List of works - Jennifer L. Reed

2H and 13C metabolic flux analysis elucidates in vivo thermodynamics of the ED pathway in Zymomonas mobilis

scientific article published on 10 May 2019

A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2

scientific article

A framework for the identification of promising bio-based chemicals

scientific article published on 10 July 2018

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

scientific article (publication date: 2007)

Adaptive evolution of synthetic cooperating communities improves growth performance

scientific article

Advances in gap-filling genome-scale metabolic models and model-driven experiments lead to novel metabolic discoveries.

scientific article published on 23 December 2017

An automated phenotype-driven approach (GeneForce) for refining metabolic and regulatory models

scientific article

An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR)

scientific article

Analysis of metabolic capabilities using singular value decomposition of extreme pathway matrices

scientific article

BioMog: a computational framework for the de novo generation or modification of essential biomass components

scientific article

Comparisons of Shewanella strains based on genome annotations, modeling, and experiments

scientific article

Complex physiology and compound stress responses during fermentation of alkali-pretreated corn stover hydrolysate by an Escherichia coli ethanologen.

scientific article

Computational approaches in metabolic engineering

scientific article published on January 2010

Computational evaluation of Synechococcus sp. PCC 7002 metabolism for chemical production

scientific article published on 24 April 2013

Computational methods in metabolic engineering for strain design.

scientific article published on 07 January 2015

Constraint-based analysis of metabolic capacity of Salmonella typhimurium during host-pathogen interaction

scientific article

Constraint-based model of Shewanella oneidensis MR-1 metabolism: a tool for data analysis and hypothesis generation

scientific article

Constraint-based strain design using continuous modifications (CosMos) of flux bounds finds new strategies for metabolic engineering.

scientific article

Correction: Directed Evolution Reveals Unexpected Epistatic Interactions That Alter Metabolic Regulation and Enable Anaerobic Xylose Use by Saccharomyces cerevisiae

scientific article published on 9 November 2016

Directed Evolution Reveals Unexpected Epistatic Interactions That Alter Metabolic Regulation and Enable Anaerobic Xylose Use by Saccharomyces cerevisiae.

scientific article

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

scientific article published on 14 October 2015

Escherichia coli as a model organism for systems metabolic engineering

scientific article

Expanding Metabolic Engineering Algorithms Using Feasible Space and Shadow Price Constraint Modules

scientific article published on December 2014

Experimental and computational assessment of conditionally essential genes in Escherichia coli

scientific article

FOCAL: an experimental design tool for systematizing metabolic discoveries and model development

scientific article published on 13 December 2012

Flux Balance Analysis Indicates that Methane Is the Lowest Cost Feedstock for Microbial Cell Factories.

scientific article published on 10 July 2017

Genome-Wide Analysis of RNA Decay in the Cyanobacterium Synechococcus sp. Strain PCC 7002

scientific article published on 04 August 2020

Genome-scale in silico models of E. coli have multiple equivalent phenotypic states: assessment of correlated reaction subsets that comprise network states.

scientific article

Genome-scale modeling of light-driven reductant partitioning and carbon fluxes in diazotrophic unicellular cyanobacterium Cyanothece sp. ATCC 51142

scientific article

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

scientific article (publication date: November 2004)

Genome-scale reconstruction of metabolic networks of Lactobacillus casei ATCC 334 and 12A.

scientific article

Hierarchical thinking in network biology: the unbiased modularization of biochemical networks.

scientific article

Identification of functional differences in metabolic networks using comparative genomics and constraint-based models

scientific article

Improving flux predictions by integrating data from multiple strains

scientific article

Inferring ancient metabolism using ancestral core metabolic models of enterobacteria

scientific article

Integrating high-throughput and computational data elucidates bacterial networks

scientific article

Integrating proteomic or transcriptomic data into metabolic models using linear bound flux balance analysis

scientific article published on 01 November 2018

Large-scale bi-level strain design approaches and mixed-integer programming solution techniques

scientific article

Light-optimized growth of cyanobacterial cultures: Growth phases and productivity of biomass and secreted molecules in light-limited batch growth

scientific article published on 27 March 2018

MapMaker and PathTracer for tracking carbon in genome-scale metabolic models.

scientific article published on 14 January 2016

Mechanistic analysis of multi-omics datasets to generate kinetic parameters for constraint-based metabolic models.

