scholarly article | Q13442814 |
P6179 | Dimensions Publication ID | 1007348192 |
P356 | DOI | 10.1038/NATURE03842 |
P698 | PubMed publication ID | 16049495 |
P5875 | ResearchGate publication ID | 7695245 |
P50 | author | Uri Alon | Q7900508 |
P2093 | author name string | Erez Dekel | |
P2860 | cites work | Mathematical model of the lac operon: inducer exclusion, catabolite repression, and diauxic growth on glucose and lactose. | Q52272848 |
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Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth | Q29397612 | ||
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From molecular to modular cell biology | Q29547493 | ||
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The population genetics of Escherichia coli | Q40080341 | ||
The protein burden of lac operon products | Q41563893 | ||
Biochemistry. How to make a superior cell | Q43642011 | ||
The organization of metabolic reaction networks. III. Application for diauxic growth on glucose and lactose | Q43776901 | ||
Dynamics and bistability in a reduced model of the lac operon. | Q44930453 | ||
P433 | issue | 7050 | |
P407 | language of work or name | English | Q1860 |
P1104 | number of pages | 5 | |
P304 | page(s) | 588-592 | |
P577 | publication date | 2005-07-01 | |
P1433 | published in | Nature | Q180445 |
P1476 | title | Optimality and evolutionary tuning of the expression level of a protein | |
P478 | volume | 436 |
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Q47097515 | Co-adaption of tRNA gene copy number and amino acid usage influences translation rates in three life domains |
Q33734356 | Comparison of the theoretical and real-world evolutionary potential of a genetic circuit |
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Q39862211 | Computational design of digital and memory biological devices. |
Q28080776 | Computing the functional proteome: recent progress and future prospects for genome-scale models |
Q53412824 | Conditional privatization of a public siderophore enables Pseudomonas aeruginosa to resist cheater invasion. |
Q34090968 | Constitutive versus responsive gene expression strategies for growth in changing environments |
Q98164531 | Contingent evolution of alternative metabolic network topologies determines whether cross-feeding evolves |
Q43578521 | Cost-benefit tradeoffs in engineered lac operons |
Q28082095 | Costs of antibiotic resistance - separating trait effects and selective effects |
Q48183188 | Counterbalancing Regulation in Response Memory of a Positively Autoregulated Two-Component System |
Q38623805 | Crosstalk between transcription and metabolism: how much enzyme is enough for a cell? |
Q37202063 | DNA looping provides stability and robustness to the bacteriophage lambda switch |
Q37120249 | Deciphering the Principles of Bacterial Nitrogen Dietary Preferences: a Strategy for Nutrient Containment |
Q37401494 | Depletion of Shine-Dalgarno Sequences within Bacterial Coding Regions Is Expression Dependent |
Q33432715 | Design principles for riboswitch function |
Q56637295 | Design principles of a bacterial signalling network |
Q33735386 | Designing and engineering evolutionary robust genetic circuits. |
Q35006962 | Determinants of translation efficiency and accuracy |
Q27316108 | Different levels of catabolite repression optimize growth in stable and variable environments |
Q39954065 | Diminishing returns epistasis among beneficial mutations decelerates adaptation |
Q36820801 | Divergent MLS1 Promoters Lie on a Fitness Plateau for Gene Expression |
Q53199647 | Division of labour and the evolution of multicellularity. |
Q90167457 | Dominance Effects and Functional Enrichments Improve Prediction of Agronomic Traits in Hybrid Maize |
Q64234595 | Dominance reversals and the maintenance of genetic variation for fitness |
Q47098313 | Dual role of starvation signaling in promoting growth and recovery |
Q46188014 | Dynamic changes in xylanases and β-1,4-endoglucanases secreted by Aspergillus niger An-76 in response to hydrolysates of lignocellulose polysaccharide |
Q47693920 | Dynamic optimization identifies optimal programmes for pathway regulation in prokaryotes. |
Q34732211 | Dynamics of nutrient uptake strategies: lessons from the tortoise and the hare |
