From DNA to FBA: How to Build Your Own Genome-Scale Metabolic Model
Abstract
Microbiological studies are increasingly relying on in silico methods to perform exploration and rapid analysis of genomic data, and functional genomics studies are supplemented by the new perspectives that genome-scale metabolic models offer. A mathematical model consisting of a microbe’s entire metabolic map can be rapidly determined from whole-genome sequencing and annotating the genomic material encoded in its DNA. Flux-balance analysis (FBA), a linear programming technique that uses metabolic models to predict the phenotypic responses imposed by environmental elements and factors, is the leading method to simulate and manipulate cellular growth in silico. However, the process of creating an accurate model to use in FBA consists of a series of steps involving a multitude of connections between bioinformatics databases, enzyme resources, and metabolic pathways. We present the methodology and procedure to obtain a metabolic model using PyFBA, an extensible Pythonbased open-source software package aimed to provide a platform where functional annotations are used to build metabolic models (http://linsalrob.github.io/PyFBA). Backed by the Model SEED biochemistry database, PyFBA contains methods to reconstruct a microbe’s metabolic map, run FBA upon different media conditions, and gap-fill its metabolism. The extensibility of PyFBA facilitates novel techniques in creating accurate genome-scale metabolic models.
- Authors:
-
- San Diego State Univ., CA (United States). Computational Science Research Center
- Argonne National Lab. (ANL), Argonne, IL (United States). Mathematics and Computer Science Division
- Fellowship for Interpretation of Genomes, Burr Ridge, IL (United States)
- San Diego State Univ., CA (United States). Dept. of Computer Science
- San Diego State Univ., CA (United States). Computational Science Research Center; San Diego State Univ., CA (United States). Dept. of Computer Science; San Diego State Univ., CA (United States). Biological and Medical Informatics Research Center; San Diego State Univ., CA (United States). Dept. of Biology
- Publication Date:
- Research Org.:
- Argonne National Laboratory (ANL), Argonne, IL (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC)
- OSTI Identifier:
- 1628146
- Grant/Contract Number:
- AC02-06CH11357
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Frontiers in Microbiology
- Additional Journal Information:
- Journal Volume: 7; Journal ID: ISSN 1664-302X
- Publisher:
- Frontiers Research Foundation
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; Microbiology; metabolic modeling; metabolic reconstruction; in silico modeling; flux-balance analysis; model SEED; genome annotation
Citation Formats
Cuevas, Daniel A., Edirisinghe, Janaka, Henry, Chris S., Overbeek, Ross, O’Connell, Taylor G., and Edwards, Robert A. From DNA to FBA: How to Build Your Own Genome-Scale Metabolic Model. United States: N. p., 2016.
Web. doi:10.3389/fmicb.2016.00907.
Cuevas, Daniel A., Edirisinghe, Janaka, Henry, Chris S., Overbeek, Ross, O’Connell, Taylor G., & Edwards, Robert A. From DNA to FBA: How to Build Your Own Genome-Scale Metabolic Model. United States. https://doi.org/10.3389/fmicb.2016.00907
Cuevas, Daniel A., Edirisinghe, Janaka, Henry, Chris S., Overbeek, Ross, O’Connell, Taylor G., and Edwards, Robert A. Fri .
"From DNA to FBA: How to Build Your Own Genome-Scale Metabolic Model". United States. https://doi.org/10.3389/fmicb.2016.00907. https://www.osti.gov/servlets/purl/1628146.
