Published in Am Nat on July 12, 2006
Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli. Proc Natl Acad Sci U S A (2008) 5.29
Trait variation in yeast is defined by population history. PLoS Genet (2011) 2.50
The Beagle in a bottle. Nature (2009) 2.11
Metabolic trade-offs and the maintenance of the fittest and the flattest. Nature (2011) 1.82
An experimental test of evolutionary trade-offs during temperature adaptation. Proc Natl Acad Sci U S A (2007) 1.62
Host imprints on bacterial genomes--rapid, divergent evolution in individual patients. PLoS Pathog (2010) 1.54
Constraint-based model of Shewanella oneidensis MR-1 metabolism: a tool for data analysis and hypothesis generation. PLoS Comput Biol (2010) 1.48
Metabolic-network-driven analysis of bacterial ecological strategies. Genome Biol (2009) 1.44
Experimental evolution with E. coli in diverse resource environments. I. Fluctuating environments promote divergence of replicate populations. BMC Evol Biol (2010) 1.30
Metabolic erosion primarily through mutation accumulation, and not tradeoffs, drives limited evolution of substrate specificity in Escherichia coli. PLoS Biol (2014) 1.29
Different levels of catabolite repression optimize growth in stable and variable environments. PLoS Biol (2014) 1.28
Economics of membrane occupancy and respiro-fermentation. Mol Syst Biol (2011) 1.23
An integrative approach to understanding microbial diversity: from intracellular mechanisms to community structure. Ecol Lett (2010) 1.21
Resource supply and the evolution of public-goods cooperation in bacteria. BMC Biol (2008) 1.16
Dissecting the logical types of network control in gene expression profiles. BMC Syst Biol (2008) 1.12
Mutational neighbourhood and mutation supply rate constrain adaptation in Pseudomonas aeruginosa. Proc Biol Sci (2009) 1.10
The ability of flux balance analysis to predict evolution of central metabolism scales with the initial distance to the optimum. PLoS Comput Biol (2013) 1.06
The multiplicity of divergence mechanisms in a single evolving population. Genome Biol (2012) 1.05
A framework for evolutionary systems biology. BMC Syst Biol (2009) 1.05
Surviving the bottleneck: transmission mutants and the evolution of microbial populations. Genetics (2008) 1.00
Availability of public goods shapes the evolution of competing metabolic strategies. Proc Natl Acad Sci U S A (2013) 0.99
A critical view of metabolic network adaptations. HFSP J (2008) 0.98
Evolution of penicillin-binding protein 2 concentration and cell shape during a long-term experiment with Escherichia coli. J Bacteriol (2008) 0.97
Cryptic fitness advantage: diploids invade haploid populations despite lacking any apparent advantage as measured by standard fitness assays. PLoS One (2011) 0.97
Pathways to extinction: beyond the error threshold. Philos Trans R Soc Lond B Biol Sci (2010) 0.97
NADH availability limits asymmetric biocatalytic epoxidation in a growing recombinant Escherichia coli strain. Appl Environ Microbiol (2008) 0.96
The components of kin competition. Evolution (2010) 0.95
Increased susceptibility to repeated freeze-thaw cycles in Escherichia coli following long-term evolution in a benign environment. BMC Evol Biol (2006) 0.92
"Ant" and "grasshopper" life-history strategies in Saccharomyces cerevisiae. PLoS One (2008) 0.89
Role of pleiotropy during adaptation of TEM-1 β-lactamase to two novel antibiotics. Evol Appl (2014) 0.89
Resource availability and competition shape the evolution of survival and growth ability in a bacterial community. PLoS One (2013) 0.88
The yield of experimental yeast populations declines during selection. Proc Biol Sci (2012) 0.85
Microbial resource utilization traits and trade-offs: implications for community structure, functioning, and biogeochemical impacts at present and in the future. Front Microbiol (2015) 0.84
Ex uno plures: clonal reinforcement drives evolution of a simple microbial community. PLoS Genet (2014) 0.83
Ube2g2-gp78-mediated HERP polyubiquitylation is involved in ER stress recovery. J Cell Sci (2014) 0.81
First steps in experimental cancer evolution. Evol Appl (2013) 0.79
Population level analysis of evolved mutations underlying improvements in plant hemicellulose and cellulose fermentation by Clostridium phytofermentans. PLoS One (2014) 0.77
Evolution of parasitism and mutualism between filamentous phage M13 and Escherichia coli. PeerJ (2016) 0.77
