Bilevel optimization techniques in computational strain design

Chowdhury, Anupam; Zomorrodi, Ali R.; Maranas, Costas D.

doi:10.1016/j.compchemeng.2014.06.007

Title: Bilevel optimization techniques in computational strain design

Authors:: Chowdhury, Anupam; Zomorrodi, Ali R.; Maranas, Costas D.

Publication Date:: Thu Jan 01 00:00:00 EST 2015

Sponsoring Org.:: USDOE

OSTI Identifier:: 1366316

Grant/Contract Number:: EEC-0813570

Resource Type:: Publisher's Accepted Manuscript

Journal Name:: Computers and Chemical Engineering

Additional Journal Information:: Journal Name: Computers and Chemical Engineering Journal Volume: 72 Journal Issue: C; Journal ID: ISSN 0098-1354

Publisher:: Elsevier

Country of Publication:: United Kingdom

Language:: English

Citation Formats


                    Chowdhury, Anupam, Zomorrodi, Ali R., and Maranas, Costas D. Bilevel optimization techniques in computational strain design.  United Kingdom: N. p., 2015. 
Web.  doi:10.1016/j.compchemeng.2014.06.007.

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                    Chowdhury, Anupam, Zomorrodi, Ali R., & Maranas, Costas D. Bilevel optimization techniques in computational strain design.  United Kingdom.  https://doi.org/10.1016/j.compchemeng.2014.06.007

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                    Chowdhury, Anupam, Zomorrodi, Ali R., and Maranas, Costas D. Thu .  
"Bilevel optimization techniques in computational strain design".  United Kingdom.  https://doi.org/10.1016/j.compchemeng.2014.06.007.

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@article{osti_1366316,

  title        = {Bilevel optimization techniques in computational strain design},

  author       = {Chowdhury, Anupam and Zomorrodi, Ali R. and Maranas, Costas D.},

  abstractNote = {},

  doi          = {10.1016/j.compchemeng.2014.06.007},

  journal      = {Computers and Chemical Engineering},

  number       = C,

  volume       = 72,

  place        = {United Kingdom},

  year         = {Thu Jan 01 00:00:00 EST 2015},

  month        = {Thu Jan 01 00:00:00 EST 2015}

}

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https://doi.org/10.1016/j.compchemeng.2014.06.007

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Title: Bilevel optimization techniques in computational strain design

Citation Formats

Recent advances in reconstruction and applications of genome-scale metabolic models journal, August 2012

In Silico Identification of Gene Amplification Targets for Improvement of Lycopene Production journal, March 2010

Integrating Flux Balance Analysis into Kinetic Models to Decipher the Dynamic Metabolism of Shewanella oneidensis MR-1 journal, February 2012

Effect of Sorghum vulgare phosphoenolpyruvate carboxylase and Lactococcus lactis pyruvate carboxylase coexpression on succinate production in mutant strains of Escherichia coli journal, November 2004

OptFlux: an open-source software platform for in silico metabolic engineering journal, April 2010

d-OptCom: Dynamic Multi-level and Multi-objective Metabolic Modeling of Microbial Communities journal, November 2013

Constraint-based strain design using continuous modifications (CosMos) of flux bounds finds new strategies for metabolic engineering journal, April 2013

Re-examination of metabolic fluxes in Escherichia coli during anaerobic fermentation of glucose using 13C labeling experiments and 2-dimensional nuclear magnetic resonance (NMR) spectroscopy journal, June 2011

Recent advances in the reconstruction of metabolic models and integration of omics data journal, October 2014

Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli W3110. journal, January 1994

Poly(butylene succinate) and its copolymers: Research, development and industrialization journal, November 2010

OptCom: A Multi-Level Optimization Framework for the Metabolic Modeling and Analysis of Microbial Communities journal, February 2012

GIM3E: condition-specific models of cellular metabolism developed from metabolomics and expression data journal, August 2013

Optknock: A bilevel programming framework for identifying gene knockout strategies for microbial strain optimization journal, October 2003

An optimization framework for identifying reaction activation/inhibition or elimination candidates for overproduction in microbial systems journal, January 2006