scientific article

Metabolic assessment of E. coli as a Biofactory for commercial products.

scientific article published on 2 February 2016

Metabolic reconstruction and modeling of nitrogen fixation in Rhizobium etli

scientific article

Model-driven analysis of mutant fitness experiments improves genome-scale metabolic models of Zymomonas mobilis ZM4

scientific article published on 17 August 2020

Model-enabled gene search (MEGS) allows fast and direct discovery of enzymatic and transport gene functions in the marine bacterium Vibrio fischeri.

scientific article published on 26 April 2017

Multi-platform 'Omics Analysis of Human Ebola Virus Disease Pathogenesis

scientific article published on 15 November 2017

Network-based analysis of metabolic regulation in the human red blood cell

scientific article (publication date: 21 November 2003)

OptORF: Optimal metabolic and regulatory perturbations for metabolic engineering of microbial strains

scientific article

Predicting outcomes of steady-state ¹³C isotope tracing experiments using Monte Carlo sampling

scientific article

Pyruvate and lactate metabolism by Shewanella oneidensis MR-1 under fermentation, oxygen limitation, and fumarate respiration conditions

scientific article published on 30 September 2011

Quantitative assessment of thermodynamic constraints on the solution space of genome-scale metabolic models.

scientific article published on July 2013

RELATCH: relative optimality in metabolic networks explains robust metabolic and regulatory responses to perturbations.

scientific article published on 5 July 2012

Refining metabolic models and accounting for regulatory effects

scientific article published on 14 March 2014

Shrinking the metabolic solution space using experimental datasets

scientific article

Software platforms to facilitate reconstructing genome-scale metabolic networks

scientific article

Synergy between (13)C-metabolic flux analysis and flux balance analysis for understanding metabolic adaptation to anaerobiosis in E. coli.

scientific article published in December 2010

Systems Metabolic Engineering of Escherichia coli Improves Coconversion of Lignocellulose-Derived Sugars

scientific article published on 05 August 2019

Systems approach to refining genome annotation

scholarly article

The evolution of metabolic networks of E. coli

scientific article published on November 2011

The global transcriptional regulatory network for metabolism in Escherichia coli exhibits few dominant functional states.

scholarly article

Thermodynamics and H2 Transfer in a Methanogenic, Syntrophic Community

scientific article published on 6 July 2015

Thirteen years of building constraint-based in silico models of Escherichia coli

scientific article

Towards environmental systems biology of Shewanella

scientific article published on 07 July 2008

Towards multidimensional genome annotation

scientific article

Transcriptional characterization of Vibrio fischeri during colonization of juvenile Euprymna scolopes

scientific article published on 2 February 2017

Transcriptional patterns in both host and bacterium underlie a daily rhythm of anatomical and metabolic change in a beneficial symbiosis

scientific article

iRsp1095: a genome-scale reconstruction of the Rhodobacter sphaeroides metabolic network

scientific article (publication date: 21 July 2011)

List of works by Jennifer L. Reed

2H and 13C metabolic flux analysis elucidates in vivo thermodynamics of the ED pathway in Zymomonas mobilis

A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2

A framework for the identification of promising bio-based chemicals

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

Adaptive evolution of synthetic cooperating communities improves growth performance

Advances in gap-filling genome-scale metabolic models and model-driven experiments lead to novel metabolic discoveries.

An automated phenotype-driven approach (GeneForce) for refining metabolic and regulatory models

An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR)

Analysis of metabolic capabilities using singular value decomposition of extreme pathway matrices

BioMog: a computational framework for the de novo generation or modification of essential biomass components

Comparisons of Shewanella strains based on genome annotations, modeling, and experiments

Complex physiology and compound stress responses during fermentation of alkali-pretreated corn stover hydrolysate by an Escherichia coli ethanologen.

Computational approaches in metabolic engineering

Computational evaluation of Synechococcus sp. PCC 7002 metabolism for chemical production

Computational methods in metabolic engineering for strain design.

Constraint-based analysis of metabolic capacity of Salmonella typhimurium during host-pathogen interaction

Constraint-based model of Shewanella oneidensis MR-1 metabolism: a tool for data analysis and hypothesis generation

Constraint-based strain design using continuous modifications (CosMos) of flux bounds finds new strategies for metabolic engineering.