Q39986409 | Effect of amino acid availability on vitamin B12 production in Lactobacillus reuteri |
Q51508276 | Effect of substrate and IPTG concentrations on the burden to growth of Escherichia coli on glycerol due to the expression of Lac proteins. |
Q43136691 | Effect on β-galactosidase synthesis and burden on growth of osmotic stress in Escherichia coli. |
Q60503746 | Effective models and the search for quantitative principles in microbial evolution |
Q28685530 | Electrostatic mis-interactions cause overexpression toxicity of proteins in E. coli |
Q30495631 | Emergent bistability by a growth-modulating positive feedback circuit |
Q34606034 | Empirical fitness landscapes reveal accessible evolutionary paths |
Q92002597 | Empirical mean-noise fitness landscapes reveal the fitness impact of gene expression noise |
Q37328414 | Engineering prokaryotic gene circuits |
Q28543209 | Environmental statistics and optimal regulation |
Q51332673 | Epistasis from functional dependence of fitness on underlying traits. |
Q57756711 | Evaluation of 244,000 synthetic sequences reveals design principles to optimize translation in Escherichia coli |
Q35083757 | Evaluation of the lower protein limit in the budding yeast Saccharomyces cerevisiae using TIPI-gTOW. |
Q34671996 | Evolution after introduction of a novel metabolic pathway consistently leads to restoration of wild-type physiology |
Q51908861 | Evolution equation of phenotype distribution: general formulation and application to error catastrophe. |
Q46774328 | Evolution of gene network activity by tuning the strength of negative-feedback regulation |
Q28749934 | Evolution of gene regulatory networks by fluctuating selection and intrinsic constraints |
Q24644443 | Evolution of penicillin-binding protein 2 concentration and cell shape during a long-term experiment with Escherichia coli |
Q88238715 | Evolutionary Convergence of Pathway-Specific Enzyme Expression Stoichiometry |
Q49206319 | Evolutionary Phase Transitions in Random Environments. |
Q55417763 | Evolutionary Plasticity of AmrZ Regulation in Pseudomonas. |
Q92751901 | Evolutionary coupling analysis identifies the impact of disease-associated variants at less-conserved sites |
Q34926385 | Evolutionary meandering of intermolecular interactions along the drift barrier |
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Q52327483 | Evolutionary trade-offs and the structure of polymorphisms. |
Q28535196 | Evolutionary tradeoffs between economy and effectiveness in biological homeostasis systems |
Q35034394 | Evolutionary tuning of protein expression levels of a positively autoregulated two-component system |
Q43148797 | Evolvability and hierarchy in rewired bacterial gene networks |
Q33300128 | Excitability constraints on voltage-gated sodium channels |
Q36429817 | Expression Differentiation Is Constrained to Low-Expression Proteins over Ecological Timescales |
Q33706863 | Expression Level, Evolutionary Rate, and the Cost of Expression |
Q40577943 | Expression divergence between Escherichia coli and Salmonella enterica serovar Typhimurium reflects their lifestyles |
Q57031370 | Feedbacks from the metabolic network to the genetic network reveal regulatory modules in E. coli and B. subtilis |
Q91989068 | Figure 1 Theory Meets Figure 2 Experiments in the Study of Gene Expression |
Q46298716 | Fitness Effects of Cis-Regulatory Variants in the Saccharomyces cerevisiae TDH3 Promoter |
Q35634242 | Fluctuations and synchrony of RNA synthesis in nucleoli |
Q28473749 | Fragilities caused by dosage imbalance in regulation of the budding yeast cell cycle |
Q33292444 | From bit to it: how a complex metabolic network transforms information into living matter |
Q37023389 | Full-Length cDNA, Prokaryotic Expression, and Antimicrobial Activity of UuHb-F-I from Urechis unicinctus |
Q36227467 | Gene Architectures that Minimize Cost of Gene Expression |
Q34439121 | Gene autoregulation via intronic microRNAs and its functions |
Q36837159 | Gene dosage and gene duplicability |
Q36439810 | Gene functional trade-offs and the evolution of pleiotropy. |
Q41365996 | Gene network requirements for regulation of metabolic gene expression to a desired state |
Q35009615 | General properties of transcriptional time series in Escherichia coli |
Q37715819 | Generic metric to quantify quorum sensing activation dynamics |
