. coli K-12

(2018) Alberto Santos-Zavaleta et al.   NUCLEIC ACIDS RESEARCH

ALEdb 1.0: a database of mutations from adaptive laboratory evolution experimentation

(2018) Patrick V Phaneuf et al.   NUCLEIC ACIDS RESEARCH

The Gene Ontology Resource: 20 years and still GOing strong

(2018)   NUCLEIC ACIDS RESEARCH

Transposon-mediated directed mutation in bacteria and eukaryotes

(2017) Milton H Saier Jr.   Frontiers in Bioscience-Landmark

Increased production of L-serine in Escherichia coli through Adaptive Laboratory Evolution

(2017) Hemanshu Mundhada et al.   METABOLIC ENGINEERING

Dissecting the genetic and metabolic mechanisms of adaptation to the knockout of a major metabolic enzyme inEscherichia coli

(2017) Christopher P. Long et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Hybrid Sankey diagrams: Visual analysis of multidimensional data for understanding resource use

(2017) R.C. Lupton et al.   RESOURCES CONSERVATION AND RECYCLING

Tempo and mode of genome evolution in a 50,000-generation experiment

(2016) Olivier Tenaillon et al.   NATURE

Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center

(2016) Alice R. Wattam et al.   NUCLEIC ACIDS RESEARCH

UniProt: the universal protein knowledgebase

(2016)   NUCLEIC ACIDS RESEARCH

The EcoCyc database: reflecting new knowledge aboutEscherichia coliK-12

(2016) Ingrid M. Keseler et al.   NUCLEIC ACIDS RESEARCH

Evolution of E. coli on [U-13C]Glucose Reveals a Negligible Isotopic Influence on Metabolism and Physiology

(2016) Troy E. Sandberg et al.   PLoS One

RegulonDB version 9.0: high-level integration of gene regulation, coexpression, motif clustering and beyond

(2015) Socorro Gama-Castro et al.   NUCLEIC ACIDS RESEARCH

Pan-Cancer Analysis of Mutation Hotspots in Protein Domains

(2015) Martin L. Miller et al.   Cell Systems

Use of Adaptive Laboratory Evolution To Discover Key Mutations Enabling Rapid Growth of Escherichia coli K-12 MG1655 on Glucose Minimal Medium

(2014) Ryan A. LaCroix et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The enduring utility of continuous culturing in experimental evolution

(2014) David Gresham et al.   GENOMICS

Evolution of Escherichia coli to 42 °C and Subsequent Genetic Engineering Reveals Adaptive Mechanisms and Novel Mutations

(2014) Troy E. Sandberg et al.   MOLECULAR BIOLOGY AND EVOLUTION

Dynamic Large-Scale Chromosomal Rearrangements Fuel Rapid Adaptation in Yeast Populations

(2013) Shang-Lin Chang et al.   PLoS Genetics

Rate and molecular spectrum of spontaneous mutations in the bacterium Escherichia coli as determined by whole-genome sequencing

(2012) H. Lee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Chromosomal duplication is a transient evolutionary solution to stress

(2012) A. H. Yona et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Molecular Diversity of Adaptive Convergence

(2012) O. Tenaillon et al.   SCIENCE

Newly Identified Genetic Variations in Common Escherichia coli MG1655 Stock Cultures

(2011) P. L. Freddolino et al.   JOURNAL OF BACTERIOLOGY

Functional and Metabolic Effects of Adaptive Glycerol Kinase (GLPK) Mutants inEscherichia coli

(2011) M. Kenyon Applebee et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Whole-genome sequencing of a laboratory-evolved yeast strain

(2010) Carlos L Araya et al.   BMC GENOMICS

Genetic Basis of Growth Adaptation of Escherichia coli after Deletion of pgi, a Major Metabolic Gene

(2010) Pep Charusanti et al.   PLoS Genetics

Role of the sRNA GcvB in regulation of cycA in Escherichia coli

(2009) S. C. Pulvermacher et al.   MICROBIOLOGY-SGM

Whole-genome resequencing of Escherichia coli K-12 MG1655 undergoing short-term laboratory evolution in lactate minimal media reveals flexible selection of adaptive mutations

(2009) Tom M Conrad et al.   GENOME BIOLOGY

The mechanisms of carbon catabolite repression in bacteria

(2008) Josef Deutscher   CURRENT OPINION IN MICROBIOLOGY

Carbon catabolite repression in bacteria: many ways to make the most out of nutrients

(2008) Boris Görke et al.   NATURE REVIEWS MICROBIOLOGY

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

(2008) Da Wei Huang et al.   NUCLEIC ACIDS RESEARCH