Systems-biology approaches for predicting genomic evolution (Q37909892)

25 August 2017

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title

Systems-biology approaches for predicting genomic evolution (English)

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25 August 2017

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25 August 2017

Richard A Notebaart

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25 August 2017

Csaba Pál

series ordinal

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25 August 2017

publication date

2 August 2011

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25 August 2017

published in

Nature Reviews Genetics

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25 August 2017

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25 August 2017

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25 August 2017

page(s)

591-602

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The loci of evolution: how predictable is genetic evolution?

25 August 2017

cites work

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Is genetic evolution predictable?

21 January 2018

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

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Directed evolution of enzymes and biosynthetic pathways

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Phenotypic consequences of 1,000 generations of selection at elevated CO2 in a green alga

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Predicting the evolution of antibiotic resistance genes

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Functional profiling of the Saccharomyces cerevisiae genome

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The chemical genomic portrait of yeast: uncovering a phenotype for all genes

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The genetic landscape of a cell

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Mechanistic approaches to the study of evolution: the functional synthesis

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Genome-scale models of microbial cells: evaluating the consequences of constraints

21 January 2018

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The danger of metabolic pathways with turbo design

21 January 2018

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Integrative analysis of cell cycle control in budding yeast

21 January 2018

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Reconstruction and logical modeling of glucose repression signaling pathways in Saccharomyces cerevisiae

21 January 2018

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Applications of genome-scale metabolic reconstructions

21 January 2018

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Dynamic analysis of integrated signaling, metabolic, and regulatory networks

21 January 2018

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Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli.

21 January 2018

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Mass action stoichiometric simulation models: incorporating kinetics and regulation into stoichiometric models

21 January 2018

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KEGG: kyoto encyclopedia of genes and genomes

21 January 2018

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BRENDA, enzyme data and metabolic information

21 January 2018

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Network biology: understanding the cell's functional organization

21 January 2018

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Model-driven analysis of experimentally determined growth phenotypes for 465 yeast gene deletion mutants under 16 different conditions

21 January 2018

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Plasticity of genetic interactions in metabolic networks of yeast

21 January 2018

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In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data

21 January 2018

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Flux coupling analysis of genome-scale metabolic network reconstructions.

21 January 2018

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Integrating quantitative proteomics and metabolomics with a genome-scale metabolic network model

21 January 2018

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Something from nothing: bridging the gap between constraint-based and kinetic modelling.

21 January 2018

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Prevalent positive epistasis in Escherichia coli and Saccharomyces cerevisiae metabolic networks

21 January 2018

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An integrated approach to characterize genetic interaction networks in yeast metabolism

21 January 2018

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Metabolic network analysis of the causes and evolution of enzyme dispensability in yeast

21 January 2018

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Metabolic functions of duplicate genes in Saccharomyces cerevisiae

21 January 2018

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Adaptive evolution of bacterial metabolic networks by horizontal gene transfer.

21 January 2018

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Asymmetric relationships between proteins shape genome evolution.

21 January 2018

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The genetic theory of adaptation: a brief history

21 January 2018

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The evolution of sex: empirical insights into the roles of epistasis and drift

21 January 2018

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Role of duplicate genes in genetic robustness against null mutations

21 January 2018

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Robustness against mutations in genetic networks of yeast.

21 January 2018

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Large-scale 13C-flux analysis reveals mechanistic principles of metabolic network robustness to null mutations in yeast

21 January 2018

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Evolution under fluctuating environments explains observed robustness in metabolic networks

21 January 2018

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Rewiring of genetic networks in response to DNA damage.