Q33544000 | Genome-scale metabolic analysis of Clostridium thermocellum for bioethanol production |
Q34708295 | Genotype to phenotype mapping and the fitness landscape of the E. coli lac promoter |
Q36830402 | Glucose becomes one of the worst carbon sources for E.coli on poor nitrogen sources due to suboptimal levels of cAMP. |
Q36932312 | Glycolytic strategy as a tradeoff between energy yield and protein cost |
Q33348349 | Growth landscape formed by perception and import of glucose in yeast |
Q64071953 | Growth strategy of microbes on mixed carbon sources |
Q92217433 | Growth-rate dependent resource investment in bacterial motile behavior quantitatively follows potential benefit of chemotaxis |
Q55031183 | Heterosis Is a Systemic Property Emerging From Non-linear Genotype-Phenotype Relationships: Evidence From in Vitro Genetics and Computer Simulations. |
Q35006510 | Hierarchy of non-glucose sugars in Escherichia coli |
Q92003649 | High Transcriptional Error Rates Vary as a Function of Gene Expression Level |
Q35930294 | High expression hampers horizontal gene transfer |
Q38494582 | High levels of gene expression explain the strong evolutionary constraint of mitochondrial protein-coding genes |
Q33251181 | High-resolution mutation mapping reveals parallel experimental evolution in yeast |
Q41077094 | How biochemical constraints of cellular growth shape evolutionary adaptations in metabolism. |
Q36337880 | How evolution learns to generalise: Using the principles of learning theory to understand the evolution of developmental organisation. |
Q42136418 | How fast-growing bacteria robustly tune their ribosome concentration to approximate growth-rate maximization |
Q36580584 | Identification of dosage-sensitive genes in Saccharomyces cerevisiae using the genetic tug-of-war method |
Q90407872 | In Vivo Thermodynamic Analysis of Glycolysis in Clostridium thermocellum and Thermoanaerobacterium saccharolyticum Using 13C and 2H Tracers |
Q35791099 | In silico evolution of diauxic growth |
Q41830880 | In silico evolved lac operons exhibit bistability for artificial inducers, but not for lactose |
Q54295703 | Increased gene dosage plays a predominant role in the initial stages of evolution of duplicate TEM-1 beta lactamase genes. |
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Q36856676 | Indirect and suboptimal control of gene expression is widespread in bacteria |
Q91821677 | Individual- versus group-optimality in the production of secreted bacterial compounds |
Q28478737 | Influence of molecular noise on the growth of single cells and bacterial populations |
Q42428611 | Information capacity of genetic regulatory elements |
Q39230129 | Informational requirements for transcriptional regulation |
Q54365525 | Insertion sequence-driven evolution of Escherichia coli in chemostats. |
Q33543179 | Interplay between pleiotropy and secondary selection determines rise and fall of mutators in stress response |
Q46357104 | Intra and Interspecific Variations of Gene Expression Levels in Yeast Are Largely Neutral: (Nei Lecture, SMBE 2016, Gold Coast). |
Q48304487 | Intrinsic adaptive value and early fate of gene duplication revealed by a bottom-up approach |
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Q92595558 | Inverted Regulation of Multidrug Efflux Pumps, Acid Resistance, and Porins in Benzoate-Evolved Escherichia coli K-12 |
Q28469291 | Is transcriptional regulation of metabolic pathways an optimal strategy for fitness? |
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Q39245826 | Laboratory evolution and multi-platform genome re-sequencing of the cellulolytic actinobacterium Thermobifida fusca |
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Q34795559 | Latent effects of Hsp90 mutants revealed at reduced expression levels |
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Q41361551 | Metabolic Complementation in Bacterial Communities: Necessary Conditions and Optimality |
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Q51298436 | Metabolic network architecture and carbon source determine metabolite production costs. |
Q38039368 | Metabolic shifts: a fitness perspective for microbial cell factories |
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Q38515559 | Metabolism at evolutionary optimal States. |
