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MEMOTE for standardized genome-scale metabolic model testing
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MEMOTE is an open-source Python software that automatically tests and scores genome-scale metabolic models.
“MEMOTE (MEtabolic MOdel TEsts) is an open-source Python software that automatically tests and scores genome-scale metabolic models [66].”
From Adapting modeling and simulation credibility standards to computational systems biology (2023) · cites this paper as [66]
MEMOTE tests check that a model is annotated according to the MIRIAM standard, that components are described using SBO terms, and that the model is properly constructed using the relevant SBML package, SBML-FBC.
“The tests check that a model is annotated according to the MIRIAM standard, that components are described using SBO terms, and that the model is properly constructed using the relevant SBML package, SBML-FBC [66, 67].”
From Adapting modeling and simulation credibility standards to computational systems biology (2023) · cites this paper as [66]
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Self-citationIntegrative systems biology approaches for analyzing microbiome dysbiosis and species interactions
Rehman, S. S. U., Nasar, M. I., Mesquita, C. S., Khodor, S. A., Notebaart, R. A., Ott, S., Mundra, S., Arasardanam, R. P., Muhammad, K., & Alam, M. T. (2025) · Briefings in Bioinformatics · doi:10.1093/bib/bbaf323 · Cited by 35
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Construction and Analysis of an Enzyme-Constrained Metabolic Model of Corynebacterium glutamicum
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Dotolo, S., Abate, R. E., Roma, C., Guido, D., Preziosi, A., Tropea, B., Palluzzi, F., Giacò, L., & Normanno, N. (2022) · Biomedicines · doi:10.3390/biomedicines10092074 · Cited by 32
Predicting microbial interactions with approaches based on flux balance analysis: an evaluation
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Self-citationEthanol-lactate transition of Lachancea thermotolerans is linked to nitrogen metabolism
Battjes, J., Melkonian, C., Mendoza, S. N., Haver, A., Al-Nakeeb, K., Koza, A., Schrübbers, L. C., Wagner, M. J., Zeidan, A. A., Molenaar, D., et al. (2022) · Food Microbiology · doi:10.1016/j.fm.2022.104167 · Cited by 31
Self-citationKoduru, L., Lakshmanan, M., Lee, Y. Q., Ho, P. L., Lim, P. Y., Ler, W. X., Ng, S. K., Kim, D., Park, D., Banu, M., et al. (2022) · Cell Reports · doi:10.1016/j.celrep.2022.111735 · Cited by 32
Self-citationModel-driven design allows growth of Mycoplasma pneumoniae on serum-free media
Gaspari, E., Malachowski, A., Garcia-Morales, L., Burgos, R., Serrano, L., Martins dos Santos, V. A. P., & Suarez-Diez, M. (2020) · npj Systems Biology and Applications · doi:10.1038/s41540-020-00153-7 · Cited by 30
Genome‐scale modeling for Bacillus coagulans to understand the metabolic characteristics
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Beck, A. E., Kleiner, M., & Garrell, A.-K. (2022) · Frontiers in Plant Science · doi:10.3389/fpls.2022.910377 · Cited by 30
Community‐scale models of microbiomes: Articulating metabolic modelling and metagenome sequencing
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A systematic evaluation of Mycobacterium tuberculosis Genome-Scale Metabolic Networks
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Contribution of genome‐scale metabolic modelling to niche theory
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Shiver, A. L., Sun, J., Culver, R., Violette, A., Wynter, C., Nieckarz, M., Mattiello, S. P., Sekhon, P. K., Bottacini, F., Friess, L., et al. (2025) · Cell · doi:10.1016/j.cell.2025.02.010 · Cited by 27
de León, A. V.-P., Hensen, T., Hoetzinger, M., Gupta, S., Weston, B. R., Johnsen, S. M., Rasmussen, J. A., Clausen, C. G., Pless, L., Verissimo, A. R., et al. (2024) · Nature Microbiology · doi:10.1038/s41564-024-01830-7 · Cited by 27