@article{osti_1628146,
title = {From DNA to FBA: How to Build Your Own Genome-Scale Metabolic Model},
author = {Cuevas, Daniel A. and Edirisinghe, Janaka and Henry, Chris S. and Overbeek, Ross and O’Connell, Taylor G. and Edwards, Robert A.},
abstractNote = {Microbiological studies are increasingly relying on in silico methods to perform exploration and rapid analysis of genomic data, and functional genomics studies are supplemented by the new perspectives that genome-scale metabolic models offer. A mathematical model consisting of a microbe’s entire metabolic map can be rapidly determined from whole-genome sequencing and annotating the genomic material encoded in its DNA. Flux-balance analysis (FBA), a linear programming technique that uses metabolic models to predict the phenotypic responses imposed by environmental elements and factors, is the leading method to simulate and manipulate cellular growth in silico. However, the process of creating an accurate model to use in FBA consists of a series of steps involving a multitude of connections between bioinformatics databases, enzyme resources, and metabolic pathways. We present the methodology and procedure to obtain a metabolic model using PyFBA, an extensible Pythonbased open-source software package aimed to provide a platform where functional annotations are used to build metabolic models (http://linsalrob.github.io/PyFBA). Backed by the Model SEED biochemistry database, PyFBA contains methods to reconstruct a microbe’s metabolic map, run FBA upon different media conditions, and gap-fill its metabolism. The extensibility of PyFBA facilitates novel techniques in creating accurate genome-scale metabolic models.},
doi = {10.3389/fmicb.2016.00907},
journal = {Frontiers in Microbiology},
number = ,
volume = 7,
place = {United States},
year = {Fri Jun 17 00:00:00 EDT 2016},
month = {Fri Jun 17 00:00:00 EDT 2016}
}
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Works referenced in this record:
Computationally efficient flux variability analysis
journal, September 2010
- Gudmundsson, Steinn; Thiele, Ines
- BMC Bioinformatics, Vol. 11, Issue 1
WIT: integrated system for high-throughput genome sequence analysis and metabolic reconstruction
journal, January 2000
- Overbeek, R.
- Nucleic Acids Research, Vol. 28, Issue 1
Reconstruction and modeling protein translocation and compartmentalization in Escherichia coli at the genome-scale
journal, September 2014
- Liu, Joanne K.; O’Brien, Edward J.; Lerman, Joshua A.
- BMC Systems Biology, Vol. 8, Issue 1
The ERGOTM genome analysis and discovery system
journal, January 2003
- Overbeek, R.
- Nucleic Acids Research, Vol. 31, Issue 1
Flux balance analysis in the era of metabolomics
journal, March 2006
- Lee, J. M.
- Briefings in Bioinformatics, Vol. 7, Issue 2
Metabolic Capabilities of Escherichia coli II. Optimal Growth Patterns
journal, December 1993
- Varma, Amit; Palsson, Bernhard O.
- Journal of Theoretical Biology, Vol. 165, Issue 4
Software platforms to facilitate reconstructing genome-scale metabolic networks: Software platforms for network reconstruction
journal, November 2013
- Hamilton, Joshua J.; Reed, Jennifer L.
- Environmental Microbiology, Vol. 16, Issue 1
Advances in flux balance analysis
journal, October 2003
- Kauffman, Kenneth J.; Prakash, Purusharth; Edwards, Jeremy S.
- Current Opinion in Biotechnology, Vol. 14, Issue 5
Optimization based automated curation of metabolic reconstructions
journal, January 2007
- Satish Kumar, Vinay; Dasika, Madhukar S.; Maranas, Costas D.
- BMC Bioinformatics, Vol. 8, Issue 1
Gene Calling and Bacterial Genome Annotation with BG7
book, January 2015
- Tobes, Raquel; Pareja-Tobes, Pablo; Manrique, Marina
- Methods in Molecular Biology
The Systems Biology Research Tool: evolvable open-source software
journal, June 2008
- Wright, Jeremiah; Wagner, Andreas
- BMC Systems Biology, Vol. 2, Issue 1
Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research
journal, August 2005
- Conesa, A.; Gotz, S.; Garcia-Gomez, J. M.
- Bioinformatics, Vol. 21, Issue 18
Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0
journal, August 2011
- Schellenberger, Jan; Que, Richard; Fleming, Ronan M. T.
- Nature Protocols, Vol. 6, Issue 9
Toward the automated generation of genome-scale metabolic networks in the SEED
journal, January 2007
- DeJongh, Matthew; Formsma, Kevin; Boillot, Paul
- BMC Bioinformatics, Vol. 8, Issue 1
Elucidating genomic gaps using phenotypic profiles
journal, January 2014
- Cuevas, Daniel A.; Garza, Daniel; Sanchez, Savannah E.
- F1000Research, Vol. 3
Automated Genome Annotation and Metabolic Model Reconstruction in the SEED and Model SEED
book, January 2013
- Devoid, Scott; Overbeek, Ross; DeJongh, Matthew
- Methods in Molecular Biology
The Escherichia coli MG1655 in silico metabolic genotype: Its definition, characteristics, and capabilities
journal, May 2000
- Edwards, J. S.; Palsson, B. O.