Q90406956 | Metabolite Sequestration Enables Rapid Recovery from Fatty Acid Depletion in Escherichia coli |
Q37017244 | Metabolite concentrations, fluxes and free energies imply efficient enzyme usage |
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Q35176401 | Microbial laboratory evolution in the era of genome-scale science |
Q33532575 | Minimization of biosynthetic costs in adaptive gene expression responses of yeast to environmental changes |
Q34490441 | Misfolded proteins impose a dosage-dependent fitness cost and trigger a cytosolic unfolded protein response in yeast |
Q42485858 | Model-based analysis of an adaptive evolution experiment with Escherichia coli in a pyruvate limited continuous culture with glycerol |
Q33812132 | Modeling the evolution of a classic genetic switch |
Q34361262 | Monitoring microbial population dynamics at low densities. |
Q36779247 | Multidimensional adaptive evolution of a feed-forward network and the illusion of compensation |
Q43431493 | Multidimensional optimality of microbial metabolism |
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Q29615325 | Network motifs: theory and experimental approaches |
Q50658281 | Neutral null models for diversity in serial transfer evolution experiments. |
Q39063396 | No Evidence That Protein Noise-Induced Epigenetic Epistasis Constrains Gene Expression Evolution |
Q34863121 | Noise and low-level dynamics can coordinate multicomponent bet hedging mechanisms |
Q35758729 | Noisy information processing through transcriptional regulation |
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Q33981298 | Nonlinear fitness landscape of a molecular pathway |
Q33726796 | Nonoptimal microbial response to antibiotics underlies suppressive drug interactions |
Q33642720 | Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models |
Q28743059 | On the Interplay between the Evolvability and Network Robustness in an Evolutionary Biological Network: A Systems Biology Approach |
Q37418706 | Operons |
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Q35610380 | Optimal programs of pathway control: dissecting the influence of pathway topology and feedback inhibition on pathway regulation. |
Q34708874 | Optimal resource allocation in cellular sensing systems |
Q33883319 | Optimal resting-growth strategies of microbial populations in fluctuating environments |
Q37300394 | Optimal tuning of bacterial sensing potential |
Q33994101 | Optimality and evolution of transcriptionally regulated gene expression |
Q37598412 | Optimality and sub-optimality in a bacterial growth law. |
Q38463994 | Optimality and thermodynamics determine the evolution of transcriptional regulatory networks |
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Q41875215 | Optimality principles in the regulation of metabolic networks |
Q35078726 | Optimization and control in bacterial lag phase |
Q42254765 | Optimization of gene expression through divergent mutational paths. |
Q41772877 | Origin of bistability in the lac Operon. |
Q30542457 | Overexpression limits of fission yeast cell-cycle regulators in vivo and in silico. |
Q35038412 | Parallel changes in global protein profiles during long-term experimental evolution in Escherichia coli |
Q64116354 | Pareto Optimality Explanation of the Glycolytic Alternatives in Nature |
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Q35636333 | Perception and regulatory principles of microbial growth control |
Q36938323 | Phenotypic Diversity Using Bimodal and Unimodal Expression of Stress Response Proteins |
Q33307180 | Phenotypic mutation rates and the abundance of abnormal proteins in yeast |
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Q38598069 | Physical limits on cooperative protein-DNA binding and the kinetics of combinatorial transcription regulation. |
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Q36380064 | Polymorphisms in the yeast galactose sensor underlie a natural continuum of nutrient-decision phenotypes. |
Q35549977 | Population diversification in a yeast metabolic program promotes anticipation of environmental shifts |
Q37330219 | Positive selection for elevated gene expression noise in yeast |
Q30494565 | Pre-dispositions and epigenetic inheritance in the Escherichia coli lactose operon bistable switch |