Biotechnology of succinic acid production and markets for derived industrial products journal, May 1999

Mathematical optimization applications in metabolic networks journal, November 2012

Development of a metabolic network design and optimization framework incorporating implementation constraints: A succinate production case study journal, January 2006

In silico aided metabolic engineering of Saccharomyces cerevisiae for improved bioethanol production journal, November 2005

Genome‐scale gene/reaction essentiality and synthetic lethality analysis journal, January 2009

Flow-injection fluorometric quantification of succinate in foodstuffs based on the use of an immobilized enzyme reactor journal, July 2000

Enhancing sesquiterpene production in Saccharomyces cerevisiae through in silico driven metabolic engineering journal, November 2009

k-Cone Analysis: Determining All Candidate Values for Kinetic Parameters on a Network Scale journal, March 2005

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EMILiO: A fast algorithm for genome-scale strain design journal, May 2011

OptForce: An Optimization Procedure for Identifying All Genetic Manipulations Leading to Targeted Overproductions journal, April 2010

GrowMatch: An Automated Method for Reconciling In Silico/In Vivo Growth Predictions journal, March 2009

k-OptForce: Integrating Kinetics with Flux Balance Analysis for Strain Design journal, February 2014

Towards a Bio-Based Industry: Benign Catalytic Esterifications of Succinic Acid in the Presence of Water journal, August 2007

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

A genome‐scale metabolic reconstruction for Escherichia coli K‐12 MG1655 that accounts for 1260 ORFs and thermodynamic information journal, January 2007

A novel fermentation pathway in anEscherichia coli mutant producing succinic acid, acetic acid, and ethanol journal, March 1998

A Kinetic Model of Transcription Initiation by RNA Polymerase journal, May 2008

Single Cell Genomics: Advances and Future Perspectives journal, January 2014

Model-driven evaluation of the production potential for growth-coupled products of Escherichia coli journal, May 2010

OptStrain: A computational framework for redesign of microbial production systems journal, November 2004

The IdhA Gene Encoding the Fermentative Lactate Dehydrogenase of Escherichia Coli journal, January 1997

OptORF: Optimal metabolic and regulatory perturbations for metabolic engineering of microbial strains journal, January 2010

Identifying gene targets for the metabolic engineering of lycopene biosynthesis in Escherichia coli journal, May 2005

Review of Biological Network Data and Its Applications journal, January 2013

Publishing 13C metabolic flux analysis studies: A review and future perspectives journal, November 2013

Basic and applied uses of genome‐scale metabolic network reconstructions of Escherichia coli journal, January 2013

Predicting metabolic engineering knockout strategies for chemical production: accounting for competing pathways journal, December 2009

In silico assessment of the metabolic capabilities of an engineered functional reversal of the β-oxidation cycle for the synthesis of longer-chain (C≥4) products journal, May 2014

Succinate production in Escherichia coli journal, September 2011

What is flux balance analysis? journal, March 2010

Improved Linear Integer Programming Formulations of Nonlinear Integer Problems journal, December 1975

Large-Scale Bi-Level Strain Design Approaches and Mixed-Integer Programming Solution Techniques journal, September 2011

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

Metabolic engineering of Escherichia coli for the production of L-valine based on transcriptome analysis and in silico gene knockout simulation journal, April 2007

Metabolic Engineering of Escherichia coli for Enhanced Production of Succinic Acid, Based on Genome Comparison and In Silico Gene Knockout Simulation journal, December 2005

Recent advances in reconstruction and applications of genome-scale metabolic models
journal, August 2012

In Silico Identification of Gene Amplification Targets for Improvement of Lycopene Production
journal, March 2010

Integrating Flux Balance Analysis into Kinetic Models to Decipher the Dynamic Metabolism of Shewanella oneidensis MR-1
journal, February 2012

Effect of Sorghum vulgare phosphoenolpyruvate carboxylase and Lactococcus lactis pyruvate carboxylase coexpression on succinate production in mutant strains of Escherichia coli
journal, November 2004

