Lista de obras -

<i>Escherichia coli</i> Data-Driven Strain Design Using Aggregated Adaptive Laboratory Evolution Mutational Data

artículo científico publicado en 2021

A Model for Designing Adaptive Laboratory Evolution Experiments

artículo científico publicado en 2017

A comprehensive genome-scale reconstruction of Escherichia coli metabolism--2011. ⬇️

artículo científico publicado en 2011

A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information

artículo científico publicado en 2007

A model-driven quantitative metabolomics analysis of aerobic and anaerobic metabolism in E. coli K-12 MG1655 that is biochemically and thermodynamically consistent

artículo científico publicado en 2013

A multi-tissue type genome-scale metabolic network for analysis of whole-body systems physiology ⬇️

artículo científico publicado el 31 de octubre de 2011

ALEdb 1.0: a database of mutations from adaptive laboratory evolution experimentation

article

Acidithiobacillus ferrooxidans's comprehensive model driven analysis of the electron transfer metabolism and synthetic strain design for biomining applications.

artículo científico publicado en 2016

Adaptation to the coupling of glycolysis to toxic methylglyoxal production in tpiA deletion strains of Escherichia coli requires synchronized and counterintuitive genetic changes

artículo científico publicado en 2018

Adaptive evolution reveals a tradeoff between growth rate and oxidative stress during naphthoquinone-based aerobic respiration

scientific article published on 25 November 2019

Adaptive laboratory evolution of Escherichia coli under acid stress

scientific article published on 18 October 2019

Adaptive laboratory evolution of Pseudomonas putida KT2440 improves p-coumaric and ferulic acid catabolism and tolerance

scientific article published on 29 August 2020

Adaptive laboratory evolution of tolerance to dicarboxylic acids in Saccharomyces cerevisiae

artículo científico publicado en 2019

Adaptive laboratory evolution resolves energy depletion to maintain high aromatic metabolite phenotypes in Escherichia coli strains lacking the Phosphotransferase System

artículo científico publicado en 2018

BOFdat: Generating biomass objective functions for genome-scale metabolic models from experimental data

artículo científico publicado en 2019

Basic and applied uses of genome‐scale metabolic network reconstructions of Escherichia coli ⬇️

artículo científico publicado el 1 de enero de 2013

Causal mutations from adaptive laboratory evolution are outlined by multiple scales of genome annotations and condition-specificity

artículo científico publicado en 2020

Cellular responses to reactive oxygen species are predicted from molecular mechanisms

scientific article published on 03 July 2019

Characterization and modelling of interspecies electron transfer mechanisms and microbial community dynamics of a syntrophic association

artículo científico publicado en 2013

Characterization of CA-MRSA TCH1516 exposed to nafcillin in bacteriological and physiological media

artículo científico publicado en 2019

Characterizing Strain Variation in Engineered E. coli Using a Multi-Omics-Based Workflow.

artículo científico publicado en 2016

Computational Methods to Assess the Production Potential of Bio-Based Chemicals

artículo científico publicado en 2018

Constraint-based modeling of carbon fixation and the energetics of electron transfer in Geobacter metallireducens

artículo científico publicado en 2014

Coupling S-adenosylmethionine-dependent methylation to growth: Design and uses

artículo científico publicado en 2019

Cumulative Number of Cell Divisions as a Meaningful Timescale for Adaptive Laboratory Evolution of Escherichia coli ⬇️

artículo científico publicado el 18 de octubre de 2011

Directed Metabolic Pathway Evolution Enables Functional Pterin-Dependent Aromatic-Amino-Acid Hydroxylation in Escherichia coli

artículo científico publicado en 2020

Dissecting the genetic and metabolic mechanisms of adaptation to the knockout of a major metabolic enzyme in Escherichia coli

artículo científico publicado en 2017

Do genome-scale models need exact solvers or clearer standards?

artículo científico publicado en 2015

Elucidating aromatic acid tolerance at low pH in Saccharomyces cerevisiae using adaptive laboratory evolution

artículo científico publicado en 2020

Enzyme promiscuity shapes adaptation to novel growth substrates

scientific article published on 08 April 2019

Enzyme promiscuity shapes evolutionary innovation and optimization

article

Evolution of E. coli on [U-13C]Glucose Reveals a Negligible Isotopic Influence on Metabolism and Physiology

artículo científico publicado en 2016

Evolution of Escherichia coli to 42 °C and subsequent genetic engineering reveals adaptive mechanisms and novel mutations

artículo científico publicado en 2014

Evolution of gene knockout strains of E. coli reveal regulatory architectures governed by metabolism