Correction: Directed Evolution Reveals Unexpected Epistatic Interactions That Alter Metabolic Regulation and Enable Anaerobic Xylose Use by Saccharomyces cerevisiae

Directed Evolution Reveals Unexpected Epistatic Interactions That Alter Metabolic Regulation and Enable Anaerobic Xylose Use by Saccharomyces cerevisiae.

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

Escherichia coli as a model organism for systems metabolic engineering

Expanding Metabolic Engineering Algorithms Using Feasible Space and Shadow Price Constraint Modules

Experimental and computational assessment of conditionally essential genes in Escherichia coli

FOCAL: an experimental design tool for systematizing metabolic discoveries and model development

Flux Balance Analysis Indicates that Methane Is the Lowest Cost Feedstock for Microbial Cell Factories.

Genome-Wide Analysis of RNA Decay in the Cyanobacterium Synechococcus sp. Strain PCC 7002

Genome-scale in silico models of E. coli have multiple equivalent phenotypic states: assessment of correlated reaction subsets that comprise network states.

Genome-scale modeling of light-driven reductant partitioning and carbon fluxes in diazotrophic unicellular cyanobacterium Cyanothece sp. ATCC 51142

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

Genome-scale reconstruction of metabolic networks of Lactobacillus casei ATCC 334 and 12A.

Hierarchical thinking in network biology: the unbiased modularization of biochemical networks.

Identification of functional differences in metabolic networks using comparative genomics and constraint-based models

Improving flux predictions by integrating data from multiple strains

Inferring ancient metabolism using ancestral core metabolic models of enterobacteria

Integrating high-throughput and computational data elucidates bacterial networks

Integrating proteomic or transcriptomic data into metabolic models using linear bound flux balance analysis

Large-scale bi-level strain design approaches and mixed-integer programming solution techniques

Light-optimized growth of cyanobacterial cultures: Growth phases and productivity of biomass and secreted molecules in light-limited batch growth

MapMaker and PathTracer for tracking carbon in genome-scale metabolic models.

Mechanistic analysis of multi-omics datasets to generate kinetic parameters for constraint-based metabolic models.

Metabolic assessment of E. coli as a Biofactory for commercial products.

Metabolic reconstruction and modeling of nitrogen fixation in Rhizobium etli

Model-driven analysis of mutant fitness experiments improves genome-scale metabolic models of Zymomonas mobilis ZM4

Model-enabled gene search (MEGS) allows fast and direct discovery of enzymatic and transport gene functions in the marine bacterium Vibrio fischeri.

Multi-platform 'Omics Analysis of Human Ebola Virus Disease Pathogenesis

Network-based analysis of metabolic regulation in the human red blood cell

OptORF: Optimal metabolic and regulatory perturbations for metabolic engineering of microbial strains

Predicting outcomes of steady-state ¹³C isotope tracing experiments using Monte Carlo sampling

Pyruvate and lactate metabolism by Shewanella oneidensis MR-1 under fermentation, oxygen limitation, and fumarate respiration conditions

Quantitative assessment of thermodynamic constraints on the solution space of genome-scale metabolic models.

RELATCH: relative optimality in metabolic networks explains robust metabolic and regulatory responses to perturbations.

Refining metabolic models and accounting for regulatory effects

Shrinking the metabolic solution space using experimental datasets

Software platforms to facilitate reconstructing genome-scale metabolic networks

Synergy between (13)C-metabolic flux analysis and flux balance analysis for understanding metabolic adaptation to anaerobiosis in E. coli.

Systems Metabolic Engineering of Escherichia coli Improves Coconversion of Lignocellulose-Derived Sugars

Systems approach to refining genome annotation

The evolution of metabolic networks of E. coli

The global transcriptional regulatory network for metabolism in Escherichia coli exhibits few dominant functional states.

Thermodynamics and H2 Transfer in a Methanogenic, Syntrophic Community

Thirteen years of building constraint-based in silico models of Escherichia coli

Towards environmental systems biology of Shewanella

Towards multidimensional genome annotation

Transcriptional characterization of Vibrio fischeri during colonization of juvenile Euprymna scolopes

Transcriptional patterns in both host and bacterium underlie a daily rhythm of anatomical and metabolic change in a beneficial symbiosis

iRsp1095: a genome-scale reconstruction of the Rhodobacter sphaeroides metabolic network