- Proceedings of the National Academy of Sciences, Vol. 97, Issue 10
Identification of Genome-Scale Metabolic Network Models Using Experimentally Measured Flux Profiles
journal, January 2006
- Herrgård, Markus J.; Fong, Stephen S.; Palsson, Bernhard Ø.
- PLoS Computational Biology, Vol. 2, Issue 7
Software applications for flux balance analysis
journal, November 2012
- Lakshmanan, M.; Koh, G.; Chung, B. K. S.
- Briefings in Bioinformatics, Vol. 15, Issue 1
Reconciliation of Genome-Scale Metabolic Reconstructions for Comparative Systems Analysis
journal, March 2011
- Oberhardt, Matthew A.; Puchałka, Jacek; Martins dos Santos, Vítor A. P.
- PLoS Computational Biology, Vol. 7, Issue 3
The RAST Server: Rapid Annotations using Subsystems Technology
journal, January 2008
- Aziz, Ramy K.; Bartels, Daniela; Best, Aaron A.
- BMC Genomics, Vol. 9, Issue 1, Article No. 75
MIRAGE: a functional genomics-based approach for metabolic network model reconstruction and its application to cyanobacteria networks
journal, January 2012
- Vitkin, Edward; Shlomi, Tomer
- Genome Biology, Vol. 13, Issue 11
COBRApy: COnstraints-Based Reconstruction and Analysis for Python
journal, January 2013
- Ebrahim, Ali; Lerman, Joshua A.; Palsson, Bernhard O.
- BMC Systems Biology, Vol. 7, Issue 1
GrowMatch: An Automated Method for Reconciling In Silico/In Vivo Growth Predictions
journal, March 2009
- Kumar, Vinay Satish; Maranas, Costas D.
- PLoS Computational Biology, Vol. 5, Issue 3
Likelihood-Based Gene Annotations for Gap Filling and Quality Assessment in Genome-Scale Metabolic Models
journal, October 2014
- Benedict, Matthew N.; Mundy, Michael B.; Henry, Christopher S.
- PLoS Computational Biology, Vol. 10, Issue 10
ExPASy: the proteomics server for in-depth protein knowledge and analysis
journal, July 2003
- Gasteiger, E.
- Nucleic Acids Research, Vol. 31, Issue 13
Prokka: rapid prokaryotic genome annotation
journal, March 2014
- Seemann, T.
- Bioinformatics, Vol. 30, Issue 14
Long-term phenotypic evolution of bacteria
journal, October 2014
- Plata, Germán; Henry, Christopher S.; Vitkup, Dennis
- Nature, Vol. 517, Issue 7534
The challenges of in silico biology
journal, November 2000
- Palsson, Bernhard
- Nature Biotechnology, Vol. 18, Issue 11
Minimal Reaction Sets for Escherichia coli Metabolism under Different Growth Requirements and Uptake Environments
journal, October 2001
- Burgard, A. P.; Vaidyaraman, S.; Maranas, C. D.
- Biotechnology Progress, Vol. 17, Issue 5
Genome-scale microbial in silico models: the constraints-based approach
journal, April 2003
- Price, Nathan D.; Papin, Jason A.; Schilling, Christophe H.
- Trends in Biotechnology, Vol. 21, Issue 4
Filling gaps in a metabolic network using expression information
journal, July 2004
- Kharchenko, P.; Vitkup, D.; Church, G. M.
- Bioinformatics, Vol. 20, Issue Suppl 1
Phage Phenomics: Physiological Approaches to Characterize Novel Viral Proteins
journal, January 2015
- Sanchez, Savannah E.; Cuevas, Daniel A.; Rostron, Jason E.
- Journal of Visualized Experiments, Issue 100
PATRIC, the bacterial bioinformatics database and analysis resource
journal, November 2013
- Wattam, Alice R.; Abraham, David; Dalay, Oral
- Nucleic Acids Research, Vol. 42, Issue D1
Optimization-based framework for inferring and testing hypothesized metabolic objective functions
journal, June 2003
- Burgard, Anthony P.; Maranas, Costas D.
- Biotechnology and Bioengineering, Vol. 82, Issue 6
RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes
journal, February 2015
- Brettin, Thomas; Davis, James J.; Disz, Terry
- Scientific Reports, Vol. 5, Issue 1
BRENDA, enzyme data and metabolic information
journal, January 2002
- Schomburg, I.