21 January 2018

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Perspective: Complex Adaptations and the Evolution of Evolvability

21 January 2018

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Negative epistasis between beneficial mutations in an evolving bacterial population

21 January 2018

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An integrated view of protein evolution

21 January 2018

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Large-scale evaluation of in silico gene deletions in Saccharomyces cerevisiae

21 January 2018

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Probing the performance limits of the Escherichia coli metabolic network subject to gene additions or deletions

21 January 2018

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Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli

21 January 2018

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The effects of alternate optimal solutions in constraint-based genome-scale metabolic models

21 January 2018

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Evolutionary origins of genomic repertoires in bacteria

21 January 2018

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Evolution of genetic redundancy

21 January 2018

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Influence of metabolic network structure and function on enzyme evolution

21 January 2018

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The distribution of fitness effects of new mutations

21 January 2018

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Conservation of expression and sequence of metabolic genes is reflected by activity across metabolic states

21 January 2018

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A genome-scale computational study of the interplay between transcriptional regulation and metabolism

21 January 2018

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Transcriptional regulation in constraints-based metabolic models of Escherichia coli

21 January 2018

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Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth

21 January 2018

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Metabolic gene-deletion strains of Escherichia coli evolve to computationally predicted growth phenotypes

21 January 2018

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Chance and necessity in the evolution of minimal metabolic networks

21 January 2018

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Comparative genome sequencing of Escherichia coli allows observation of bacterial evolution on a laboratory timescale

21 January 2018

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Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models

21 January 2018

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Metabolic modeling of endosymbiont genome reduction on a temporal scale

21 January 2018

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The process of genome shrinkage in the obligate symbiont Buchnera aphidicola

21 January 2018

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A framework for evolutionary systems biology

21 January 2018

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In silico model-driven assessment of the effects of single nucleotide polymorphisms (SNPs) on human red blood cell metabolism

21 January 2018

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Comparative systems biology: from bacteria to man

21 January 2018

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Reconciliation of genome-scale metabolic reconstructions for comparative systems analysis

21 January 2018

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Comparative methods for explaining adaptations

21 January 2018

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Network Archaeology: Uncovering Ancient Networks from Present-Day Interactions

21 January 2018

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Environments that induce synthetic microbial ecosystems

21 January 2018

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Emergent cooperation in microbial metabolism

21 January 2018

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Large-scale reconstruction and phylogenetic analysis of metabolic environments

21 January 2018

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Topological signatures of species interactions in metabolic networks

21 January 2018

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Comparative genome-scale metabolic reconstruction and flux balance analysis of multiple Staphylococcus aureus genomes identify novel antimicrobial drug targets

21 January 2018

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Programming cells by multiplex genome engineering and accelerated evolution

21 January 2018

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Avida: a software platform for research in computational evolutionary biology

21 January 2018

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Digital genetics: unravelling the genetic basis of evolution

21 January 2018

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Optimality and evolutionary tuning of the expression level of a protein

21 January 2018

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The yeast cell-cycle network is robustly designed

21 January 2018

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Using a logical model to predict the growth of yeast

21 January 2018

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Dynamic flux balance analysis of diauxic growth in Escherichia coli

21 January 2018

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Evolvability and hierarchy in rewired bacterial gene networks

21 January 2018

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Neutralism and selectionism: a network-based reconciliation

21 January 2018

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Evolutionary plasticity and innovations in complex metabolic reaction networks

21 January 2018

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Enzyme promiscuity: a mechanistic and evolutionary perspective

21 January 2018

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The locus of evolution: evo devo and the genetics of adaptation

21 January 2018

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Convergent evolution of gene circuits

21 January 2018

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Mechanisms of haploinsufficiency revealed by genome-wide profiling in yeast

21 January 2018

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Connecting extracellular metabolomic measurements to intracellular flux states in yeast

21 January 2018

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Correction: Dynamic Analysis of Integrated Signaling, Metabolic, and Regulatory Networks.

21 January 2018

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Modular epistasis in yeast metabolism.

31 March 2020

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PERSPECTIVE: COMPLEX ADAPTATIONS AND THE EVOLUTION OF EVOLVABILITY.

31 March 2020

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High-throughput generation, optimization and analysis of genome-scale metabolic models

31 March 2020

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Network-based prediction of human tissue-specific metabolism

31 March 2020

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Putative regulatory sites unraveled by network-embedded thermodynamic analysis of metabolome data

31 March 2020

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31 March 2020

Underground metabolism

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Muller's ratchet under epistatic selection

31 March 2020

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PubMed

https://pubmed.ncbi.nlm.nih.gov/21808261

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1038/NRG3033

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25 August 2017

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