OptFlux: an open-source software platform for in silico metabolic engineering
journal, April 2010

d-OptCom: Dynamic Multi-level and Multi-objective Metabolic Modeling of Microbial Communities
journal, November 2013

Constraint-based strain design using continuous modifications (CosMos) of flux bounds finds new strategies for metabolic engineering
journal, April 2013

Re-examination of metabolic fluxes in Escherichia coli during anaerobic fermentation of glucose using 13C labeling experiments and 2-dimensional nuclear magnetic resonance (NMR) spectroscopy
journal, June 2011

Recent advances in the reconstruction of metabolic models and integration of omics data
journal, October 2014

Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli W3110.
journal, January 1994

Poly(butylene succinate) and its copolymers: Research, development and industrialization
journal, November 2010

OptCom: A Multi-Level Optimization Framework for the Metabolic Modeling and Analysis of Microbial Communities
journal, February 2012

GIM3E: condition-specific models of cellular metabolism developed from metabolomics and expression data
journal, August 2013

Optknock: A bilevel programming framework for identifying gene knockout strategies for microbial strain optimization
journal, October 2003

An optimization framework for identifying reaction activation/inhibition or elimination candidates for overproduction in microbial systems
journal, January 2006

Biotechnology of succinic acid production and markets for derived industrial products
journal, May 1999

Mathematical optimization applications in metabolic networks
journal, November 2012

Development of a metabolic network design and optimization framework incorporating implementation constraints: A succinate production case study
journal, January 2006

In silico aided metabolic engineering of Saccharomyces cerevisiae for improved bioethanol production
journal, November 2005

Genome‐scale gene/reaction essentiality and synthetic lethality analysis
journal, January 2009

Flow-injection fluorometric quantification of succinate in foodstuffs based on the use of an immobilized enzyme reactor
journal, July 2000

Enhancing sesquiterpene production in Saccharomyces cerevisiae through in silico driven metabolic engineering
journal, November 2009

k-Cone Analysis: Determining All Candidate Values for Kinetic Parameters on a Network Scale
journal, March 2005

Integrated stoichiometric, thermodynamic and kinetic modelling of steady state metabolism
journal, June 2010

EMILiO: A fast algorithm for genome-scale strain design
journal, May 2011

OptForce: An Optimization Procedure for Identifying All Genetic Manipulations Leading to Targeted Overproductions
journal, April 2010

GrowMatch: An Automated Method for Reconciling In Silico/In Vivo Growth Predictions
journal, March 2009

k-OptForce: Integrating Kinetics with Flux Balance Analysis for Strain Design
journal, February 2014

Towards a Bio-Based Industry: Benign Catalytic Esterifications of Succinic Acid in the Presence of Water
journal, August 2007

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

A genome‐scale metabolic reconstruction for Escherichia coli K‐12 MG1655 that accounts for 1260 ORFs and thermodynamic information
journal, January 2007

A novel fermentation pathway in anEscherichia coli mutant producing succinic acid, acetic acid, and ethanol
journal, March 1998

A Kinetic Model of Transcription Initiation by RNA Polymerase
journal, May 2008

Single Cell Genomics: Advances and Future Perspectives
journal, January 2014

Model-driven evaluation of the production potential for growth-coupled products of Escherichia coli
journal, May 2010

OptStrain: A computational framework for redesign of microbial production systems
journal, November 2004

The IdhA Gene Encoding the Fermentative Lactate Dehydrogenase of Escherichia Coli
journal, January 1997

OptORF: Optimal metabolic and regulatory perturbations for metabolic engineering of microbial strains
journal, January 2010

Identifying gene targets for the metabolic engineering of lycopene biosynthesis in Escherichia coli
journal, May 2005

Review of Biological Network Data and Its Applications
journal, January 2013

Publishing 13C metabolic flux analysis studies: A review and future perspectives
journal, November 2013

Basic and applied uses of genome‐scale metabolic network reconstructions of Escherichia coli
journal, January 2013

Predicting metabolic engineering knockout strategies for chemical production: accounting for competing pathways
journal, December 2009

In silico assessment of the metabolic capabilities of an engineered functional reversal of the β-oxidation cycle for the synthesis of longer-chain (C≥4) products
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