- Nucleic Acids Research, Vol. 30, Issue 1
An integrative, multi‐scale, genome‐wide model reveals the phenotypic landscape of E scherichia coli
journal, July 2014
- Carrera, Javier; Estrela, Raissa; Luo, Jing
- Molecular Systems Biology, Vol. 10, Issue 7
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
Genome‐scale models of metabolism and gene expression extend and refine growth phenotype prediction
journal, January 2013
- O'Brien, Edward J.; Lerman, Joshua A.; Chang, Roger L.
- Molecular Systems Biology, Vol. 9, Issue 1
An application programming interface for CellNetAnalyzer
journal, August 2011
- Klamt, Steffen; von Kamp, Axel
- Biosystems, Vol. 105, Issue 2
The KEGG resource for deciphering the genome
journal, January 2004
- Kanehisa, M.
- Nucleic Acids Research, Vol. 32, Issue 90001
The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)
journal, November 2013
- Overbeek, Ross; Olson, Robert; Pusch, Gordon D.
- Nucleic Acids Research, Vol. 42, Issue D1
BASys: a web server for automated bacterial genome annotation
journal, July 2005
- Van Domselaar, G. H.; Stothard, P.; Shrivastava, S.
- Nucleic Acids Research, Vol. 33, Issue Web Server
Solving Puzzles With Missing Pieces: The Power of Systems Biology
journal, January 2016
- Yurkovich, James T.; Palsson, Bernhard O.
- Proceedings of the IEEE, Vol. 104, Issue 1
Metabolic modelling of microbes: the flux-balance approach
journal, March 2002
- Edwards, Jeremy S.; Covert, Markus; Palsson, Bernhard
- Environmental Microbiology, Vol. 4, Issue 3
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases
journal, November 2013
- Caspi, Ron; Altman, Tomer; Billington, Richard
- Nucleic Acids Research, Vol. 42, Issue D1
What is flux balance analysis?
journal, March 2010
- Orth, Jeffrey D.; Thiele, Ines; Palsson, Bernhard Ø
- Nature Biotechnology, Vol. 28, Issue 3
Computer-aided analyses of transport protein sequences: gleaning evidence concerning function, structure, biogenesis, and evolution.
journal, January 1994
- Saier, M. H.
- Microbiological Reviews, Vol. 58, Issue 1
Flux balance analysis of biological systems: applications and challenges
journal, March 2009
- Raman, K.; Chandra, N.
- Briefings in Bioinformatics, Vol. 10, Issue 4
Frontiers in metabolic reconstruction and modeling of plant genomes
journal, January 2012
- Seaver, S. M. D.; Henry, C. S.; Hanson, A. D.
- Journal of Experimental Botany, Vol. 63, Issue 6
A major superfamily of transmembrane facilitators that catalyse uniport, symport and antiport
journal, January 1993
- Marger, Michael D.; Saier, Milton H.
- Trends in Biochemical Sciences, Vol. 18, Issue 1
Metabolic Capabilities of Escherichia coli II. Optimal Growth Patterns
journal, December 1993
- Varma, Amit; Palsson, Bernhard O.
- Journal of Theoretical Biology, Vol. 165, Issue 4
Gene Calling and Bacterial Genome Annotation with BG7
book, January 2015
- Tobes, Raquel; Pareja-Tobes, Pablo; Manrique, Marina
- Methods in Molecular Biology
An application programming interface for CellNetAnalyzer
journal, August 2011
- Klamt, Steffen; von Kamp, Axel
- Biosystems, Vol. 105, Issue 2
Advances in flux balance analysis
journal, October 2003
- Kauffman, Kenneth J.; Prakash, Purusharth; Edwards, Jeremy S.
- Current Opinion in Biotechnology, Vol. 14, Issue 5
The challenges of in silico biology
journal, November 2000
- Palsson, Bernhard
- Nature Biotechnology, Vol. 18, Issue 11
Genome‐scale models of metabolism and gene expression extend and refine growth phenotype prediction
journal, January 2013
- O'Brien, Edward J.; Lerman, Joshua A.; Chang, Roger L.
- Molecular Systems Biology, Vol. 9, Issue 1
Long-term phenotypic evolution of bacteria
journal, October 2014
- Plata, Germán; Henry, Christopher S.; Vitkup, Dennis
- Nature, Vol. 517, Issue 7534
Commensal Pseudomonas protect Arabidopsis thaliana from a coexisting pathogen via multiple lineage-dependent mechanisms
journal, December 2021
- Shalev, Or; Ashkenazy, Haim; Neumann, Manuela
- The ISME Journal, Vol. 16, Issue 5
Analysis of histological and microRNA profiles changes in rabbit skin development
journal, January 2020
- Ding, Haisheng; Cheng, Guanglong; Leng, Jianjian
- Scientific Reports, Vol. 10, Issue 1
RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes
journal, February 2015
- Brettin, Thomas; Davis, James J.; Disz, Terry
- Scientific Reports, Vol. 5, Issue 1
Metabolic modelling of microbes: the flux-balance approach
journal, March 2002
- Edwards, Jeremy S.; Covert, Markus; Palsson, Bernhard
- Environmental Microbiology, Vol. 4, Issue 3
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
The Escherichia coli MG1655 in silico metabolic genotype: Its definition, characteristics, and capabilities
journal, May 2000
- Edwards, J. S.; Palsson, B. O.
- Proceedings of the National Academy of Sciences, Vol. 97, Issue 10
Software applications for flux balance analysis
journal, November 2012
- Lakshmanan, M.; Koh, G.; Chung, B. K. S.
- Briefings in Bioinformatics, Vol. 15, Issue 1
Filling gaps in a metabolic network using expression information
journal, July 2004
- Kharchenko, P.; Vitkup, D.; Church, G. M.
- Bioinformatics, Vol. 20, Issue Suppl 1
Frontiers in metabolic reconstruction and modeling of plant genomes
journal, January 2012
- Seaver, S. M. D.; Henry, C. S.; Hanson, A. D.
- Journal of Experimental Botany, Vol. 63, Issue 6
BRENDA, enzyme data and metabolic information
journal, January 2002
- Schomburg, I.
- Nucleic Acids Research, Vol. 30, Issue 1
The ERGOTM genome analysis and discovery system
journal, January 2003
- Overbeek, R.
- Nucleic Acids Research, Vol. 31, Issue 1
BASys: a web server for automated bacterial genome annotation
journal, July 2005
- Van Domselaar, G. H.; Stothard, P.; Shrivastava, S.
- Nucleic Acids Research, Vol. 33, Issue Web Server
KEGG for integration and interpretation of large-scale molecular data sets
journal, November 2011
- Kanehisa, M.; Goto, S.; Sato, Y.
- Nucleic Acids Research, Vol. 40, Issue D1
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases
journal, November 2013
- Caspi, Ron; Altman, Tomer; Billington, Richard
- Nucleic Acids Research, Vol. 42, Issue D1
The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)
journal, November 2013
- Overbeek, Ross; Olson, Robert; Pusch, Gordon D.
- Nucleic Acids Research, Vol. 42, Issue D1
Software platforms to facilitate reconstructing genome-scale metabolic networks: Software platforms for network reconstruction
journal, November 2013
- Hamilton, Joshua J.; Reed, Jennifer L.
- Environmental Microbiology, Vol. 16, Issue 1
Computer-aided analyses of transport protein sequences: gleaning evidence concerning function, structure, biogenesis, and evolution
journal, March 1994
- Saier, M. H.
- Microbiological Reviews, Vol. 58, Issue 1
Computationally efficient flux variability analysis
journal, September 2010
- Gudmundsson, Steinn; Thiele, Ines
- BMC Bioinformatics, Vol. 11, Issue 1
FASIMU: flexible software for flux-balance computation series in large metabolic networks
journal, January 2011
- Hoppe, Andreas; Hoffmann, Sabrina; Gerasch, Andreas
- BMC Bioinformatics, Vol. 12, Issue 1
Optimization based automated curation of metabolic reconstructions
journal, January 2007
- Satish Kumar, Vinay; Dasika, Madhukar S.; Maranas, Costas D.
- BMC Bioinformatics, Vol. 8, Issue 1
Emiliania huxleyi endures N-limitation with an efficient metabolic budgeting and effective ATP synthesis
journal, January 2014
- Rokitta, Sebastian D.; Von Dassow, Peter; Rost, Björn
- BMC Genomics, Vol. 15, Issue 1
The RAST Server: Rapid Annotations using Subsystems Technology
journal, January 2008
- Aziz, Ramy K.; Bartels, Daniela; Best, Aaron A.
- BMC Genomics, Vol. 9, Issue 1, Article No. 75
The Systems Biology Research Tool: evolvable open-source software
journal, June 2008
- Wright, Jeremiah; Wagner, Andreas
- BMC Systems Biology, Vol. 2, Issue 1
MIRAGE: a functional genomics-based approach for metabolic network model reconstruction and its application to cyanobacteria networks
journal, January 2012
- Vitkin, Edward; Shlomi, Tomer
- Genome Biology, Vol. 13, Issue 11
Identification of Genome-Scale Metabolic Network Models Using Experimentally Measured Flux Profiles
journal, January 2006
- Herrgård, Markus J.; Fong, Stephen S.; Palsson, Bernhard Ø.
- PLoS Computational Biology, Vol. 2, Issue 7
GrowMatch: An Automated Method for Reconciling In Silico/In Vivo Growth Predictions
journal, March 2009
- Kumar, Vinay Satish; Maranas, Costas D.
- PLoS Computational Biology, Vol. 5, Issue 3
Reconciliation of Genome-Scale Metabolic Reconstructions for Comparative Systems Analysis
journal, March 2011
- Oberhardt, Matthew A.; Puchałka, Jacek; Martins dos Santos, Vítor A. P.
- PLoS Computational Biology, Vol. 7, Issue 3
Likelihood-Based Gene Annotations for Gap Filling and Quality Assessment in Genome-Scale Metabolic Models
journal, October 2014
- Benedict, Matthew N.; Mundy, Michael B.; Henry, Christopher S.
- PLoS Computational Biology, Vol. 10, Issue 10
Phage Phenomics: Physiological Approaches to Characterize Novel Viral Proteins
journal, June 2015
- Sanchez, Savannah E.; Cuevas, Daniel A.; Rostron, Jason E.
- Journal of Visualized Experiments, Issue 100
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journal, December 2018
- Karlsen, Emil; Schulz, Christian; Almaas, Eivind
- BMC Bioinformatics, Vol. 19, Issue 1
Methane utilization in Methylomicrobium alcaliphilum 20ZR: a systems approach
journal, February 2018
- Akberdin, Ilya R.; Thompson, Merlin; Hamilton, Richard
- Scientific Reports, Vol. 8, Issue 1
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journal, April 2019
- Henson, Michael A.; Orazi, Giulia; Phalak, Poonam
- mSystems, Vol. 4, Issue 2
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journal, February 2019
- Pham, Nhung; van Heck, Ruben; van Dam, Jesse
- Metabolites, Vol. 9, Issue 2
Constraint-based modeling in microbial food biotechnology
journal, March 2018
- Rau, Martin H.; Zeidan, Ahmad A.
- Biochemical Society Transactions, Vol. 46, Issue 2
Constraint-based modeling in microbial food biotechnology
journal, March 2018
- Rau, Martin H.; Zeidan, Ahmad A.
- Biochemical Society Transactions, Vol. 46, Issue 2
PMAnalyzer: a new web interface for bacterial growth curve analysis
journal, February 2017
- Cuevas, Daniel A.; Edwards, Robert A.
- Bioinformatics, Vol. 33, Issue 12
Metabolic Modeling of Cystic Fibrosis Airway Communities Predicts Mechanisms of Pathogen Dominance
journal, April 2019
- Henson, Michael A.; Orazi, Giulia; Phalak, Poonam
- mSystems, Vol. 4, Issue 2
Human Systems Biology and Metabolic Modelling: A Review—From Disease Metabolism to Precision Medicine
journal, June 2019
- Angione, Claudio
- BioMed Research International, Vol. 2019
Automated generation of genome-scale metabolic draft reconstructions based on KEGG
journal, December 2018
- Karlsen, Emil; Schulz, Christian; Almaas, Eivind
- BMC Bioinformatics, Vol. 19, Issue 1
Consistency, Inconsistency, and Ambiguity of Metabolite Names in Biochemical Databases Used for Genome-Scale Metabolic Modelling
journal, February 2019
- Pham, Nhung; van Heck, Ruben; van Dam, Jesse
- Metabolites, Vol. 9, Issue 2