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High-Quality Genome-Scale Reconstruction of Corynebacterium glutamicum ATCC 13032
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Self-citationBenito-Vaquerizo, S., Olm, I. P., de Vroet, T., Schaap, P. J., Sousa, D. Z., dos Santos, V. A. P. M., & Diez, M. S. (2022) · Microbial Cell Factories · doi:10.1186/s12934-022-01841-1 · Cited by 27
Self-citationGenome-scale modeling of Chinese hamster ovary cells by hybrid semi-parametric flux balance analysis
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Path to improving the life cycle and quality of genome-scale models of metabolism
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Self-citationet i Bsu1209: A comprehensive multiscale metabolic model for Bacillus subtilis
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Adapting modeling and simulation credibility standards to computational systems biology
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Metadata
- Authors
- Lieven, C., Beber, M. E., Olivier, B. G., Bergmann, F. T., Ataman, M., Babaei, P., Bartell, J. A., Blank, L. M., Chauhan, S., Correia, K., Diener, C., Dräger, A., Ebert, B. E., Edirisinghe, J. N., Faria, J. P., Feist, A. M., Fengos, G., Fleming, R. M. T., García-Jiménez, B., Hatzimanikatis, V., van Helvoirt, W., Henry, C. S., Hermjakob, H., Herrgård, M. J., Kaafarani, A., Kim, H. U., King, Z., Klamt, S., Klipp, E., Koehorst, J. J., König, M., Lakshmanan, M., Lee, D.-Y., Lee, S. Y., Lee, S., Lewis, N. E., Liu, F., Ma, H., Machado, D., Mahadevan, R., Maia, P., Mardinoglu, A., Medlock, G. L., Monk, J. M., Nielsen, J., Nielsen, L. K., Nogales, J., Nookaew, I., Palsson, B. O., Papin, J. A., Patil, K. R., Poolman, M., Price, N. D., Resendis-Antonio, O., Richelle, A., Rocha, I., Sánchez, B. J., Schaap, P. J., Malik Sheriff, R. S., Shoaie, S., Sonnenschein, N., Teusink, B., Vilaça, P., Vik, J. O., Wodke, J. A. H., Xavier, J. C., Yuan, Q., Zakhartsev, M., & Zhang, C.
- Affiliations
- Novo Nordisk Foundation (DK)
- Vrije Universiteit Amsterdam (NL)
- Heidelberg University (DE)
- RWTH Aachen University (DE)
- University of California System (US)
- University of Toronto (CA)
- Institute for Systems Biology (US)
- German Center for Infection Research (DE)
- The University of Queensland (AU)
- Argonne National Laboratory (US)
- École Polytechnique Fédérale de Lausanne (CH)
- Leiden University (NL)
- Consejo Superior de Investigaciones Científicas (ES)
- European Bioinformatics Institute (GB)
- Korea Advanced Institute of Science and Technology (KR)
- Max Planck Institute for Dynamics of Complex Technical Systems (DE)
- Humboldt-Universität zu Berlin (DE)
- Wageningen University & Research (NL)
- Agency for Science, Technology and Research (SG)
- Chinese Academy of Sciences (CN)
- European Molecular Biology Laboratory (DE)
- SilicoLife (Portugal) (PT)
- University of Virginia (US)
- University of Arkansas Medical Center (US)
- Oxford Brookes University (GB)
- University of California San Diego (US)
- Instituto de Tecnologia Química e Biológica António Xavier (PT)
- King's College London (GB)
- Norwegian University of Life Sciences (NO)
- Heinrich Heine University Düsseldorf (DE)
- Science for Life Laboratory (SE)
- Corresponding author
- Sonnenschein, Nikolaus
- ORCID
- Lieven, Christian
- Beber, Moritz E.
- Olivier, Brett G.
- Bergmann, Frank T.
- Babaei, Parizad
- Bartell, Jennifer A.
- Blank, Lars M.
- Chauhan, Siddharth
- Correia, Kevin
- Diener, Christian
- Dräger, Andreas
- Ebert, Birgitta E.
- Edirisinghe, Janaka N.
- Faria, José P.
- Feist, Adam M.
- Fengos, Georgios
- Fleming, Ronan M. T.
- García-Jiménez, Beatriz
- Hatzimanikatis, Vassily
- van Helvoirt, Wout
- Henry, Christopher S.
- Hermjakob, Henning
- Herrgård, Markus J.