scientific article published in Nature Communications

Fast growth phenotype of E. coli K-12 from adaptive laboratory evolution does not require intracellular flux rewiring

artículo científico publicado en 2017

Gapless, Unambiguous Genome Sequence for Escherichia coli C, a Workhorse of Industrial Biology

scientific article published on 04 October 2018

Generation of a platform strain for ionic liquid tolerance using adaptive laboratory evolution

artículo científico publicado en 2017

Generation of an E. coli platform strain for improved sucrose utilization using adaptive laboratory evolution

scientific article published on 29 June 2019

Generation of an atlas for commodity chemical production in Escherichia coli and a novel pathway prediction algorithm, GEM-Path

artículo científico publicado en 2014

Genetic Determinants Enabling Medium-Dependent Adaptation to Nafcillin in Methicillin-Resistant Staphylococcus aureus

scientific article published on 31 March 2020

Genome-Scale Reconstruction, Modeling, and Simulation of E. coli℉s Metabolic Network

scholarly article published 2009

Genome-scale metabolic modeling reveals key features of a minimal gene set

artículo científico publicado en 2021

Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments

artículo científico publicado en 2013

Genome-scale reconstruction and in silico analysis of the Clostridium acetobutylicum ATCC 824 metabolic network

artículo científico publicado en 2008

Genomically and biochemically accurate metabolic reconstruction of Methanosarcina barkeri Fusaro, iMG746

artículo científico publicado en 2013

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

artículo científico publicado en 2016

Growth Adaptation of and Deletion Strains Diverges From a Similar Initial Perturbation of the Transcriptome

article published in 2018

High-quality genome-scale metabolic modelling of Pseudomonas putida highlights its broad metabolic capabilities

scientific article published on 11 November 2019

Identification of growth-coupled production strains considering protein costs and kinetic variability

Increased production of L-serine in Escherichia coli through Adaptive Laboratory Evolution

artículo científico publicado en 2016

Kinetic profiling of metabolic specialists demonstrates stability and consistency of in vivo enzyme turnover numbers

scientific article published on 01 September 2020

Laboratory Evolution to Alternating Substrate Environments Yields Distinct Phenotypic and Genetic Adaptive Strategies

artículo científico publicado en 2017

Laboratory evolution reveals a two-dimensional rate-yield tradeoff in microbial metabolism

scientific article published on 03 June 2019

Laboratory evolution reveals regulatory and metabolic trade-offs of glycerol utilization in Saccharomyces cerevisiae.

artículo científico publicado en 2018

Literature mining supports a next-generation modeling approach to predict cellular byproduct secretion

artículo científico publicado en 2016

MEMOTE for standardized genome-scale metabolic model testing

artículo científico publicado en 2020

MID Max: LC-MS/MS Method for Measuring the Precursor and Product Mass Isotopomer Distributions of Metabolic Intermediates and Cofactors for Metabolic Flux Analysis Applications

artículo científico publicado en 2015

Maximizing biomass productivity and cell density of Chlorella vulgaris by using light-emitting diode-based photobioreactor

artículo científico publicado en 2012

Memote: A community-driven effort towards a standardized genome-scale metabolic model test suite

Model-driven discovery of underground metabolic functions in Escherichia coli

artículo científico publicado en 2015

Model-driven evaluation of the production potential for growth-coupled products of Escherichia coli

artículo científico publicado en 2009

Modeling Method for Increased Precision and Scope of Directly Measurable Fluxes at a Genome-Scale

artículo científico publicado en 2016

Modeling methanogenesis with a genome-scale metabolic reconstruction of Methanosarcina barkeri

artículo científico publicado en 2006

Multi-omic data integration enables discovery of hidden biological regularities

artículo científico publicado en 2016

Multi-omics Quantification of Species Variation of Escherichia coli Links Molecular Features with Strain Phenotypes

artículo científico publicado en 2016

Multiple Optimal Phenotypes Overcome Redox and Glycolytic Intermediate Metabolite Imbalances in Escherichia coli pgi Knockout Evolutions

scientific article published on 17 September 2018

Next-generation genome-scale models for metabolic engineering.