Q37062923 | Predicting evolution from genomics: experimental evolution of bacteriophage T7. |
Q41106561 | PrfA regulation offsets the cost of Listeria virulence outside the host |
Q41578142 | Principles of cellular resource allocation revealed by condition-dependent proteome profiling. |
Q42021181 | Principles of transcriptional regulation and evolution of the metabolic system in E. coli |
Q35904949 | Probing the Limits to MicroRNA-Mediated Control of Gene Expression |
Q28481785 | Probing the informational and regulatory plasticity of a transcription factor DNA-binding domain |
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Q39035713 | Proteome reallocation in Escherichia coli with increasing specific growth rate |
Q33521246 | Proteomic detection of non-annotated protein-coding genes in Pseudomonas fluorescens Pf0-1. |
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Q33551343 | Quantifying absolute protein synthesis rates reveals principles underlying allocation of cellular resources |
Q37518583 | Quantitative influence of macromolecular crowding on gene regulation kinetics. |
Q36455398 | Quantitative nature of overexpression experiments |
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Q35882597 | Regulatory architecture determines optimal regulation of gene expression in metabolic pathways |
Q28473536 | Regulatory control and the costs and benefits of biochemical noise |
Q35602100 | Regulatory evolution and voltage-gated ion channel expression in squid axon: selection-mutation balance and fitness cliffs |
Q35849084 | Resource constrained flux balance analysis predicts selective pressure on the global structure of metabolic networks |
Q39369193 | Rethinking cell growth models. |
Q41959990 | Reverse-engineering the Arabidopsis thaliana transcriptional network under changing environmental conditions |
Q51622296 | Revisiting demand rules for gene regulation. |
Q46874291 | Ribosomal mutations affecting the translation of genes that use non-optimal codons |
Q38888646 | Robust Analysis of Fluxes in Genome-Scale Metabolic Pathways |
Q34450045 | Robust circadian clocks from coupled protein-modification and transcription-translation cycles. |
Q34424966 | Rules for biological regulation based on error minimization |
Q34388337 | Sex linkage, sex-specific selection, and the role of recombination in the evolution of sexually dimorphic gene expression |
Q42242972 | Shifts in growth strategies reflect tradeoffs in cellular economics |
Q46323399 | Signaling Architectures that Transmit Unidirectional Information Despite Retroactivity |
Q28487113 | Simulation of E. coli gene regulation including overlapping cell cycles, growth, division, time delays and noise |
Q34700543 | Single-cell dynamics reveals sustained growth during diauxic shifts |
Q35931760 | Single-cell zeroth-order protein degradation enhances the robustness of synthetic oscillator |
Q35006971 | Social interaction in synthetic and natural microbial communities |
Q38966277 | Social interactions in bacterial cell-cell signaling. |
Q34136699 | Social interactions, information use, and the evolution of collective migration |
Q40366148 | Spanning high-dimensional expression space using ribosome-binding site combinatorics |
Q91070610 | Stimulus response-based fine-tuning of polyhydroxyalkanoate pathway in Halomonas |
Q64991598 | Stochastic protein multimerization, activity, and fitness. |
Q37634302 | Strategies for cellular decision-making |
Q33275962 | Strategy of transcription regulation in the budding yeast. |
Q46283683 | Stress Introduction Rate Alters the Benefit of AcrAB-TolC Efflux Pumps |
Q41023000 | Stress-response balance drives the evolution of a network module and its host genome |
Q89571421 | Structural optimality and neurogenetic expression mediate functional dynamics in the human brain |
Q34598769 | Structure and function of negative feedback loops at the interface of genetic and metabolic networks |
Q35013239 | Structure of deviations from optimality in biological systems. |
Q46004771 | Substrate concentration and enzyme allocation can affect rates of microbial decomposition. |
Q28651496 | Sulfur isotope fractionation during the evolutionary adaptation of a sulfate-reducing bacterium |
Q38017457 | Synthetic approaches to understanding biological constraints |
