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Title: Improving flux predictions by integrating data from multiple strains


Not provided.

Publication Date:
Research Org.:
Univ. of Wisconsin, Madison, WI (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
DOE Contract Number:  
Resource Type:
Journal Article
Journal Name:
Additional Journal Information:
Journal Volume: 33; Journal Issue: 6; Journal ID: ISSN 1367-4803
Oxford University Press
Country of Publication:
United States
Biochemistry & Molecular Biology; Biotechnology & Applied Microbiology; Computer Science; Mathematical & Computational Biology; Mathematics

Citation Formats

Long, Matthew R., and Reed, Jennifer L. Improving flux predictions by integrating data from multiple strains. United States: N. p., 2016. Web. doi:10.1093/bioinformatics/btw706.
Long, Matthew R., & Reed, Jennifer L. Improving flux predictions by integrating data from multiple strains. United States. doi:10.1093/bioinformatics/btw706.
Long, Matthew R., and Reed, Jennifer L. Tue . "Improving flux predictions by integrating data from multiple strains". United States. doi:10.1093/bioinformatics/btw706.
title = {Improving flux predictions by integrating data from multiple strains},
author = {Long, Matthew R. and Reed, Jennifer L.},
abstractNote = {Not provided.},
doi = {10.1093/bioinformatics/btw706},
journal = {Bioinformatics},
issn = {1367-4803},
number = 6,
volume = 33,
place = {United States},
year = {2016},
month = {12}

Works referenced in this record:

Context-Specific Metabolic Networks Are Consistent with Experiments
journal, May 2008

Integration of expression data in genome-scale metabolic network reconstructions
journal, January 2012

Probabilistic integrative modeling of genome-scale metabolic and regulatory networks in Escherichia coli and Mycobacterium tuberculosis
journal, September 2010

  • Chandrasekaran, Sriram; Price, Nathan D.
  • Proceedings of the National Academy of Sciences, Vol. 107, Issue 41
  • DOI: 10.1073/pnas.1005139107

Drug Off-Target Effects Predicted Using Structural Analysis in the Context of a Metabolic Network Model
journal, September 2010

Interpreting Expression Data with Metabolic Flux Models: Predicting Mycobacterium tuberculosis Mycolic Acid Production
journal, August 2009

In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data
journal, February 2001

  • Edwards, Jeremy S.; Ibarra, Rafael U.; Palsson, Bernhard O.
  • Nature Biotechnology, Vol. 19, Issue 2
  • DOI: 10.1038/84379

Metabolic gene–deletion strains of Escherichia coli evolve to computationally predicted growth phenotypes
journal, September 2004

  • Fong, Stephen S.; Palsson, Bernhard Ø
  • Nature Genetics, Vol. 36, Issue 10
  • DOI: 10.1038/ng1432

Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth
journal, November 2002

  • Ibarra, Rafael U.; Edwards, Jeremy S.; Palsson, Bernhard O.
  • Nature, Vol. 420, Issue 6912
  • DOI: 10.1038/nature01149

Multiple High-Throughput Analyses Monitor the Response of E. coli to Perturbations
journal, April 2007

Functional integration of a metabolic network model and expression data without arbitrary thresholding
journal, December 2010

Integrative genome‐scale metabolic analysis of Vibrio vulnificus for drug targeting and discovery
journal, January 2011

  • Kim, Hyun Uk; Kim, Soo Young; Jeong, Haeyoung
  • Molecular Systems Biology, Vol. 7, Issue 1
  • DOI: 10.1038/msb.2010.115

RELATCH: relative optimality in metabolic networks explains robust metabolic and regulatory responses to perturbations
journal, January 2012

COMPLETE-MFA: Complementary parallel labeling experiments technique for metabolic flux analysis
journal, November 2013

Omic data from evolved E. coli are consistent with computed optimal growth from genome‐scale models
journal, January 2010

  • Lewis, Nathan E.; Hixson, Kim K.; Conrad, Tom M.
  • Molecular Systems Biology, Vol. 6, Issue 1
  • DOI: 10.1038/msb.2010.47

Characterization of physiological responses to 22 gene knockouts in Escherichia coli central carbon metabolism
journal, September 2016

Systematic Evaluation of Methods for Integration of Transcriptomic Data into Constraint-Based Models of Metabolism
journal, April 2014

The effects of alternate optimal solutions in constraint-based genome-scale metabolic models
journal, October 2003

In Silico Constraint-Based Strain Optimization Methods: the Quest for Optimal Cell Factories
journal, November 2015

  • Maia, Paulo; Rocha, Miguel; Rocha, Isabel
  • Microbiology and Molecular Biology Reviews, Vol. 80, Issue 1
  • DOI: 10.1128/MMBR.00014-15

A comprehensive genome‐scale reconstruction of Escherichia coli metabolism—2011
journal, January 2011

  • Orth, Jeffrey D.; Conrad, Tom M.; Na, Jessica
  • Molecular Systems Biology, Vol. 7, Issue 1
  • DOI: 10.1038/msb.2011.65

Equations and calculations for fermentations of butyric acid bacteria
journal, February 1984

  • Papoutsakis, Eleftherios Terry
  • Biotechnology and Bioengineering, Vol. 26, Issue 2
  • DOI: 10.1002/bit.260260210

Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli
journal, January 2007

  • Schuetz, Robert; Kuepfer, Lars; Sauer, Uwe
  • Molecular Systems Biology, Vol. 3, Issue 1
  • DOI: 10.1038/msb4100162

Analysis of optimality in natural and perturbed metabolic networks
journal, November 2002

  • Segre, D.; Vitkup, D.; Church, G. M.
  • Proceedings of the National Academy of Sciences, Vol. 99, Issue 23
  • DOI: 10.1073/pnas.232349399

Regulatory on/off minimization of metabolic flux changes after genetic perturbations
journal, May 2005

  • Shlomi, T.; Berkman, O.; Ruppin, E.
  • Proceedings of the National Academy of Sciences, Vol. 102, Issue 21
  • DOI: 10.1073/pnas.0406346102

13C-based metabolic flux analysis
journal, May 2009

  • Zamboni, Nicola; Fendt, Sarah-Maria; Rühl, Martin
  • Nature Protocols, Vol. 4, Issue 6
  • DOI: 10.1038/nprot.2009.58

iMAT: an integrative metabolic analysis tool
journal, November 2010