artículo científico

Optimal cofactor swapping can increase the theoretical yield for chemical production in Escherichia coli and Saccharomyces cerevisiae

artículo científico publicado en 2014

OxyR Is a Convergent Target for Mutations Acquired during Adaptation to Oxidative Stress-Prone Metabolic States

scientific article published on 01 March 2020

Profiling the effect of nafcillin on HA-MRSA D712 using bacteriological and physiological media

scientific article published on 17 December 2019

Pseudogene repair driven by selection pressure applied in experimental evolution

scientific article published on 28 January 2019

Publisher Correction: MEMOTE for standardized genome-scale metabolic model testing

artículo científico publicado en 2020

Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0

artículo científico publicado en 2011

Reconstruction and modeling protein translocation and compartmentalization in Escherichia coli at the genome-scale

artículo científico publicado en 2014

Reframing gene essentiality in terms of adaptive flexibility

article

Selection for Cell Yield Does Not Reduce Overflow Metabolism in <i>Escherichia coli</i>

artículo científico publicado en 2021

Strain-Specific Metabolic Requirements Revealed by a Defined Minimal Medium for Systems Analyses of Staphylococcus aureus

scientific article published on 16 October 2019

Sulfide-driven microbial electrosynthesis.

artículo científico publicado en 2012

The biomass objective function

artículo científico publicado en 2010

The emergence of adaptive laboratory evolution as an efficient tool for biological discovery and industrial biotechnology

artículo científico publicado en 2019

The genetic basis for adaptation of model-designed syntrophic co-cultures

article

The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli

artículo científico publicado en 2008

Tracing compartmentalized NADPH metabolism in the cytosol and mitochondria of mammalian cells

artículo científico publicado en 2014

Use of adaptive laboratory evolution to discover key mutations enabling rapid growth of Escherichia coli K-12 MG1655 on glucose minimal medium

artículo científico publicado en 2014

What do cells actually want?

artículo científico publicado en 2016

iML1515, a knowledgebase that computes Escherichia coli traits.

artículo científico publicado en 2017

Lista de obras de

<i>Escherichia coli</i> Data-Driven Strain Design Using Aggregated Adaptive Laboratory Evolution Mutational Data

A Model for Designing Adaptive Laboratory Evolution Experiments

A comprehensive genome-scale reconstruction of Escherichia coli metabolism--2011. ⬇️

A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information

A model-driven quantitative metabolomics analysis of aerobic and anaerobic metabolism in E. coli K-12 MG1655 that is biochemically and thermodynamically consistent

A multi-tissue type genome-scale metabolic network for analysis of whole-body systems physiology ⬇️

ALEdb 1.0: a database of mutations from adaptive laboratory evolution experimentation

Acidithiobacillus ferrooxidans's comprehensive model driven analysis of the electron transfer metabolism and synthetic strain design for biomining applications.

Adaptation to the coupling of glycolysis to toxic methylglyoxal production in tpiA deletion strains of Escherichia coli requires synchronized and counterintuitive genetic changes

Adaptive evolution reveals a tradeoff between growth rate and oxidative stress during naphthoquinone-based aerobic respiration

Adaptive laboratory evolution of Escherichia coli under acid stress

Adaptive laboratory evolution of Pseudomonas putida KT2440 improves p-coumaric and ferulic acid catabolism and tolerance

Adaptive laboratory evolution of tolerance to dicarboxylic acids in Saccharomyces cerevisiae

Adaptive laboratory evolution resolves energy depletion to maintain high aromatic metabolite phenotypes in Escherichia coli strains lacking the Phosphotransferase System

BOFdat: Generating biomass objective functions for genome-scale metabolic models from experimental data

Basic and applied uses of genome‐scale metabolic network reconstructions of Escherichia coli ⬇️

Causal mutations from adaptive laboratory evolution are outlined by multiple scales of genome annotations and condition-specificity

Cellular responses to reactive oxygen species are predicted from molecular mechanisms

Characterization and modelling of interspecies electron transfer mechanisms and microbial community dynamics of a syntrophic association

Characterization of CA-MRSA TCH1516 exposed to nafcillin in bacteriological and physiological media

Characterizing Strain Variation in Engineered E. coli Using a Multi-Omics-Based Workflow.

Computational Methods to Assess the Production Potential of Bio-Based Chemicals

Constraint-based modeling of carbon fixation and the energetics of electron transfer in Geobacter metallireducens

Coupling S-adenosylmethionine-dependent methylation to growth: Design and uses

Cumulative Number of Cell Divisions as a Meaningful Timescale for Adaptive Laboratory Evolution of Escherichia coli ⬇️

Directed Metabolic Pathway Evolution Enables Functional Pterin-Dependent Aromatic-Amino-Acid Hydroxylation in Escherichia coli

Dissecting the genetic and metabolic mechanisms of adaptation to the knockout of a major metabolic enzyme in Escherichia coli

Do genome-scale models need exact solvers or clearer standards?