Bacterial Quorum Sensing Stabilizes Cooperation by Optimizing Growth Strategies. Appl Environ Microbiol (2016) 0.76
Trade-offs drive resource specialization and the gradual establishment of ecotypes. BMC Evol Biol (2014) 0.76
The complex relationship between microbial growth rate and yield and its implications for ecosystem processes. Front Microbiol (2015) 0.75
Saturating effects of species diversity on life-history evolution in bacteria. Proc Biol Sci (2015) 0.75
Algae for biofuel: will the evolution of weeds limit the enterprise? Evolution (2012) 0.75
Metabolic variability in micro-populations. PLoS One (2012) 0.75
Nitrous Oxide Reduction Kinetics Distinguish Bacteria Harboring Clade I NosZ from Those Harboring Clade II NosZ. Appl Environ Microbiol (2016) 0.75
Competing metabolic strategies in a multilevel selection model. R Soc Open Sci (2016) 0.75
Experimental evolution of the grain of metabolic specialization in yeast. Ecol Evol (2016) 0.75
Difference in C3-C4 metabolism underlies tradeoff between growth rate and biomass yield in Methylobacterium extorquens AM1. BMC Microbiol (2016) 0.75
Metabolism at evolutionary optimal States. Metabolites (2015) 0.75
Constraints, Trade-offs and the Currency of Fitness. J Mol Evol (2016) 0.75
Evolution of organismal stoichiometry in a long-term experiment with Escherichia coli. R Soc Open Sci (2017) 0.75
Genome evolution and adaptation in a long-term experiment with Escherichia coli. Nature (2009) 11.36
Evolution experiments with microorganisms: the dynamics and genetic bases of adaptation. Nat Rev Genet (2003) 10.52
Robustness of cellular functions. Cell (2004) 6.65
Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli. Proc Natl Acad Sci U S A (2008) 5.29
Parallel changes in gene expression after 20,000 generations of evolution in Escherichiacoli. Proc Natl Acad Sci U S A (2003) 4.63
Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli. Mol Syst Biol (2007) 4.61
A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology. Nat Biotechnol (2008) 4.55
Negative epistasis between beneficial mutations in an evolving bacterial population. Science (2011) 4.47
Genomic analysis of a key innovation in an experimental Escherichia coli population. Nature (2012) 4.35
Metabolic flux profiling of Escherichia coli mutants in central carbon metabolism using GC-MS. Eur J Biochem (2003) 3.51
Tests of parallel molecular evolution in a long-term experiment with Escherichia coli. Proc Natl Acad Sci U S A (2006) 3.39
Genome sequences of Escherichia coli B strains REL606 and BL21(DE3). J Mol Biol (2009) 3.10
Multidimensional optimality of microbial metabolism. Science (2012) 3.09
Metabolic flux responses to pyruvate kinase knockout in Escherichia coli. J Bacteriol (2002) 3.06
Second-order selection for evolvability in a large Escherichia coli population. Science (2011) 3.02
Experimental evolution. Trends Ecol Evol (2012) 3.02
Repeatability and contingency in the evolution of a key innovation in phage lambda. Science (2012) 2.95
Large-scale in vivo flux analysis shows rigidity and suboptimal performance of Bacillus subtilis metabolism. Nat Genet (2005) 2.82
Does evolutionary theory need a rethink? Nature (2014) 2.82
(13)C-based metabolic flux analysis. Nat Protoc (2009) 2.75
High-throughput metabolic flux analysis based on gas chromatography-mass spectrometry derived 13C constraints. Anal Biochem (2004) 2.73
Impact of global transcriptional regulation by ArcA, ArcB, Cra, Crp, Cya, Fnr, and Mlc on glucose catabolism in Escherichia coli. J Bacteriol (2005) 2.70
Natural prevalence of hepatitis C virus variants with decreased sensitivity to NS3.4A protease inhibitors in treatment-naive subjects. J Infect Dis (2008) 2.69
Large-scale 13C-flux analysis reveals mechanistic principles of metabolic network robustness to null mutations in yeast. Genome Biol (2005) 2.68
Metabolic functions of duplicate genes in Saccharomyces cerevisiae. Genome Res (2005) 2.68
A systems analysis of mutational effects in HIV-1 protease and reverse transcriptase. Nat Genet (2011) 2.66
The Black Queen Hypothesis: evolution of dependencies through adaptive gene loss. MBio (2012) 2.58
Emergence of drug-resistant influenza virus: population dynamical considerations. Science (2006) 2.46
Cryptic population dynamics: rapid evolution masks trophic interactions. PLoS Biol (2007) 2.44
Quantitative phosphoproteomics reveal mTORC1 activates de novo pyrimidine synthesis. Science (2013) 2.44
FiatFlux--a software for metabolic flux analysis from 13C-glucose experiments. BMC Bioinformatics (2005) 2.42
Increased systemic perfusion pressure during cardiopulmonary bypass is associated with less early postoperative cognitive dysfunction and delirium. Eur J Cardiothorac Surg (2010) 2.38
Global network reorganization during dynamic adaptations of Bacillus subtilis metabolism. Science (2012) 2.38
Experimental identification and quantification of glucose metabolism in seven bacterial species. J Bacteriol (2005) 2.24
Molecular epidemiology reveals long-term changes in HIV type 1 subtype B transmission in Switzerland. J Infect Dis (2010) 2.21
Dynamic variation in cycling of hematopoietic stem cells in steady state and inflammation. J Exp Med (2011) 2.18
Emergence of minor populations of human immunodeficiency virus type 1 carrying the M184V and L90M mutations in subjects undergoing structured treatment interruptions. J Infect Dis (2003) 2.17
The effect of opinion clustering on disease outbreaks. J R Soc Interface (2008) 2.12
Population biological principles of drug-resistance evolution in infectious diseases. Lancet Infect Dis (2011) 2.11
Latent pathway activation and increased pathway capacity enable Escherichia coli adaptation to loss of key metabolic enzymes. J Biol Chem (2005) 2.10
Long-term experimental evolution in Escherichia coli. XII. DNA topology as a key target of selection. Genetics (2004) 2.10
Long-term dynamics of adaptation in asexual populations. Science (2013) 2.09
A novel metabolic cycle catalyzes glucose oxidation and anaplerosis in hungry Escherichia coli. J Biol Chem (2003) 2.09
Birth-death skyline plot reveals temporal changes of epidemic spread in HIV and hepatitis C virus (HCV). Proc Natl Acad Sci U S A (2012) 2.07
Genome dynamics during experimental evolution. Nat Rev Genet (2013) 2.07
Quantitative constraints on the scope of negative selection. Trends Immunol (2003) 2.06
Ultrahigh performance liquid chromatography-tandem mass spectrometry method for fast and robust quantification of anionic and aromatic metabolites. Anal Chem (2010) 2.05
Evolution of global regulatory networks during a long-term experiment with Escherichia coli. Bioessays (2007) 2.03
Parallel changes in global protein profiles during long-term experimental evolution in Escherichia coli. Genetics (2006) 2.00
Evolution of cooperation by generalized reciprocity. Proc Biol Sci (2005) 1.96
Identification of furfural as a key toxin in lignocellulosic hydrolysates and evolution of a tolerant yeast strain. Microb Biotechnol (2008) 1.88
Is maximization of molar yield in metabolic networks favoured by evolution? J Theor Biol (2007) 1.88
Using an epidemiological model for phylogenetic inference reveals density dependence in HIV transmission. Mol Biol Evol (2013) 1.88
Estimating the basic reproductive number from viral sequence data. Mol Biol Evol (2011) 1.86
Adaptive radiation from resource competition in digital organisms. Science (2004) 1.86
Ensemble modeling for analysis of cell signaling dynamics. Nat Biotechnol (2007) 1.84
Dynamics of insertion sequence elements during experimental evolution of bacteria. Res Microbiol (2004) 1.83
Cross-platform comparison of methods for quantitative metabolomics of primary metabolism. Anal Chem (2009) 1.83
Stable virulence levels in the HIV epidemic of Switzerland over two decades. AIDS (2006) 1.81
Epistasis between deleterious mutations and the evolution of recombination. Trends Ecol Evol (2007) 1.79
Determination of metabolic flux ratios from 13C-experiments and gas chromatography-mass spectrometry data: protocol and principles. Methods Mol Biol (2007) 1.76
The HIV coreceptor switch: a population dynamical perspective. Trends Microbiol (2005) 1.76
Long-term experimental evolution in Escherichia coli. XI. Rejection of non-transitive interactions as cause of declining rate of adaptation. BMC Evol Biol (2002) 1.71
Entry and transcription as key determinants of differences in CD4 T-cell permissiveness to human immunodeficiency virus type 1 infection. J Virol (2004) 1.68
Metabolic-flux and network analysis in fourteen hemiascomycetous yeasts. FEMS Yeast Res (2005) 1.65
Ambiguous nucleotide calls from population-based sequencing of HIV-1 are a marker for viral diversity and the age of infection. Clin Infect Dis (2011) 1.64
Phylogenetic approach reveals that virus genotype largely determines HIV set-point viral load. PLoS Pathog (2010) 1.63
An experimental test of evolutionary trade-offs during temperature adaptation. Proc Natl Acad Sci U S A (2007) 1.62
Natural selection fails to optimize mutation rates for long-term adaptation on rugged fitness landscapes. PLoS Comput Biol (2008) 1.58
Stochastic or deterministic: what is the effective population size of HIV-1? Trends Microbiol (2006) 1.58
Convergent peripheral pathways catalyze initial glucose catabolism in Pseudomonas putida: genomic and flux analysis. J Bacteriol (2007) 1.57
Mutation rate dynamics in a bacterial population reflect tension between adaptation and genetic load. Proc Natl Acad Sci U S A (2012) 1.56
Large-scale 13C-flux analysis reveals distinct transcriptional control of respiratory and fermentative metabolism in Escherichia coli. Mol Syst Biol (2011) 1.55
Sexual reproduction reshapes the genetic architecture of digital organisms. Proc Biol Sci (2006) 1.55
An evolutionary scenario for the transition to undifferentiated multicellularity. Proc Natl Acad Sci U S A (2003) 1.55
Genome engineering reveals large dispensable regions in Bacillus subtilis. Mol Biol Evol (2003) 1.55
The evolution of connectivity in metabolic networks. PLoS Biol (2005) 1.54
Recombination in HIV and the evolution of drug resistance: for better or for worse? Bioessays (2004) 1.54
Mutation Rate Inferred From Synonymous Substitutions in a Long-Term Evolution Experiment With Escherichia coli. G3 (Bethesda) (2011) 1.53
Tradeoff between enzyme and metabolite efficiency maintains metabolic homeostasis upon perturbations in enzyme capacity. Mol Syst Biol (2010) 1.50
Long-term trends of HIV type 1 drug resistance prevalence among antiretroviral treatment-experienced patients in Switzerland. Clin Infect Dis (2009) 1.50
Nonlinear dependency of intracellular fluxes on growth rate in miniaturized continuous cultures of Escherichia coli. Appl Environ Microbiol (2006) 1.50
Pervasive joint influence of epistasis and plasticity on mutational effects in Escherichia coli. Nat Genet (2004) 1.49
Inferring epidemic contact structure from phylogenetic trees. PLoS Comput Biol (2012) 1.47
PhoR autokinase activity is controlled by an intermediate in wall teichoic acid metabolism that is sensed by the intracellular PAS domain during the PhoPR-mediated phosphate limitation response of Bacillus subtilis. Mol Microbiol (2014) 1.47
Death and cannibalism in a seasonal environment facilitate bacterial coexistence. Ecol Lett (2008) 1.46
Understanding the differences between genome sequences of Escherichia coli B strains REL606 and BL21(DE3) and comparison of the E. coli B and K-12 genomes. J Mol Biol (2009) 1.46
Evolution of cross-feeding in microbial populations. Am Nat (2004) 1.46
Evolutionary engineering of Saccharomyces cerevisiae for anaerobic growth on xylose. Appl Environ Microbiol (2003) 1.45
Fumarate reductase activity maintains an energized membrane in anaerobic Mycobacterium tuberculosis. PLoS Pathog (2011) 1.45
TCA cycle activity in Saccharomyces cerevisiae is a function of the environmentally determined specific growth and glucose uptake rates. Microbiology (2004) 1.44
Escherichia coli rpoB mutants have increased evolvability in proportion to their fitness defects. Mol Biol Evol (2010) 1.41
Fermentation performance of engineered and evolved xylose-fermenting Saccharomyces cerevisiae strains. Biotechnol Bioeng (2004) 1.38
Long-term experimental evolution in Escherichia coli. XIII. Phylogenetic history of a balanced polymorphism. J Mol Evol (2005) 1.37
Systematic identification of allosteric protein-metabolite interactions that control enzyme activity in vivo. Nat Biotechnol (2013) 1.36
Estimating the stoichiometry of human immunodeficiency virus entry. J Virol (2008) 1.36
Comprehensive quantitative analysis of central carbon and amino-acid metabolism in Saccharomyces cerevisiae under multiple conditions by targeted proteomics. Mol Syst Biol (2011) 1.35
Compensatory mutations cause excess of antagonistic epistasis in RNA secondary structure folding. BMC Evol Biol (2003) 1.34
Metabolic-flux profiling of the yeasts Saccharomyces cerevisiae and Pichia stipitis. Eukaryot Cell (2003) 1.33
Systems biology of microbial metabolism. Curr Opin Microbiol (2010) 1.33