Q39782355 | Synthetic biology: a foundation for multi-scale molecular biology |
Q38081904 | Synthetic biology: advancing the design of diverse genetic systems |
Q30584192 | Systematic exploration of ubiquitin sequence, E1 activation efficiency, and experimental fitness in yeast |
Q37945283 | Systems biology of lactic acid bacteria: a critical review. |
Q37909892 | Systems-biology approaches for predicting genomic evolution |
Q28307788 | Testing optimality with experimental evolution: lysis time in a bacteriophage |
Q90099269 | The Evolution of Variance Control |
Q30402322 | The Evolutionary Basis of Translational Accuracy in Plants |
Q51285896 | The Landscape of Evolution: Reconciling Structural and Dynamic Properties of Metabolic Networks in Adaptive Diversifications. |
Q36182002 | The Protein Cost of Metabolic Fluxes: Prediction from Enzymatic Rate Laws and Cost Minimization |
Q38810233 | The Response to 2-Aminoacrylate Differs in Escherichia coli and Salmonella enterica, despite Shared Metabolic Components. |
Q35996823 | The Role of Genome Accessibility in Transcription Factor Binding in Bacteria |
Q34789242 | The ability of flux balance analysis to predict evolution of central metabolism scales with the initial distance to the optimum |
Q41516802 | The architecture of eukaryotic translation |
Q37134524 | The cost of gene expression underlies a fitness trade-off in yeast |
Q35137906 | The decoupling between genetic structure and metabolic phenotypes in Escherichia coli leads to continuous phenotypic diversity |
Q90571606 | The ecology of heterogeneity: soil bacterial communities and C dynamics |
Q82241869 | The econometrics of evolution |
Q33288725 | The effect of stochasticity on the lac operon: an evolutionary perspective |
Q92544990 | The emergence of adaptive laboratory evolution as an efficient tool for biological discovery and industrial biotechnology |
Q51563018 | The evolution of salinity tolerance in Daphnia: a functional genomics approach. |
Q64067570 | The fitness cost and benefit of phase-separated protein deposits |
Q28474970 | The fitness landscapes of cis-acting binding sites in different promoter and environmental contexts |
Q35698892 | The genetic code is nearly optimal for allowing additional information within protein-coding sequences |
Q36850446 | The lag-phase during diauxic growth is a trade-off between fast adaptation and high growth rate |
Q34636989 | The last generation of bacterial growth in limiting nutrient |
Q33247453 | The life-cycle of operons |
Q34247630 | The rate of the molecular clock and the cost of gratuitous protein synthesis |
Q89876204 | The relation between crosstalk and gene regulation form revisited |
Q28752207 | The relationship among gene expression, the evolution of gene dosage, and the rate of protein evolution |
Q54310563 | The robustness and evolvability of transcription factor binding sites. |
Q33868449 | The role of cellular objectives and selective pressures in metabolic pathway evolution. |
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Q97067846 | Time-resolved multi-omics analysis reveals the role of nutrient stress-induced resource reallocation for TAG accumulation in oleaginous fungus Mortierella alpina |
Q92610747 | Titrating gene expression using libraries of systematically attenuated CRISPR guide RNAs |
Q26998624 | Towards physiological complexity with in vitro single-molecule biophysics |
Q36925231 | Transcriptional regulation constrains the organization of genes on eukaryotic chromosomes |
Q28740288 | Transcriptional regulation is a major controller of cell cycle transition dynamics |
Q37524872 | Transient protein-protein interactions perturb E. coli metabolome and cause gene dosage toxicity. |
Q36021783 | Translation elicits a growth rate-dependent, genome-wide, differential protein production in Bacillus subtilis. |
Q34678372 | Translational signatures and mRNA levels are highly correlated in human stably expressed genes |
Q37203938 | Tuning gene expression to changing environments: from rapid responses to evolutionary adaptation |
Q51067465 | Tuning transcription of nutrient utilization genes to catabolic rate promotes growth in a gut bacterium. |
Q37197219 | Underlying principles of natural selection in network evolution: systems biology approach. |
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