3.9 Article

NetFlow: A tool for isolating carbon flows in genome-scale metabolic networks

Related references

Note: Only part of the references are listed.
Article Biochemical Research Methods

Improving the organization and interactivity of metabolic pathfinding with precomputed pathways

Sarah M. Kim et al.

BMC BIOINFORMATICS (2020)

Article Biochemical Research Methods

Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0

Laurent Heirendt et al.

NATURE PROTOCOLS (2019)

Article Chemistry, Medicinal

Machine Learning Guided Atom Mapping of Metabolic Reactions

Eleni E. Litsa et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2019)

Article Multidisciplinary Sciences

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

Douglas McCloskey et al.

NATURE COMMUNICATIONS (2018)

Article Biochemistry & Molecular Biology

The EcoCyc database: reflecting new knowledge about Escherichia coli K-12

Ingrid M. Keseler et al.

NUCLEIC ACIDS RESEARCH (2017)

Article Chemistry, Multidisciplinary

Comparative evaluation of atom mapping algorithms for balanced metabolic reactions: application to Recon 3D

German A. Preciat Gonzalez et al.

JOURNAL OF CHEMINFORMATICS (2017)

Article Biochemical Research Methods

Reconstruction of biological pathways and metabolic networks from in silico labeled metabolites

Noushin Hadadi et al.

BIOTECHNOLOGY JOURNAL (2017)

Review Biotechnology & Applied Microbiology

Quantitative intracellular flux modeling and applications in biotherapeutic development and production using CHO cell cultures

Zhuangrong Huang et al.

BIOTECHNOLOGY AND BIOENGINEERING (2017)

Article Chemistry, Analytical

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

Douglas McCloskey et al.

ANALYTICAL CHEMISTRY (2016)

Article Biochemical Research Methods

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

Christopher J. Tervo et al.

BIOTECHNOLOGY JOURNAL (2016)

Article Biochemical Research Methods

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

Christopher J. Tervo et al.

BIOTECHNOLOGY JOURNAL (2016)

Article Biotechnology & Applied Microbiology

13C metabolic flux analysis at a genome-scale

Saratram Gopalakrishnan et al.

METABOLIC ENGINEERING (2015)

Article Multidisciplinary Sciences

Designing overall stoichiometric conversions and intervening metabolic reactions

Anupam Chowdhury et al.

SCIENTIFIC REPORTS (2015)

Article Biochemical Research Methods

Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways

Zachary A. King et al.

PLOS COMPUTATIONAL BIOLOGY (2015)

Article Biochemical Research Methods

Refining carbon flux paths using atomic trace data

Jon Pey et al.

BIOINFORMATICS (2014)

Article Chemistry, Medicinal

CLCA: Maximum Common Molecular Substructure Queries within the MetRxn Database

Akhil Kumar et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2014)

Article Biochemistry & Molecular Biology

Genome-scale models of metabolism and gene expression extend and refine growth phenotype prediction

Edward J. O'Brien et al.

MOLECULAR SYSTEMS BIOLOGY (2013)

Article Biotechnology & Applied Microbiology

Potentiating antibacterial activity by predictably enhancing endogenous microbial ROS production

Mark P. Brynildsen et al.

NATURE BIOTECHNOLOGY (2013)

Article Chemistry, Medicinal

Accurate Atom-Mapping Computation for Biochemical Reactions

Mario Latendresse et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2012)

Article Biochemistry & Molecular Biology

Predicting selective drug targets in cancer through metabolic networks

Ori Folger et al.

MOLECULAR SYSTEMS BIOLOGY (2011)

Article Biotechnology & Applied Microbiology

Path finding methods accounting for stoichiometry in metabolic networks

Jon Pey et al.

GENOME BIOLOGY (2011)

Article Biochemical Research Methods

Finding metabolic pathways using atom tracking

Allison P. Heath et al.

BIOINFORMATICS (2010)

Article Biotechnology & Applied Microbiology

What is flux balance analysis?

Jeffrey D. Orth et al.

NATURE BIOTECHNOLOGY (2010)

Article Biochemistry & Molecular Biology

Inferring meaningful pathways in weighted metabolic networks

D Croes et al.

JOURNAL OF MOLECULAR BIOLOGY (2006)

Article Biochemistry & Molecular Biology

Metabolic PathFinding: inferring relevant pathways in biochemical networks

D Croes et al.

NUCLEIC ACIDS RESEARCH (2005)

Article Biotechnology & Applied Microbiology

Identifying gene targets for the metabolic engineering of lycopene biosynthesis in Escherichia coli

H Alper et al.

METABOLIC ENGINEERING (2005)

Article Biochemistry & Molecular Biology

The principle of flux minimization and its application to estimate stationary fluxes in metabolic networks

HG Holzhütter

EUROPEAN JOURNAL OF BIOCHEMISTRY (2004)

Article Biochemistry & Molecular Biology

OptStrain: A computational framework for redesign of microbial production systems

P Pharkya et al.

GENOME RESEARCH (2004)

Article Biotechnology & Applied Microbiology

OptKnock: A bilevel programming framework for identifying gene knockout strategies for microbial strain optimization

AP Burgard et al.

BIOTECHNOLOGY AND BIOENGINEERING (2003)

Article Multidisciplinary Sciences

Analysis of optimality in natural and perturbed metabolic networks

D Segrè et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2002)