Elucidating aromatic acid tolerance at low pH in Saccharomyces cerevisiae using adaptive laboratory evolution

Enzyme promiscuity shapes adaptation to novel growth substrates

Enzyme promiscuity shapes evolutionary innovation and optimization

Evolution of E. coli on [U-13C]Glucose Reveals a Negligible Isotopic Influence on Metabolism and Physiology

Evolution of Escherichia coli to 42 °C and subsequent genetic engineering reveals adaptive mechanisms and novel mutations

Evolution of gene knockout strains of E. coli reveal regulatory architectures governed by metabolism

Fast growth phenotype of E. coli K-12 from adaptive laboratory evolution does not require intracellular flux rewiring

Gapless, Unambiguous Genome Sequence for Escherichia coli C, a Workhorse of Industrial Biology

Generation of a platform strain for ionic liquid tolerance using adaptive laboratory evolution

Generation of an E. coli platform strain for improved sucrose utilization using adaptive laboratory evolution

Generation of an atlas for commodity chemical production in Escherichia coli and a novel pathway prediction algorithm, GEM-Path

Genetic Determinants Enabling Medium-Dependent Adaptation to Nafcillin in Methicillin-Resistant Staphylococcus aureus

Genome-Scale Reconstruction, Modeling, and Simulation of E. coli℉s Metabolic Network

Genome-scale metabolic modeling reveals key features of a minimal gene set

Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments

Genome-scale reconstruction and in silico analysis of the Clostridium acetobutylicum ATCC 824 metabolic network

Genomically and biochemically accurate metabolic reconstruction of Methanosarcina barkeri Fusaro, iMG746

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

Growth Adaptation of and Deletion Strains Diverges From a Similar Initial Perturbation of the Transcriptome

High-quality genome-scale metabolic modelling of Pseudomonas putida highlights its broad metabolic capabilities

Identification of growth-coupled production strains considering protein costs and kinetic variability

Increased production of L-serine in Escherichia coli through Adaptive Laboratory Evolution

Kinetic profiling of metabolic specialists demonstrates stability and consistency of in vivo enzyme turnover numbers

Laboratory Evolution to Alternating Substrate Environments Yields Distinct Phenotypic and Genetic Adaptive Strategies

Laboratory evolution reveals a two-dimensional rate-yield tradeoff in microbial metabolism

Laboratory evolution reveals regulatory and metabolic trade-offs of glycerol utilization in Saccharomyces cerevisiae.

Literature mining supports a next-generation modeling approach to predict cellular byproduct secretion

MEMOTE for standardized genome-scale metabolic model testing

MID Max: LC-MS/MS Method for Measuring the Precursor and Product Mass Isotopomer Distributions of Metabolic Intermediates and Cofactors for Metabolic Flux Analysis Applications

Maximizing biomass productivity and cell density of Chlorella vulgaris by using light-emitting diode-based photobioreactor

Memote: A community-driven effort towards a standardized genome-scale metabolic model test suite

Model-driven discovery of underground metabolic functions in Escherichia coli

Model-driven evaluation of the production potential for growth-coupled products of Escherichia coli

Modeling Method for Increased Precision and Scope of Directly Measurable Fluxes at a Genome-Scale

Modeling methanogenesis with a genome-scale metabolic reconstruction of Methanosarcina barkeri

Multi-omic data integration enables discovery of hidden biological regularities

Multi-omics Quantification of Species Variation of Escherichia coli Links Molecular Features with Strain Phenotypes

Multiple Optimal Phenotypes Overcome Redox and Glycolytic Intermediate Metabolite Imbalances in Escherichia coli pgi Knockout Evolutions

Next-generation genome-scale models for metabolic engineering.

Optimal cofactor swapping can increase the theoretical yield for chemical production in Escherichia coli and Saccharomyces cerevisiae

OxyR Is a Convergent Target for Mutations Acquired during Adaptation to Oxidative Stress-Prone Metabolic States

Profiling the effect of nafcillin on HA-MRSA D712 using bacteriological and physiological media

Pseudogene repair driven by selection pressure applied in experimental evolution

Publisher Correction: MEMOTE for standardized genome-scale metabolic model testing

Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0

Reconstruction and modeling protein translocation and compartmentalization in Escherichia coli at the genome-scale

Reframing gene essentiality in terms of adaptive flexibility

Selection for Cell Yield Does Not Reduce Overflow Metabolism in <i>Escherichia coli</i>

Strain-Specific Metabolic Requirements Revealed by a Defined Minimal Medium for Systems Analyses of Staphylococcus aureus

Sulfide-driven microbial electrosynthesis.

The biomass objective function