Experimental evolution of diverse Escherichia coli metabolic mutants identifies genetic loci for convergent adaptation of growth rate

Synthetic rescue couples NADPH generation to metabolite overproduction in Saccharomyces cerevisiae

(2017) Siavash Partow et al.   METABOLIC ENGINEERING

Genomewide Mutational Diversity in Escherichia coli Population Evolving in Prolonged Stationary Phase

(2017) Savita Chib et al.   mSphere

Structure and function of bacterial H-NS protein

(2016) D. C. Grainger   BIOCHEMICAL SOCIETY TRANSACTIONS

PANTHER version 11: expanded annotation data from Gene Ontology and Reactome pathways, and data analysis tool enhancements

(2016) Huaiyu Mi 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

Exploring genetic suppression interactions on a global scale

(2016) J. van Leeuwen et al.   SCIENCE

A global genetic interaction network maps a wiring diagram of cellular function

(2016) M. Costanzo et al.   SCIENCE

Global Rebalancing of Cellular Resources by Pleiotropic Point Mutations Illustrates a Multi-scale Mechanism of Adaptive Evolution

(2016) Jose Utrilla et al.   Cell Systems

Bacterial protein networks: properties and functions

(2015) Athanasios Typas et al.   NATURE REVIEWS MICROBIOLOGY

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

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

Structural Basis of Transcription Inhibition by CBR Hydroxamidines and CBR Pyrazoles

(2015) Yu Feng et al.   STRUCTURE

Decoding genome-wide GadEWX-transcriptional regulatory networks reveals multifaceted cellular responses to acid stress in Escherichia coli

(2015) Sang Woo Seo et al.   Nature Communications

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

Resistance to rifampicin: a review

(2014) Beth P Goldstein   JOURNAL OF ANTIBIOTICS

An integrative, multi-scale, genome-wide model reveals the phenotypic landscape of Escherichia coli

(2014) J. Carrera et al.   Molecular Systems Biology

The predictability of molecular evolution during functional innovation

(2014) D. Blank et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CBR antimicrobials alter coupling between the bridge helix and the β subunit in RNA polymerase

(2014) Anssi M. Malinen et al.   Nature Communications

The Genomic Landscape of Compensatory Evolution

(2014) Béla Szamecz et al.   PLOS BIOLOGY

Dimerization of Bacterial Diaminopimelate Epimerase Is Essential for Catalysis

(2013) Lilian Hor et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The Magic Spot: A ppGpp Binding Site on E. coli RNA Polymerase Responsible for Regulation of Transcription Initiation

(2013) Wilma Ross et al.   MOLECULAR CELL

Genome dynamics during experimental evolution

(2013) Jeffrey E. Barrick et al.   NATURE REVIEWS GENETICS

The genetic causes of convergent evolution

(2013) David L. Stern   NATURE REVIEWS GENETICS

Computational analysis of bacterial RNA-Seq data

(2013) Ryan McClure et al.   NUCLEIC ACIDS RESEARCH

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

(2012) M. Kearse et al.   BIOINFORMATICS

Isolation and Characterization of RNA PolymeraserpoBMutations That Alter Transcription Slippage during Elongation inEscherichia coli

(2012) Yan Ning Zhou et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The Molecular Diversity of Adaptive Convergence

(2012) O. Tenaillon et al.   SCIENCE

Structural Basis of Transcription Initiation

(2012) Y. Zhang et al.   SCIENCE

Evolution combined with genomic study elucidates genetic bases of isobutanol tolerance in Escherichia coli

(2011) Jeremy J Minty et al.   Microbial Cell Factories

The Base-Pairing RNA Spot 42 Participates in a Multioutput Feedforward Loop to Help Enact Catabolite Repression in Escherichia coli

(2011) Chase L. Beisel et al.   MOLECULAR CELL

Assembly and stability of flagellar motor in Escherichia coli

(2011) Hui Li et al.   MOLECULAR MICROBIOLOGY

Microbial laboratory evolution in the era of genome-scale science

(2011) T. M. Conrad et al.   Molecular Systems Biology

Evolutionary paths to antibiotic resistance under dynamically sustained drug selection

(2011) Erdal Toprak et al.   NATURE GENETICS

Dispensability of Escherichia coli's latent pathways

(2011) S. P. Cornelius et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Stress-induced evolution of Escherichia coli points to original concepts in respiratory cofactor selectivity

(2011) C. Auriol et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Diminishing Returns Epistasis Among Beneficial Mutations Decelerates Adaptation

(2011) H.-H. Chou et al.   SCIENCE

Adaptive Evolution of Escherichia coli K-12 MG1655 during Growth on a Nonnative Carbon Source, L-1,2-Propanediol

(2010) D.-H. Lee et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Improved network performance via antagonism: From synthetic rescues to multi-drug combinations

(2010) Adilson E. Motter   BIOESSAYS

Divergence Involving Global Regulatory Gene Mutations in an Escherichia coli Population Evolving under Phosphate Limitation

(2010) Lei Wang et al.   Genome Biology and Evolution

The NusA N-Terminal Domain Is Necessary and Sufficient for Enhancement of Transcriptional Pausing via Interaction with the RNA Exit Channel of RNA Polymerase

(2010) Kook Sun Ha et al.   JOURNAL OF MOLECULAR BIOLOGY

The Effect of Mobile Element IS10 on Experimental Regulatory Evolution in Escherichia coli

(2010) D. M. Stoebel et al.   MOLECULAR BIOLOGY AND EVOLUTION

Antagonistic regulation of motility and transcriptome expression by RpoN and RpoS in Escherichia coli

(2010) Tao Dong et al.   MOLECULAR MICROBIOLOGY

RNA polymerase mutants found through adaptive evolution reprogram Escherichia coli for optimal growth in minimal media

(2010) T. M. Conrad et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Complete Structural Model of Escherichia coli RNA Polymerase from a Hybrid Approach

(2010) Natacha Opalka et al.   PLOS BIOLOGY

Transition from Positive to Neutral in Mutation Fixation along with Continuing Rising Fitness in Thermal Adaptive Evolution

(2010) Toshihiko Kishimoto et al.   PLoS Genetics

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

(2010) Pep Charusanti et al.   PLoS Genetics

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Structures of RNA polymerase–antibiotic complexes

(2009) Mary X Ho et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Genome evolution and adaptation in a long-term experiment with Escherichia coli

(2009) Jeffrey E. Barrick et al.   NATURE

Global discovery of adaptive mutations

(2009) Hani Goodarzi et al.   NATURE METHODS

Control of RpoS in global gene expression of Escherichia coli in minimal media

(2008) Tao Dong et al.   MOLECULAR GENETICS AND GENOMICS

Predicting synthetic rescues in metabolic networks

(2008) Adilson E Motter et al.   Molecular Systems Biology

eSGA: E. coli synthetic genetic array analysis

(2008) Gareth Butland et al.   NATURE METHODS

High-throughput, quantitative analyses of genetic interactions in E. coli

(2008) Athanasios Typas et al.   NATURE METHODS

Spontaneous Reaction Silencing in Metabolic Optimization

(2008) Takashi Nishikawa et al.   PLoS Computational Biology