Evolutionary potential, cross-stress behavior and the genetic basis of acquired stress resistance in Escherichia coli

Visualizing evolution in real time to determine the molecular mechanisms of n-butanol tolerance in Escherichia coli

(2012) Luis H. Reyes et al.   METABOLIC ENGINEERING

A memory-efficient data structure representing exact-match overlap graphs with application for next-generation DNA assembly

(2011) H. Dinh et al.   BIOINFORMATICS

Newly Identified Genetic Variations in Common Escherichia coli MG1655 Stock Cultures

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

Microbial laboratory evolution in the era of genome-scale science

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

Multiple Means to the Same End: The Genetic Basis of Acquired Stress Resistance in Yeast

(2011) David B. Berry et al.   PLoS Genetics

Functional Genomic Study of Exogenous n-Butanol Stress in Escherichia coli

(2010) B. J. Rutherford et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Scaffolding pre-assembled contigs using SSPACE

(2010) Marten Boetzer et al.   BIOINFORMATICS

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

Experimental evolution with E. coli in diverse resource environments. I. Fluctuating environments promote divergence of replicate populations

(2010) Tim F Cooper et al.   BMC EVOLUTIONARY BIOLOGY

Whole-genome sequencing of a laboratory-evolved yeast strain

(2010) Carlos L Araya et al.   BMC GENOMICS

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

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

Escherichia coli rpoB Mutants Have Increased Evolvability in Proportion to Their Fitness Defects

(2010) J. E. Barrick et al.   MOLECULAR BIOLOGY AND EVOLUTION

Regulatory and metabolic rewiring during laboratory evolution of ethanol tolerance in E. coli

(2010) Hani Goodarzi et al.   Molecular Systems Biology

Evolution, genomic analysis, and reconstruction of isobutanol tolerance in Escherichia coli

(2010) Shota Atsumi et al.   Molecular Systems Biology

EcoCyc: a comprehensive database of Escherichia coli biology

(2010) I. M. Keseler et al.   NUCLEIC ACIDS RESEARCH

progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement

(2010) Aaron E. Darling et al.   PLoS One

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

Mutagenesis of the Bacterial RNA Polymerase Alpha Subunit for Improvement of Complex Phenotypes

(2009) D. Klein-Marcuschamer et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Indigenous and Environmental Modulation of Frequencies of Mutation in Lactobacillus plantarum

(2009) R. Machielsen et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Reordering contigs of draft genomes using the Mauve Aligner

(2009) Anna I. Rissman et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Molecular Mechanism of Transcriptional Cascade Initiated by the EvgS/EvgA System inEscherichia coliK-12

(2009) Junji ITOU et al.   BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY

Ischemic Postconditioning as a Novel Avenue to Protect against Brain Injury after Stroke

(2009) Heng Zhao   JOURNAL OF CEREBRAL BLOOD FLOW AND METABOLISM

Adaptive prediction of environmental changes by microorganisms

(2009) Amir Mitchell et al.   NATURE

Changes in Escherichia coli outer membrane subproteome under environmental conditions inducing the viable but nonculturable state

(2008) Alicia Muela et al.   FEMS MICROBIOLOGY ECOLOGY

Genetic Basis of Evolutionary Adaptation by Escherichia coli to Stressful Cycles of Freezing, Thawing and Growth

(2008) S. C. Sleight et al.   GENETICS

Outer Membrane Antigens of the Uropathogen Proteus mirabilis Recognized by the Humoral Response during Experimental Murine Urinary Tract Infection

(2008) G. R. Nielubowicz et al.   INFECTION AND IMMUNITY

Genome-Wide Transcriptional Responses of Escherichia coli K-12 to Continuous Osmotic and Heat Stresses

(2008) T. S. Gunasekera et al.   JOURNAL OF BACTERIOLOGY

Low temperature (23  C) increases expression of biofilm-, cold-shock- and RpoS-dependent genes in Escherichia coli K-12

(2008) C. A. White-Ziegler et al.   MICROBIOLOGY-SGM

Stress-activated Genomic Expression Changes Serve a Preparative Role for Impending Stress in Yeast

(2008) David B. Berry et al.   MOLECULAR BIOLOGY OF THE CELL

Non-fermentative pathways for synthesis of branched-chain higher alcohols as biofuels

(2008) Shota Atsumi et al.   NATURE

Starvation-dependent differential stress resistance protects normal but not cancer cells against high-dose chemotherapy

(2008) L. Raffaghello et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli

(2008) Z. D. Blount et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Predictive Behavior Within Microbial Genetic Networks

(2008) I. Tagkopoulos et al.   SCIENCE

Robustness and evolvability: a paradox resolved

(2007) A. Wagner   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES