BiGG Models: A platform for integrating, standardizing and sharing genome-scale models
Abstract
In this study, genome-scale metabolic models are mathematically structured knowledge bases that can be used to predict metabolic pathway usage and growth phenotypes. Furthermore, they can generate and test hypotheses when integrated with experimental data. To maximize the value of these models, centralized repositories of high-quality models must be established, models must adhere to established standards and model components must be linked to relevant databases. Tools for model visualization further enhance their utility. To meet these needs, we present BiGG Models (http://bigg.ucsd.edu), a completely redesigned Biochemical, Genetic and Genomic knowledge base. BiGG Models contains more than 75 high-quality, manually-curated genome-scale metabolic models. On the website, users can browse, search and visualize models. BiGG Models connects genome-scale models to genome annotations and external databases. Reaction and metabolite identifiers have been standardized across models to conform to community standards and enable rapid comparison across models. Furthermore, BiGG Models provides a comprehensive application programming interface for accessing BiGG Models with modeling and analysis tools. As a resource for highly curated, standardized and accessible models of metabolism, BiGG Models will facilitate diverse systems biology studies and support knowledge-based analysis of diverse experimental data.
- Authors:
-
- Univ. of California, San Diego, La Jolla, CA (United States)
- Univ. of California, San Diego, La Jolla, CA (United States); Univ. of Tuebingen, Tubingen (Germany)
- Publication Date:
- Research Org.:
- Univ. of California, San Diego, La Jolla, CA (United States)
- Sponsoring Org.:
- USDOE
- OSTI Identifier:
- 1253623
- Grant/Contract Number:
- SC0008701
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Nucleic Acids Research
- Additional Journal Information:
- Journal Volume: 44; Journal Issue: D1; Journal ID: ISSN 0305-1048
- Publisher:
- Oxford University Press
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES
Citation Formats
King, Zachary A., Lu, Justin, Drager, Andreas, Miller, Philip, Federowicz, Stephen, Lerman, Joshua A., Ebrahim, Ali, Palsson, Bernhard O., and Lewis, Nathan E. BiGG Models: A platform for integrating, standardizing and sharing genome-scale models. United States: N. p., 2015.
Web. doi:10.1093/nar/gkv1049.
King, Zachary A., Lu, Justin, Drager, Andreas, Miller, Philip, Federowicz, Stephen, Lerman, Joshua A., Ebrahim, Ali, Palsson, Bernhard O., & Lewis, Nathan E. BiGG Models: A platform for integrating, standardizing and sharing genome-scale models. United States. https://doi.org/10.1093/nar/gkv1049
King, Zachary A., Lu, Justin, Drager, Andreas, Miller, Philip, Federowicz, Stephen, Lerman, Joshua A., Ebrahim, Ali, Palsson, Bernhard O., and Lewis, Nathan E. Sat .
"BiGG Models: A platform for integrating, standardizing and sharing genome-scale models". United States. https://doi.org/10.1093/nar/gkv1049. https://www.osti.gov/servlets/purl/1253623.
@article{osti_1253623,
title = {BiGG Models: A platform for integrating, standardizing and sharing genome-scale models},
author = {King, Zachary A. and Lu, Justin and Drager, Andreas and Miller, Philip and Federowicz, Stephen and Lerman, Joshua A. and Ebrahim, Ali and Palsson, Bernhard O. and Lewis, Nathan E.},
abstractNote = {In this study, genome-scale metabolic models are mathematically structured knowledge bases that can be used to predict metabolic pathway usage and growth phenotypes. Furthermore, they can generate and test hypotheses when integrated with experimental data. To maximize the value of these models, centralized repositories of high-quality models must be established, models must adhere to established standards and model components must be linked to relevant databases. Tools for model visualization further enhance their utility. To meet these needs, we present BiGG Models (http://bigg.ucsd.edu), a completely redesigned Biochemical, Genetic and Genomic knowledge base. BiGG Models contains more than 75 high-quality, manually-curated genome-scale metabolic models. On the website, users can browse, search and visualize models. BiGG Models connects genome-scale models to genome annotations and external databases. Reaction and metabolite identifiers have been standardized across models to conform to community standards and enable rapid comparison across models. Furthermore, BiGG Models provides a comprehensive application programming interface for accessing BiGG Models with modeling and analysis tools. As a resource for highly curated, standardized and accessible models of metabolism, BiGG Models will facilitate diverse systems biology studies and support knowledge-based analysis of diverse experimental data.},
doi = {10.1093/nar/gkv1049},
journal = {Nucleic Acids Research},
number = D1,
volume = 44,
place = {United States},
year = {Sat Oct 17 00:00:00 EDT 2015},
month = {Sat Oct 17 00:00:00 EDT 2015}
}
Web of Science
Works referenced in this record:
Implications of Big Data for cell biology
journal, July 2015
- Dolinski, Kara; Troyanskaya, Olga G.
- Molecular Biology of the Cell, Vol. 26, Issue 14
The National Institutes of Health's Big Data to Knowledge (BD2K) initiative: capitalizing on biomedical big data
journal, November 2014
- Margolis, Ronald; Derr, Leslie; Dunn, Michelle
- Journal of the American Medical Informatics Association, Vol. 21, Issue 6
Data, information, knowledge and principle: back to metabolism in KEGG
journal, November 2013
- Kanehisa, Minoru; Goto, Susumu; Sato, Yoko
- Nucleic Acids Research, Vol. 42, 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
Saccharomyces genome database provides new regulation data
journal, November 2013
- Costanzo, Maria C.; Engel, Stacia R.; Wong, Edith D.
- Nucleic Acids Research, Vol. 42, Issue D1
The Mouse Genome Database (MGD): facilitating mouse as a model for human biology and disease
journal, October 2014
- Eppig, Janan T.; Blake, Judith A.; Bult, Carol J.
- Nucleic Acids Research, Vol. 43, Issue D1
Reconstruction of biochemical networks in microorganisms
journal, December 2008
- Feist, Adam M.; Herrgård, Markus J.; Thiele, Ines
- Nature Reviews Microbiology, Vol. 7, Issue 2
Constraint-based models predict metabolic and associated cellular functions
journal, January 2014
- Bordbar, Aarash; Monk, Jonathan M.; King, Zachary A.
- Nature Reviews Genetics, Vol. 15, Issue 2
Constraining the metabolic genotype–phenotype relationship using a phylogeny of in silico methods
journal, February 2012
- Lewis, Nathan E.; Nagarajan, Harish; Palsson, Bernhard O.
- Nature Reviews Microbiology, Vol. 10, Issue 4
The evolution of genome-scale models of cancer metabolism
journal, January 2013
- Lewis, Nathan E.; Abdel-Haleem, Alyaa M.
- Frontiers in Physiology, Vol. 4
Analysis of omics data with genome-scale models of metabolism
journal, January 2013
- Hyduke, Daniel R.; Lewis, Nathan E.; Palsson, Bernhard Ø.
- Mol. BioSyst., Vol. 9, Issue 2
Next-generation genome-scale models for metabolic engineering
journal, December 2015
- King, Zachary A.; Lloyd, Colton J.; Feist, Adam M.
- Current Opinion in Biotechnology, Vol. 35
Co-evolution of strain design methods based on flux balance and elementary mode analysis
journal, December 2015
- Machado, Daniel; Herrgård, Markus J.
- Metabolic Engineering Communications, Vol. 2
Basic and applied uses of genome‐scale metabolic network reconstructions of Escherichia coli
journal, January 2013
- McCloskey, Douglas; Palsson, Bernhard Ø; Feist, Adam M.
- Molecular Systems Biology, Vol. 9, Issue 1
Towards multidimensional genome annotation
journal, February 2006
- Reed, Jennifer L.; Famili, Iman; Thiele, Ines
- Nature Reviews Genetics, Vol. 7, Issue 2
A protocol for generating a high-quality genome-scale metabolic reconstruction
journal, January 2010
- Thiele, Ines; Palsson, Bernhard Ø
- Nature Protocols, Vol. 5, Issue 1
Optimizing genome-scale network reconstructions
journal, May 2014
- Monk, Jonathan; Nogales, Juan; Palsson, Bernhard O.
- Nature Biotechnology, Vol. 32, Issue 5
BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions
journal, January 2010
- Schellenberger, Jan; Park, Junyoung O.; Conrad, Tom M.
- BMC Bioinformatics, Vol. 11, Issue 1
The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models
journal, March 2003
- Hucka, M.; Finney, A.; Sauro, H. M.
- Bioinformatics, Vol. 19, Issue 4
MetaNetX.org: a website and repository for accessing, analysing and manipulating metabolic networks
journal, January 2013
- Ganter, M.; Bernard, T.; Moretti, S.
- Bioinformatics, Vol. 29, Issue 6
HMDB 3.0—The Human Metabolome Database in 2013
journal, November 2012
- Wishart, David S.; Jewison, Timothy; Guo, An Chi
- Nucleic Acids Research, Vol. 41, Issue D1
Using Bioconductor Package BiGGR for Metabolic Flux Estimation Based on Gene Expression Changes in Brain
journal, March 2015
- Gavai, Anand K.; Supandi, Farahaniza; Hettling, Hannes
- PLOS ONE, Vol. 10, Issue 3
MetRxn: a knowledgebase of metabolites and reactions spanning metabolic models and databases
journal, January 2012
- Kumar, Akhil; Suthers, Patrick F.; Maranas, Costas D.
- BMC Bioinformatics, Vol. 13, Issue 1
Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways
journal, August 2015
- King, Zachary A.; Dräger, Andreas; Ebrahim, Ali
- PLOS Computational Biology, Vol. 11, Issue 8
Improving Collaboration by Standardization Efforts in Systems Biology
journal, December 2014
- Dräger, Andreas; Palsson, Bernhard Ø.
- Frontiers in Bioengineering and Biotechnology, Vol. 2
RefSeq: an update on mammalian reference sequences
journal, November 2013
- Pruitt, Kim D.; Brown, Garth R.; Hiatt, Susan M.
- Nucleic Acids Research, Vol. 42, Issue D1
The Reactome pathway knowledgebase
journal, November 2013
- Croft, David; Mundo, Antonio Fabregat; Haw, Robin
- Nucleic Acids Research, Vol. 42, Issue D1
The RCSB Protein Data Bank: views of structural biology for basic and applied research and education
journal, November 2014
- Rose, Peter W.; Prlić, Andreas; Bi, Chunxiao
- Nucleic Acids Research, Vol. 43, Issue D1
High-throughput generation, optimization and analysis of genome-scale metabolic models
journal, August 2010
- Henry, Christopher S.; DeJongh, Matthew; Best, Aaron A.
- Nature Biotechnology, Vol. 28, Issue 9
Gene: a gene-centered information resource at NCBI
journal, October 2014
- Brown, Garth R.; Hem, Vichet; Katz, Kenneth S.
- Nucleic Acids Research, Vol. 43, Issue D1
Computing the functional proteome: recent progress and future prospects for genome-scale models
journal, August 2015
- O’Brien, Edward J.; Palsson, Bernhard O.
- Current Opinion in Biotechnology, Vol. 34
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
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
GenBank
journal, November 2014
- Benson, Dennis A.; Clark, Karen; Karsch-Mizrachi, Ilene
- Nucleic Acids Research, Vol. 43, Issue D1
Identifiers.org and MIRIAM Registry: community resources to provide persistent identification
journal, December 2011
- Juty, N.; Le Novere, N.; Laibe, C.
- Nucleic Acids Research, Vol. 40, Issue D1
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
JSBML 1.0: providing a smorgasbord of options to encode systems biology models: Table 1.
journal, June 2015
- Rodriguez, Nicolas; Thomas, Alex; Watanabe, Leandro
- Bioinformatics, Vol. 31, Issue 20
Controlled vocabularies and semantics in systems biology
journal, January 2011
- Courtot, Mélanie; Juty, Nick; Knüpfer, Christian
- Molecular Systems Biology, Vol. 7, Issue 1
GATA3 and stemness of high-grade serous ovarian carcinoma: novel hope for the deadliest type of ovarian cancer
journal, May 2020
- El-Arabey, Amr Ahmed; Abdalla, Mohnad; Abd-Allah, Adel Rashad
- Human Cell, Vol. 33, Issue 3
The Reactome Pathway Knowledgebase
journal, November 2017
- Fabregat, Antonio; Jupe, Steven; Matthews, Lisa
- Nucleic Acids Research, Vol. 46, Issue D1
MetaNetX.org: A website and repository for accessing, analysing and manipulating metabolic networks
text, January 2013
- Ganter, Mathias; Bernard, Thomas; Moretti, Sébastien
- ETH Zurich
The reactome pathway knowledgebase
journal, November 2019
- Jassal, Bijay; Matthews, Lisa; Viteri, Guilherme
- Nucleic Acids Research
Co-evolution of strain design methods based on flux balance and elementary mode analysis
journal, December 2015
- Machado, Daniel; Herrgård, Markus J.
- Metabolic Engineering Communications, Vol. 2
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
Controlled vocabularies and semantics in systems biology
journal, January 2011
- Courtot, Mélanie; Juty, Nick; Knüpfer, Christian
- Molecular Systems Biology, Vol. 7, Issue 1
Basic and applied uses of genome‐scale metabolic network reconstructions of Escherichia coli
journal, January 2013
- McCloskey, Douglas; Palsson, Bernhard Ø; Feist, Adam M.
- Molecular Systems Biology, Vol. 9, Issue 1
High-throughput generation, optimization and analysis of genome-scale metabolic models
journal, August 2010
- Henry, Christopher S.; DeJongh, Matthew; Best, Aaron A.
- Nature Biotechnology, Vol. 28, Issue 9
Constraint-based models predict metabolic and associated cellular functions
journal, January 2014
- Bordbar, Aarash; Monk, Jonathan M.; King, Zachary A.
- Nature Reviews Genetics, Vol. 15, Issue 2
Reconstruction of biochemical networks in microorganisms
journal, December 2008
- Feist, Adam M.; Herrgård, Markus J.; Thiele, Ines
- Nature Reviews Microbiology, Vol. 7, Issue 2
Constraining the metabolic genotype–phenotype relationship using a phylogeny of in silico methods
journal, February 2012
- Lewis, Nathan E.; Nagarajan, Harish; Palsson, Bernhard O.
- Nature Reviews Microbiology, Vol. 10, Issue 4
The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models
journal, March 2003
- Hucka, M.; Finney, A.; Sauro, H. M.
- Bioinformatics, Vol. 19, Issue 4
JSBML 1.0: providing a smorgasbord of options to encode systems biology models: Table 1.
journal, June 2015
- Rodriguez, Nicolas; Thomas, Alex; Watanabe, Leandro
- Bioinformatics, Vol. 31, Issue 20
Identifiers.org and MIRIAM Registry: community resources to provide persistent identification
journal, December 2011
- Juty, N.; Le Novere, N.; Laibe, C.
- Nucleic Acids Research, Vol. 40, Issue D1
Data, information, knowledge and principle: back to metabolism in KEGG
journal, November 2013
- Kanehisa, Minoru; Goto, Susumu; Sato, Yoko
- Nucleic Acids Research, Vol. 42, Issue D1
RefSeq: an update on mammalian reference sequences
journal, November 2013
- Pruitt, Kim D.; Brown, Garth R.; Hiatt, Susan M.
- Nucleic Acids Research, Vol. 42, Issue D1
Gene: a gene-centered information resource at NCBI
journal, October 2014
- Brown, Garth R.; Hem, Vichet; Katz, Kenneth S.
- Nucleic Acids Research, Vol. 43, Issue D1
The RCSB Protein Data Bank: views of structural biology for basic and applied research and education
journal, November 2014
- Rose, Peter W.; Prlić, Andreas; Bi, Chunxiao
- Nucleic Acids Research, Vol. 43, Issue D1
GenBank
journal, November 2014
- Benson, Dennis A.; Clark, Karen; Karsch-Mizrachi, Ilene
- Nucleic Acids Research, Vol. 43, Issue D1
The Mouse Genome Database (MGD): facilitating mouse as a model for human biology and disease
journal, October 2014
- Eppig, Janan T.; Blake, Judith A.; Bult, Carol J.
- Nucleic Acids Research, Vol. 43, Issue D1
The reactome pathway knowledgebase
journal, November 2019
- Jassal, Bijay; Matthews, Lisa; Viteri, Guilherme
- Nucleic Acids Research
MetRxn: a knowledgebase of metabolites and reactions spanning metabolic models and databases
journal, January 2012
- Kumar, Akhil; Suthers, Patrick F.; Maranas, Costas D.
- BMC Bioinformatics, Vol. 13, Issue 1
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
Improving Collaboration by Standardization Efforts in Systems Biology
journal, December 2014
- Dräger, Andreas; Palsson, Bernhard Ø.
- Frontiers in Bioengineering and Biotechnology, Vol. 2
A fractal approach to dynamic inference and distribution analysis
journal, January 2013
- van Rooij, Marieke M. J. W.; Nash, Bertha A.; Rajaraman, Srinivasan
- Frontiers in Physiology, Vol. 4
MetaNetX.org: A website and repository for accessing, analysing and manipulating metabolic networks
text, January 2013
- Ganter, Mathias; Bernard, Thomas; Moretti, Sébastien
- ETH Zurich
Works referencing / citing this record:
Predicting Strain Engineering Strategies Using iKS1317: A Genome‐Scale Metabolic Model of Streptomyces coelicolor
journal, January 2019
- Kumelj, Tjaša; Sulheim, Snorre; Wentzel, Alexander
- Biotechnology Journal, Vol. 14, Issue 4
Meta‐Omics‐ and Metabolic Modeling‐Assisted Deciphering of Human Microbiota Metabolism
journal, July 2019
- Sieow, Brendan Fu‐Long; Nurminen, Toni Juhani; Ling, Hua
- Biotechnology Journal, Vol. 14, Issue 9
Expanding Metabolic Capabilities Using Novel Pathway Designs: Computational Tools and Case Studies
journal, July 2019
- Saa, Pedro A.; Cortés, María P.; López, Javiera
- Biotechnology Journal, Vol. 14, Issue 9
Genomic and metabolic analysis of Komagataeibacter xylinus DSM 2325 producing bacterial cellulose nanofiber
journal, September 2019
- Jang, Woo Dae; Kim, Tae Yong; Kim, Hyun Uk
- Biotechnology and Bioengineering, Vol. 116, Issue 12
Multi-objective optimization of genome-scale metabolic models: the case of ethanol production
journal, April 2018
- Patané, Andrea; Jansen, Giorgio; Conca, Piero
- Annals of Operations Research, Vol. 276, Issue 1-2
Challenges in modeling the human gut microbiome
journal, August 2018
- Babaei, Parizad; Shoaie, Saeed; Ji, Boyang
- Nature Biotechnology, Vol. 36, Issue 8
Genome-scale metabolic reconstructions of multiple Salmonella strains reveal serovar-specific metabolic traits
journal, September 2018
- Seif, Yara; Kavvas, Erol; Lachance, Jean-Christophe
- Nature Communications, Vol. 9, Issue 1
Machine learning applied to enzyme turnover numbers reveals protein structural correlates and improves metabolic models
journal, December 2018
- Heckmann, David; Lloyd, Colton J.; Mih, Nathan
- Nature Communications, Vol. 9, Issue 1
MoVE identifies metabolic valves to switch between phenotypic states
journal, December 2018
- Venayak, Naveen; von Kamp, Axel; Klamt, Steffen
- Nature Communications, Vol. 9, Issue 1
Strain-level metagenomic assignment and compositional estimation for long reads with MetaMaps
journal, July 2019
- Dilthey, Alexander T.; Jain, Chirag; Koren, Sergey
- Nature Communications, Vol. 10, Issue 1
Microbial carbon use efficiency predicted from genome-scale metabolic models
journal, August 2019
- Saifuddin, Mustafa; Bhatnagar, Jennifer M.; Segrè, Daniel
- Nature Communications, Vol. 10, Issue 1
A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism
journal, August 2019
- Lu, Hongzhong; Li, Feiran; Sánchez, Benjamín J.
- Nature Communications, Vol. 10, Issue 1
Identification of bioactive metabolites using activity metabolomics
journal, February 2019
- Rinschen, Markus M.; Ivanisevic, Julijana; Giera, Martin
- Nature Reviews Molecular Cell Biology, Vol. 20, Issue 6
MEMOTE for standardized genome-scale metabolic model testing
journal, March 2020
- Lieven, Christian; Beber, Moritz E.; Olivier, Brett G.
- Nature Biotechnology, Vol. 38, Issue 3
A workflow for generating multi-strain genome-scale metabolic models of prokaryotes
journal, December 2019
- Norsigian, Charles J.; Fang, Xin; Seif, Yara
- Nature Protocols, Vol. 15, 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
Genome-driven cell engineering review: in vivo and in silico metabolic and genome engineering
journal, June 2019
- Landon, Sophie; Rees-Garbutt, Joshua; Marucci, Lucia
- Essays in Biochemistry, Vol. 63, Issue 2
Bioengineering tools for the production of pharmaceuticals: current perspective and future outlook
journal, January 2019
- Sarsaiya, Surendra; Shi, Jingshan; Chen, Jishuang
- Bioengineered, Vol. 10, Issue 1
Structural and functional analyses of microbial metabolic networks reveal novel insights into genome-scale metabolic fluxes
journal, March 2018
- Li, Gaoyang; Cao, Huansheng; Xu, Ying
- Briefings in Bioinformatics, Vol. 20, Issue 4
Harmonizing semantic annotations for computational models in biology
journal, November 2018
- Neal, Maxwell Lewis; König, Matthias; Nickerson, David
- Briefings in Bioinformatics, Vol. 20, Issue 2
Characterizing and ranking computed metabolic engineering strategies
journal, January 2019
- Schneider, Philipp; Klamt, Steffen
- Bioinformatics, Vol. 35, Issue 17
Gsmodutils: a python based framework for test-driven genome scale metabolic model development
journal, February 2019
- Gilbert, James; Pearcy, Nicole; Norman, Rupert
- Bioinformatics, Vol. 35, Issue 18
De novo design of biosynthetic pathways for bacterial production of bulk chemicals and biofuels
journal, August 2018
- Okano, Kenji; Honda, Kohsuke; Taniguchi, Hironori
- FEMS Microbiology Letters, Vol. 365, Issue 20
Compartment and hub definitions tune metabolic networks for metabolomic interpretations
journal, January 2020
- Waller, T. Cameron; Berg, Jordan A.; Lex, Alexander
- GigaScience, Vol. 9, Issue 1
MetExplore: collaborative edition and exploration of metabolic networks
journal, April 2018
- Cottret, Ludovic; Frainay, Clément; Chazalviel, Maxime
- Nucleic Acids Research, Vol. 46, Issue W1
Phenotypic innovation through recombination in genome-scale metabolic networks
journal, September 2016
- Hosseini, Sayed-Rzgar; Martin, Olivier C.; Wagner, Andreas
- Proceedings of the Royal Society B: Biological Sciences, Vol. 283, Issue 1839
Model-driven design allows growth of Mycoplasma pneumoniae on serum-free media
journal, December 2019
- Gaspari, Erika; Malachowski, Antoni; Garcia-Morales, Luis
- npj Systems Biology and Applications
MINREACT: an efficient algorithm for identifying minimal metabolic networks
posted_content, January 2020
- Sambamoorthy, Gayathri; Raman, Karthik
- bioRxiv
Metabolic mechanisms of interaction within a defined gut microbiota
posted_content, January 2018
- Medlock, Gregory L.; Carey, Maureen A.; McDuffie, Dennis G.
Metabolic modeling of Pectobacterium parmentieri SCC3193 provides insights into metabolic pathways of plant pathogenic bacteria
journal, March 2018
- Zoledowska, Sabina; Presta, Luana; Fondi, Marco
- Microorganisms
Transcriptome-guided parsimonious flux analysis improves predictions with metabolic networks in complex environments
posted_content, January 2020
- Jenior, Matthew L.; Moutinho, Jr., Thomas J.; Dougherty, Bonnie V.
- PLOS Computational Biology
Community standards to facilitate development and address challenges in metabolic modeling
posted_content, July 2019
- Carey, Maureen A.; Dräger, Andreas; Papin, Jason A.
- bioRxiv
Comparative analyses of parasites with a comprehensive database of genome-scale metabolic models
journal, September 2019
- Carey, Maureen A.; Medlock, Gregory L.; Stolarczyk, Michał
- PLOS Computational Biology
Designing Metabolic Division of Labor in Microbial Communities
journal, April 2019
- Thommes, Meghan; Wang, Taiyao; Zhao, Qi
- mSystems, Vol. 4, Issue 2
Metabolic Modeling of Streptococcus mutans Reveals Complex Nutrient Requirements of an Oral Pathogen
journal, October 2019
- Jijakli, Kenan; Jensen, Paul A.
- mSystems, Vol. 4, Issue 5
Identification of critical connectors in the directed reaction-centric graphs of microbial metabolic networks
journal, June 2019
- Kim, Eun-Youn; Ashlock, Daniel; Yoon, Sung Ho
- BMC Bioinformatics, Vol. 20, Issue 1
Automatic construction of metabolic models with enzyme constraints
journal, January 2020
- Bekiaris, Pavlos Stephanos; Klamt, Steffen
- BMC Bioinformatics, Vol. 21, Issue 1
Development and validation of an updated computational model of Streptomyces coelicolor primary and secondary metabolism
journal, July 2018
- Amara, Adam; Takano, Eriko; Breitling, Rainer
- BMC Genomics, Vol. 19, Issue 1
Updated and standardized genome-scale reconstruction of Mycobacterium tuberculosis H37Rv, iEK1011, simulates flux states indicative of physiological conditions
journal, March 2018
- Kavvas, Erol S.; Seif, Yara; Yurkovich, James T.
- BMC Systems Biology, Vol. 12, Issue 1
Towards creating an extended metabolic model (EMM) for E. coli using enzyme promiscuity prediction and metabolomics data
journal, June 2019
- Amin, Sara A.; Chavez, Elizabeth; Porokhin, Vladimir
- Microbial Cell Factories, Vol. 18, Issue 1
A metabolic reconstruction of Lactobacillus reuteri JCM 1112 and analysis of its potential as a cell factory
journal, October 2019
- Kristjansdottir, Thordis; Bosma, Elleke F.; Branco dos Santos, Filipe
- Microbial Cell Factories, Vol. 18, Issue 1
In silico identification of metabolic engineering strategies for improved lipid production in Yarrowia lipolytica by genome-scale metabolic modeling
journal, July 2019
- Kim, Minsuk; Park, Beom Gi; Kim, Eun-Jung
- Biotechnology for Biofuels, Vol. 12, Issue 1
A reverse metabolic approach to weaning: in silico identification of immune-beneficial infant gut bacteria, mining their metabolism for prebiotic feeds and sourcing these feeds in the natural product space
journal, September 2018
- Michelini, Samanta; Balakrishnan, Biju; Parolo, Silvia
- Microbiome, Vol. 6, Issue 1
Challenges in the construction of knowledge bases for human microbiome-disease associations
journal, September 2019
- Badal, Varsha Dave; Wright, Dustin; Katsis, Yannis
- Microbiome, Vol. 7, Issue 1
Functional interrogation of Plasmodium genus metabolism identifies species- and stage-specific differences in nutrient essentiality and drug targeting
journal, January 2018
- Abdel-Haleem, Alyaa M.; Hefzi, Hooman; Mineta, Katsuhiko
- PLOS Computational Biology, Vol. 14, Issue 1
Traceability, reproducibility and wiki-exploration for “à-la-carte” reconstructions of genome-scale metabolic models
journal, May 2018
- Aite, Méziane; Chevallier, Marie; Frioux, Clémence
- PLOS Computational Biology, Vol. 14, Issue 5
A computational knowledge-base elucidates the response of Staphylococcus aureus to different media types
journal, January 2019
- Seif, Yara; Monk, Jonathan M.; Mih, Nathan
- PLOS Computational Biology, Vol. 15, Issue 1
BOFdat: Generating biomass objective functions for genome-scale metabolic models from experimental data
journal, April 2019
- Lachance, Jean-Christophe; Lloyd, Colton J.; Monk, Jonathan M.
- PLOS Computational Biology, Vol. 15, Issue 4
Metabolic adaptations underlying genome flexibility in prokaryotes
journal, October 2018
- Goyal, Akshit
- PLOS Genetics, Vol. 14, Issue 10
Metabolic network reconstruction and phenome analysis of the industrial microbe, Escherichia coli BL21(DE3)
journal, September 2018
- Kim, Hanseol; Kim, Sinyeon; Yoon, Sung Ho
- PLOS ONE, Vol. 13, Issue 9
Reconstruction of a regulated two-cell metabolic model to study biohydrogen production in a diazotrophic cyanobacterium Anabaena variabilis ATCC 29413
journal, January 2020
- Malek Shahkouhi, Ali; Motamedian, Ehsan
- PLOS ONE, Vol. 15, Issue 1
Enzyme promiscuity shapes adaptation to novel growth substrates
journal, April 2019
- Guzmán, Gabriela I.; Sandberg, Troy E.; LaCroix, Ryan A.
- Molecular Systems Biology, Vol. 15, Issue 4
Modeling Meets Metabolomics—The WormJam Consensus Model as Basis for Metabolic Studies in the Model Organism Caenorhabditis elegans
journal, November 2018
- Witting, Michael; Hastings, Janna; Rodriguez, Nicolas
- Frontiers in Molecular Biosciences, Vol. 5
In Silico Toxicology Data Resources to Support Read-Across and (Q)SAR
journal, June 2019
- Pawar, Gopal; Madden, Judith C.; Ebbrell, David
- Frontiers in Pharmacology, Vol. 10
The Role of Soil Microorganisms in Plant Mineral Nutrition—Current Knowledge and Future Directions
journal, September 2017
- Jacoby, Richard; Peukert, Manuela; Succurro, Antonella
- Frontiers in Plant Science, Vol. 8
Metabolic Modeling of Human Gut Microbiota on a Genome Scale: An Overview
journal, January 2019
- Sen, Partho; Orešič, Matej
- Metabolites, Vol. 9, Issue 2
Comparison of Multi-Objective Evolutionary Algorithms to Solve the Modular Cell Design Problem for Novel Biocatalysis
journal, June 2019
- Garcia, Sergio; Trinh, Cong T.
- Processes, Vol. 7, Issue 6
Metabolomics: Basic Principles and Strategies
book, November 2019
- Nalbantoglu, Sinem
- Molecular Medicine
Metabolic network percolation quantifies biosynthetic capabilities across the human oral microbiome
journal, June 2019
- Bernstein, David B.; Dewhirst, Floyd E.; Segrè, Daniel
- eLife, Vol. 8
Horizons of Systems Biocatalysis and Renaissance of Metabolite Synthesis
journal, May 2018
- Wohlgemuth, Roland
- Biotechnology Journal
Finding MEMo: minimum sets of elementary flux modes
journal, August 2019
- Röhl, Annika; Bockmayr, Alexander
- Journal of Mathematical Biology, Vol. 79, Issue 5
Reconstruction, verification and in-silico analysis of a genome-scale metabolic model of bacterial cellulose producing Komagataeibacter xylinus
journal, February 2020
- Rezazadeh, Mohammad; Babaeipour, Valiollah; Motamedian, Ehsan
- Bioprocess and Biosystems Engineering, Vol. 43, Issue 6
From correlation to causation: analysis of metabolomics data using systems biology approaches
journal, February 2018
- Rosato, Antonio; Tenori, Leonardo; Cascante, Marta
- Metabolomics, Vol. 14, Issue 4
Recon3D enables a three-dimensional view of gene variation in human metabolism
journal, February 2018
- Brunk, Elizabeth; Sahoo, Swagatika; Zielinski, Daniel C.
- Nature Biotechnology, Vol. 36, Issue 3
An analytic approximation of the feasible space of metabolic networks
journal, April 2017
- Braunstein, Alfredo; Muntoni, Anna Paola; Pagnani, Andrea
- Nature Communications, Vol. 8, Issue 1
Genome-scale metabolic model of the rat liver predicts effects of diet restriction
journal, July 2019
- Baloni, Priyanka; Sangar, Vineet; Yurkovich, James T.
- Scientific Reports, Vol. 9, Issue 1
FlySilico: Flux balance modeling of Drosophila larval growth and resource allocation
journal, November 2019
- Schönborn, Jürgen Wilhelm; Jehrke, Lisa; Mettler-Altmann, Tabea
- Scientific Reports, Vol. 9, Issue 1
BiKEGG: a COBRA toolbox extension for bridging the BiGG and KEGG databases
journal, January 2016
- Jamialahmadi, Oveis; Motamedian, Ehsan; Hashemi-Najafabadi, Sameereh
- Molecular BioSystems, Vol. 12, Issue 11
Marine Proteobacteria as a source of natural products: advances in molecular tools and strategies
journal, January 2019
- Buijs, Yannick; Bech, Pernille Kjersgaard; Vazquez-Albacete, Dario
- Natural Product Reports, Vol. 36, Issue 9
GEMtractor: extracting views into genome-scale metabolic models
journal, January 2020
- Scharm, Martin; Wolkenhauer, Olaf; Jalili, Mahdi
- Bioinformatics, Vol. 36, Issue 10
MOOMIN – Mathematical explOration of ’Omics data on a MetabolIc Network
journal, August 2019
- Pusa, Taneli; Ferrarini, Mariana Galvão; Andrade, Ricardo
- Bioinformatics
Enzyme annotation in UniProtKB using Rhea
journal, November 2019
- Morgat, Anne; Lombardot, Thierry; Coudert, Elisabeth
- Bioinformatics
TCSBN: a database of tissue and cancer specific biological networks
journal, October 2017
- Lee, Sunjae; Zhang, Cheng; Arif, Muhammad
- Nucleic Acids Research, Vol. 46, Issue D1
BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree
journal, November 2019
- Norsigian, Charles J.; Pusarla, Neha; McConn, John Luke
- Nucleic Acids Research
Constraint-based stoichiometric modelling from single organisms to microbial communities
journal, November 2016
- Gottstein, Willi; Olivier, Brett G.; Bruggeman, Frank J.
- Journal of The Royal Society Interface, Vol. 13, Issue 124
MAMMOTh: a new database for curated MAthematical Models of bioMOlecular sysTems
journal, May 2016
- Kazantsev, Fedor; Akberdin, Ilya; Lashin, Sergey
- Journal of Bioinformatics
On the deformability of an empirical fitness landscape by microbial evolution
journal, April 2018
- Bajić, Djordje; Vila, Jean C. C.; Blount, Zachary D.
- Proceedings of the National Academy of Sciences
Integration of Metabolomics and Transcriptomics Reveals a Complex Diet of Mycobacterium tuberculosis during Early Macrophage Infection
journal, August 2017
- Zimmermann, Michael; Kogadeeva, Maria; Gengenbacher, Martin
- mSystems, Vol. 2, Issue 4
Visualizing metabolic network dynamics through time-series metabolomic data
journal, July 2020
- Buchweitz, Lea F.; Yurkovich, James T.; Blessing, Christoph
- BMC Bioinformatics, Vol. 21, Issue 1
SSER: Species specific essential reactions database
journal, April 2017
- Labena, Abraham A.; Ye, Yuan-Nong; Dong, Chuan
- BMC Systems Biology, Vol. 11, Issue 1
Escher-FBA: a web application for interactive flux balance analysis
journal, September 2018
- Rowe, Elliot; Palsson, Bernhard O.; King, Zachary A.
- BMC Systems Biology, Vol. 12, Issue 1
Current status and applications of genome-scale metabolic models
journal, June 2019
- Gu, Changdai; Kim, Gi Bae; Kim, Won Jun
- Genome Biology, Vol. 20, Issue 1
Review on natural products databases: where to find data in 2020
journal, April 2020
- Sorokina, Maria; Steinbeck, Christoph
- Journal of Cheminformatics, Vol. 12, Issue 1
The bacterial interlocked process ONtology (BiPON): a systemic multi-scale unified representation of biological processes in prokaryotes
journal, November 2017
- Henry, Vincent J.; Goelzer, Anne; Ferré, Arnaud
- Journal of Biomedical Semantics, Vol. 8, Issue 1
NG-meta-profiler: fast processing of metagenomes using NGLess, a domain-specific language
journal, June 2019
- Coelho, Luis Pedro; Alves, Renato; Monteiro, Paulo
- Microbiome, Vol. 7, Issue 1
OptMDFpathway: Identification of metabolic pathways with maximal thermodynamic driving force and its application for analyzing the endogenous CO2 fixation potential of Escherichia coli
journal, September 2018
- Hädicke, Oliver; von Kamp, Axel; Aydogan, Timur
- PLOS Computational Biology, Vol. 14, Issue 9
Investigating the deregulation of metabolic tasks via Minimum Network Enrichment Analysis (MiNEA) as applied to nonalcoholic fatty liver disease using mouse and human omics data
journal, April 2019
- Pandey, Vikash; Hatzimanikatis, Vassily
- PLOS Computational Biology, Vol. 15, Issue 4
biochem4j: Integrated and extensible biochemical knowledge through graph databases
journal, July 2017
- Swainston, Neil; Batista-Navarro, Riza; Carbonell, Pablo
- PLOS ONE, Vol. 12, Issue 7
A genome-scale metabolic network reconstruction of extremely halophilic bacterium Salinibacter ruber
journal, May 2019
- Bagheri, Maryam; Marashi, Sayed-Amir; Amoozegar, Mohammad Ali
- PLOS ONE, Vol. 14, Issue 5
BioModelKit – An Integrative Framework for Multi-Scale Biomodel-Engineering
journal, September 2018
- Blätke, Mary-Ann
- Journal of Integrative Bioinformatics, Vol. 15, Issue 3
Fatty Acid Biosynthesis Pathways in Methylomicrobium buryatense 5G(B1)
journal, January 2017
- Demidenko, Aleksandr; Akberdin, Ilya R.; Allemann, Marco
- Frontiers in Microbiology, Vol. 7
Computational Systems Biology of Metabolism in Infection
book, January 2018
- Cesur, Müberra Fatma; Abdik, Ecehan; Güven-Gülhan, Ünzile
- Metabolic Interaction in Infection
Enzyme-Constrained Models and Omics Analysis of Streptomyces coelicolor Reveal Metabolic Changes that Enhance Heterologous Production
journal, September 2020
- Sulheim, Snorre; Kumelj, Tjaša; van Dissel, Dino
- iScience, Vol. 23, Issue 9
Costless metabolic secretions as drivers of interspecies interactions in microbial ecosystems
journal, January 2019
- Pacheco, Alan R.; Moel, Mauricio; Segrè, Daniel
- Nature Communications, Vol. 10, Issue 1
On the deformability of an empirical fitness landscape by microbial evolution
journal, October 2018
- Bajić, Djordje; Vila, Jean C. C.; Blount, Zachary D.
- Proceedings of the National Academy of Sciences, Vol. 115, Issue 44
Closing the gap between formats for storing layout information in systems biology
journal, February 2020
- Hoksza, David; Gawron, Piotr; Ostaszewski, Marek
- Briefings in Bioinformatics, Vol. 22, Issue 1
Biological Filtering and Substrate Promiscuity Prediction for Annotating Untargeted Metabolomics
posted_content, March 2019
- Hassanpour, Neda; Alden, Nicholas; Menon, Rani
- BioRxiv
GEMtractor: Extracting Views into Genome-scale Metabolic Models
journal, October 2019
- Scharm, Martin; Wolkenhauer, Olaf; Jalili, Mahdi
- Bioinformatics
Systems Medicine as an Emerging Tool for Cardiovascular Genetics
journal, August 2016
- Haase, Tina; Börnigen, Daniela; Müller, Christian
- Frontiers in Cardiovascular Medicine, Vol. 3
iCN718, an Updated and Improved Genome-Scale Metabolic Network Reconstruction of Acinetobacter baumannii AYE
journal, April 2018
- Norsigian, Charles J.; Kavvas, Erol; Seif, Yara
- Frontiers in Genetics, Vol. 9
In Silico Analysis of the Small Molecule Content of Outer Membrane Vesicles Produced by Bacteroides thetaiotaomicron Indicates an Extensive Metabolic Link between Microbe and Host
journal, December 2017
- Bryant, William A.; Stentz, Régis; Le Gall, Gwenaelle
- Frontiers in Microbiology, Vol. 8
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
Essential metabolism for a minimal cell
journal, January 2019
- Breuer, Marian; Earnest, Tyler M.; Merryman, Chuck
- eLife, Vol. 8
Fast automated reconstruction of genome-scale metabolic models for microbial species and communities
journal, June 2018
- Machado, Daniel; Andrejev, Sergej; Tramontano, Melanie
- Nucleic Acids Research, Vol. 46, Issue 15
A systematic assessment of current genome-scale metabolic reconstruction tools
journal, August 2019
- Mendoza, Sebastián N.; Olivier, Brett G.; Molenaar, Douwe
- Genome Biology, Vol. 20, Issue 1
Transcriptome-guided parsimonious flux analysis improves predictions with metabolic networks in complex environments
journal, April 2020
- Jenior, Matthew L.; Moutinho, Thomas J.; Dougherty, Bonnie V.
- PLOS Computational Biology, Vol. 16, Issue 4
Flux-based hierarchical organization of Escherichia coli’s metabolic network
journal, April 2020
- Robaina-Estévez, Semidán; Nikoloski, Zoran
- PLOS Computational Biology, Vol. 16, Issue 4
MEMOTE for standardized genome-scale metabolic model testing
text, January 2020
- Lieven, Christian; Beber, Moritz E.; Olivier, Brett G.
- RWTH Aachen University
A Genome-Scale Metabolic Model for Methylococcus capsulatus (Bath) Suggests Reduced Efficiency Electron Transfer to the Particulate Methane Monooxygenase
journal, December 2018
- Lieven, Christian; Petersen, Leander A. H.; Jørgensen, Sten Bay
- Frontiers in Microbiology, Vol. 9
Model-driven design allows growth of Mycoplasma pneumoniae on serum-free media
journal, October 2020
- Gaspari, Erika; Malachowski, Antoni; Garcia-Morales, Luis
- npj Systems Biology and Applications, Vol. 6, Issue 1
Updates in Rhea: SPARQLing biochemical reaction data
journal, October 2018
- Lombardot, Thierry; Morgat, Anne; Axelsen, Kristian B.
- Nucleic Acids Research, Vol. 47, Issue D1
Gsmodutils: A python based framework for test-driven genome scale metabolic model development
journal, September 2018
- Gilbert, James P.; Pearcy, Nicole; Norman, Rupert
- Bioinformatics
Modeling Meets Metabolomics-The WormJam Consensus Model as Basis for Metabolic Studies in the Model Organism Caenorhabditis elegans.
journalarticle, January 2018
- Witting, Michael; Hastings, Janna; Rodriguez, Nicolas
- Frontiers Media SA
Inferring Biochemical Reactions and Metabolite Structures to Understand Metabolic Pathway Drift
journal, February 2020
- Belcour, Arnaud; Girard, Jean; Aite, Méziane
- iScience, Vol. 23, Issue 2
Horizontal Gene Transfer Drives the Evolution of Dependencies in Bacteria
journal, January 2021
- Goyal, Akshit
- SSRN Electronic Journal
Integration of Metabolomics and Transcriptomics Reveals a Complex Diet of Mycobacterium tuberculosis during Early Macrophage Infection
text, January 2017
- Michael, Zimmermann,; Maria, Kogadeeva,; Gayle, McEwen,
- ETH Zurich
Phenotypic innovation through recombination in genome-scale metabolic networks
interactiveresource, January 2016
- Sayed-Rzgar, Hosseini,; C., Martin, Olivier; Andreas, Wagner,
- Royal Society Publishing
From correlation to causation: analysis of metabolomics data using systems biology approaches
journal, February 2018
- Rosato, Antonio; Tenori, Leonardo; Cascante, Marta
- Metabolomics, Vol. 14, Issue 4
A system architecture for parallel analysis of flux-balanced metabolic pathways
journal, October 2020
- Arabzadeh, Mona; Sedighi, Mehdi; Saheb Zamani, Morteza
- Computational Biology and Chemistry, Vol. 88
OptFill: A Tool for Infeasible Cycle-Free Gapfilling of Stoichiometric Metabolic Models
journal, January 2020
- Schroeder, Wheaton L.; Saha, Rajib
- iScience, Vol. 23, Issue 1
Inferring Biochemical Reactions and Metabolite Structures to Understand Metabolic Pathway Drift
journal, February 2020
- Belcour, Arnaud; Girard, Jean; Aite, Méziane
- iScience, Vol. 23, Issue 2
Metabolic anchor reactions for robust biorefining
journal, March 2017
- Jouhten, Paula; Huerta-Cepas, Jaime; Bork, Peer
- Metabolic Engineering, Vol. 40
Machine learning applied to enzyme turnover numbers reveals protein structural correlates and improves metabolic models
journal, December 2018
- Heckmann, David; Lloyd, Colton J.; Mih, Nathan
- Nature Communications, Vol. 9, Issue 1
Costless metabolic secretions as drivers of interspecies interactions in microbial ecosystems
journal, January 2019
- Pacheco, Alan R.; Moel, Mauricio; Segrè, Daniel
- Nature Communications, Vol. 10, Issue 1
A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism
journal, August 2019
- Lu, Hongzhong; Li, Feiran; Sánchez, Benjamín J.
- Nature Communications, Vol. 10, Issue 1
FlySilico: Flux balance modeling of Drosophila larval growth and resource allocation
journal, November 2019
- Schönborn, Jürgen Wilhelm; Jehrke, Lisa; Mettler-Altmann, Tabea
- Scientific Reports, Vol. 9, Issue 1
Genome-scale metabolic models of Microbacterium species isolated from a high altitude desert environment
journal, March 2020
- Mandakovic, Dinka; Cintolesi, Ángela; Maldonado, Jonathan
- Scientific Reports, Vol. 10, Issue 1
Elucidating dynamic metabolic physiology through network integration of quantitative time-course metabolomics
journal, April 2017
- Bordbar, Aarash; Yurkovich, James T.; Paglia, Giuseppe
- Scientific Reports, Vol. 7, Issue 1
Genome-driven cell engineering review: in vivo and in silico metabolic and genome engineering
journal, June 2019
- Landon, Sophie; Rees-Garbutt, Joshua; Marucci, Lucia
- Essays in Biochemistry, Vol. 63, Issue 2
Metabolic and genetic basis for auxotrophies in Gram-negative species
journal, March 2020
- Seif, Yara; Choudhary, Kumari Sonal; Hefner, Ying
- Proceedings of the National Academy of Sciences, Vol. 117, Issue 11
Characterizing and ranking computed metabolic engineering strategies
journal, January 2019
- Schneider, Philipp; Klamt, Steffen
- Bioinformatics, Vol. 35, Issue 17
Genome-scale metabolic modeling of responses to polymyxins inPseudomonas aeruginosa
journal, March 2018
- Zhu, Yan; Czauderna, Tobias; Zhao, Jinxin
- GigaScience, Vol. 7, Issue 4
Updates in Rhea: SPARQLing biochemical reaction data
journal, October 2018
- Lombardot, Thierry; Morgat, Anne; Axelsen, Kristian B.
- Nucleic Acids Research, Vol. 47, Issue D1
Model-driven design allows growth of Mycoplasma pneumoniae on serum-free media
journal, December 2019
- Gaspari, Erika; Malachowski, Antoni; Garcia-Morales, Luis
- npj Systems Biology and Applications
High-quality genome-scale metabolic model of Aurantiochytrium sp. T66
journal, November 2020
- Simensen, Vetle; Voigt, André; Almaas, Eivind
- Biotechnology and Bioengineering
Gsmodutils: A python based framework for test-driven genome scale metabolic model development
journal, September 2018
- Gilbert, James P.; Pearcy, Nicole; Norman, Rupert
- Bioinformatics
MCS2: Minimal coordinated supports for fast enumeration of minimal cut sets in metabolic networks
journal, February 2019
- Miraskarshahi, Reza; Zabeti, Hooman; Stephen, Tamon
- Bioinformatics
Designing Metabolic Division of Labor in Microbial Communities
journal, April 2019
- Thommes, Meghan; Wang, Taiyao; Zhao, Qi
- mSystems, Vol. 4, Issue 2
Metabolic Analyses of Nitrogen Fixation in the Soybean Microsymbiont Sinorhizobium fredii Using Constraint-Based Modeling
journal, February 2020
- Contador, Carolina A.; Lo, Siu-Kit; Chan, Siu H. J.
- mSystems, Vol. 5, Issue 1
Estimating Cellular Goals from High-Dimensional Biological Data
conference, July 2019
- Yang, Laurence; Saunders, Michael A.; Lachance, Jean-Christophe
- Proceedings of the 25th ACM SIGKDD International Conference on Knowledge Discovery & Data Mining
Identification of critical connectors in the directed reaction-centric graphs of microbial metabolic networks
journal, June 2019
- Kim, Eun-Youn; Ashlock, Daniel; Yoon, Sung Ho
- BMC Bioinformatics, Vol. 20, Issue 1
Updated and standardized genome-scale reconstruction of Mycobacterium tuberculosis H37Rv, iEK1011, simulates flux states indicative of physiological conditions
journal, March 2018
- Kavvas, Erol S.; Seif, Yara; Yurkovich, James T.
- BMC Systems Biology, Vol. 12, Issue 1
Escher-FBA: a web application for interactive flux balance analysis
journal, September 2018
- Rowe, Elliot; Palsson, Bernhard O.; King, Zachary A.
- BMC Systems Biology, Vol. 12, Issue 1
Towards creating an extended metabolic model (EMM) for E. coli using enzyme promiscuity prediction and metabolomics data
journal, June 2019
- Amin, Sara A.; Chavez, Elizabeth; Porokhin, Vladimir
- Microbial Cell Factories, Vol. 18, Issue 1
Current status and applications of genome-scale metabolic models
journal, June 2019
- Gu, Changdai; Kim, Gi Bae; Kim, Won Jun
- Genome Biology, Vol. 20, Issue 1
A systematic assessment of current genome-scale metabolic reconstruction tools
journal, August 2019
- Mendoza, Sebastián N.; Olivier, Brett G.; Molenaar, Douwe
- Genome Biology, Vol. 20, Issue 1
Exploring eukaryotic formate metabolisms to enhance microbial growth and lipid accumulation
journal, January 2017
- Liu, Zhiguo; Oyetunde, Tolutola; Hollinshead, Whitney D.
- Biotechnology for Biofuels, Vol. 10, Issue 1
In silico identification of metabolic engineering strategies for improved lipid production in Yarrowia lipolytica by genome-scale metabolic modeling
journal, July 2019
- Kim, Minsuk; Park, Beom Gi; Kim, Eun-Jung
- Biotechnology for Biofuels, Vol. 12, Issue 1
The bacterial interlocked process ONtology (BiPON): a systemic multi-scale unified representation of biological processes in prokaryotes
journal, November 2017
- Henry, Vincent J.; Goelzer, Anne; Ferré, Arnaud
- Journal of Biomedical Semantics, Vol. 8, Issue 1
Challenges in the construction of knowledge bases for human microbiome-disease associations
journal, September 2019
- Badal, Varsha Dave; Wright, Dustin; Katsis, Yannis
- Microbiome, Vol. 7, Issue 1
Functional interrogation of Plasmodium genus metabolism identifies species- and stage-specific differences in nutrient essentiality and drug targeting
journal, January 2018
- Abdel-Haleem, Alyaa M.; Hefzi, Hooman; Mineta, Katsuhiko
- PLOS Computational Biology, Vol. 14, Issue 1
A computational knowledge-base elucidates the response of Staphylococcus aureus to different media types
journal, January 2019
- Seif, Yara; Monk, Jonathan M.; Mih, Nathan
- PLOS Computational Biology, Vol. 15, Issue 1
Investigating the deregulation of metabolic tasks via Minimum Network Enrichment Analysis (MiNEA) as applied to nonalcoholic fatty liver disease using mouse and human omics data
journal, April 2019
- Pandey, Vikash; Hatzimanikatis, Vassily
- PLOS Computational Biology, Vol. 15, Issue 4
BOFdat: Generating biomass objective functions for genome-scale metabolic models from experimental data
journal, April 2019
- Lachance, Jean-Christophe; Lloyd, Colton J.; Monk, Jonathan M.
- PLOS Computational Biology, Vol. 15, Issue 4
Parametric studies of metabolic cooperativity in Escherichia coli colonies: Strain and geometric confinement effects
journal, August 2017
- Peterson, Joseph R.; Cole, John A.; Luthey-Schulten, Zaida
- PLOS ONE, Vol. 12, Issue 8
Metabolic network reconstruction and phenome analysis of the industrial microbe, Escherichia coli BL21(DE3)
journal, September 2018
- Kim, Hanseol; Kim, Sinyeon; Yoon, Sung Ho
- PLOS ONE, Vol. 13, Issue 9
MEMOTE for standardized genome-scale metabolic model testing
text, January 2020
- Lieven, Christian; Beber, Moritz E.; Olivier, Brett G.
- RWTH Aachen University
Are Microbes Thermodynamically Optimised Self-Reproducing Machines?
posted_content, December 2019
- Saadat, Nima P.; Nies, Tim; Rousset, Yvan
- Preprints.org
Metabolic Modeling of Microbial Community Interactions for Health, Environmental and Biotechnological Applications
journal, October 2018
- Ang, Kok Siong; Lakshmanan, Meiyappan; Lee, Na-Rae
- Current Genomics, Vol. 19, Issue 8
Systems Medicine as an Emerging Tool for Cardiovascular Genetics
journal, August 2016
- Haase, Tina; Börnigen, Daniela; Müller, Christian
- Frontiers in Cardiovascular Medicine, Vol. 3
iCN718, an Updated and Improved Genome-Scale Metabolic Network Reconstruction of Acinetobacter baumannii AYE
journal, April 2018
- Norsigian, Charles J.; Kavvas, Erol; Seif, Yara
- Frontiers in Genetics, Vol. 9
Fatty Acid Biosynthesis Pathways in Methylomicrobium buryatense 5G(B1)
journal, January 2017
- Demidenko, Aleksandr; Akberdin, Ilya R.; Allemann, Marco
- Frontiers in Microbiology, Vol. 7
Approaches to Computational Strain Design in the Multiomics Era
journal, April 2019
- St. John, Peter C.; Bomble, Yannick J.
- Frontiers in Microbiology, Vol. 10
Modeling Meets Metabolomics—The WormJam Consensus Model as Basis for Metabolic Studies in the Model Organism Caenorhabditis elegans
journal, November 2018
- Witting, Michael; Hastings, Janna; Rodriguez, Nicolas
- Frontiers in Molecular Biosciences, Vol. 5
ToxiM: A Toxicity Prediction Tool for Small Molecules Developed Using Machine Learning and Chemoinformatics Approaches
journal, November 2017
- Sharma, Ashok K.; Srivastava, Gopal N.; Roy, Ankita
- Frontiers in Pharmacology, Vol. 8
In Silico Toxicology Data Resources to Support Read-Across and (Q)SAR
journal, June 2019
- Pawar, Gopal; Madden, Judith C.; Ebbrell, David
- Frontiers in Pharmacology, Vol. 10
A Constraint-Based Model Analysis of Enterocyte Mitochondrial Adaptation to Dietary Interventions of Lipid Type and Lipid Load
journal, June 2018
- Sinha, Neeraj; Suarez-Diez, Maria; Hooiveld, Guido J. E. J.
- Frontiers in Physiology, Vol. 9
ESS: A Tool for Genome-Scale Quantification of Essentiality Score for Reaction/Genes in Constraint-Based Modeling
journal, September 2018
- Zhang, Cheng; Bidkhori, Gholamreza; Benfeitas, Rui
- Frontiers in Physiology, Vol. 9
The Role of Soil Microorganisms in Plant Mineral Nutrition—Current Knowledge and Future Directions
journal, September 2017
- Jacoby, Richard; Peukert, Manuela; Succurro, Antonella
- Frontiers in Plant Science, Vol. 8
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
Reliable and efficient solution of genome-scale models of Metabolism and macromolecular Expression
preprint, January 2016
- Ma, Ding; Yang, Laurence; Fleming, Ronan M. T.
- arXiv
On the effects of alternative optima in context-specific metabolic model predictions
text, January 2016
- Robaina-Estévez, Semidán; Nikoloski, Zoran
- arXiv
Metabolic network percolation quantifies biosynthetic capabilities across the human oral microbiome
journal, June 2019
- Bernstein, David B.; Dewhirst, Floyd E.; Segrè, Daniel
- eLife, Vol. 8