- Kaafarani, Ali
- Kim, Hyun Uk
- King, Zachary
- Klamt, Steffen
- Klipp, Edda
- Koehorst, Jasper J.
- König, Matthias
- Lakshmanan, Meiyappan
- Lee, Dong-Yup
- Lee, Sang Yup
- Lee, Sunjae
- Lewis, Nathan E.
- Liu, Filipe
- Ma, Hongwu
- Machado, Daniel
- Mahadevan, Radhakrishnan
- Maia, Paulo
- Mardinoglu, Adil
- Medlock, Gregory L.
- Monk, Jonathan M.
- Nielsen, Jens
- Nielsen, Lars Keld
- Nogales, Juan
- Nookaew, Intawat
- Palsson, Bernhard O.
- Papin, Jason A.
- Patil, Kiran R.
- Poolman, Mark
- Price, Nathan D.
- Richelle, Anne
- Rocha, Isabel
- Sánchez, Benjamín J.
- Schaap, Peter J.
- Shoaie, Saeed
- Sonnenschein, Nikolaus
- Teusink, Bas
- Vilaça, Paulo
- Vik, Jon Olav
- Xavier, Joana C.
- Yuan, Qianqian
- Zakhartsev, Maksim
- Zhang, Cheng
- Venue
- Nature Biotechnology
- Published
- 2020-03-01
- Volume
- 38
- Issue
- 3
- Pages
- 272-276
- ISSN
- 0733-222X (ISSN-L)
- 1087-0156
- 1546-1696
- PMC
- PMC7082222
- OpenAlex
- W3010629926
- Cited by
- 509
- References
- 31
- Citations by year
- 2026: 79 · 2025: 73 · 2024: 81 · 2023: 87 · 2022: 69 · 2021: 87 · 2020: 33
- FWCI
- 22.87
- Type
- journal article
- Language
- en
- Update notices
- correction (2020-03-19)
- Open access
- bronze
- doi.org
- Locations
- Nature Biotechnology (publishedVersion)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Socio-Environmental Systems Modeling (acceptedVersion, cc-by)
- Infoscience (Ecole Polytechnique Fédérale de Lausanne) (submittedVersion, cc-by-nc-nd)
- OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion)
- Technical University of Denmark, DTU Orbit (Technical University of Denmark, DTU) (submittedVersion, cc-by)
- DIGITAL.CSIC (Spanish National Research Council (CSIC)) (submittedVersion)
- UCL Discovery (University College London) (submittedVersion)
- Research Portal (King's College London) (submittedVersion, other-oa)
- KAIST Institutional Repository (KAIST) (submittedVersion)
- NORA - Norwegian Open Research Archives (submittedVersion, other-oa)
- RWTH Publications (RWTH Aachen) (submittedVersion, other-oa)
- MPG.PuRe (Max Planck Society) (submittedVersion, other-oa)
- Portuguese National Funding Agency for Science, Research and Technology (RCAAP Project by FCT) (submittedVersion, other-oa)
- Portuguese National Funding Agency for Science, Research and Technology (RCAAP Project by FCT) (submittedVersion, cc-by-nc-nd)
- Chalmers Research (Chalmers University of Technology) (submittedVersion)
- VU Research Portal (submittedVersion, other-oa)
- Data Archiving and Networked Services (DANS) (submittedVersion, other-oa)
- Data Archiving and Networked Services (DANS) (submittedVersion, cc-by)
- Funders
- National Science Foundation (NNF10CC1016517)
- U.S. Department of Energy (DESC0010429)
- Bill and Melinda Gates Foundation (OPP1211869)
- W. M. Keck Foundation
- Washington Research Foundation
- Eli Lilly and Company
- Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria
- University of Arkansas for Medical Sciences
- Deutsches Zentrum für Infektionsforschung
- Oxford Brookes University
- Wellcome Trust
- European Bioinformatics Institute
- Innovationsfonden
- European Molecular Biology Laboratory
- King's College London
- European Commission (633962, HORIZON2020, 244164, 686585, 34,35, 686070)
- Commonwealth Scientific and Industrial Research Organisation
- National Research Foundation (NRF‐2012M1A2A2026557, NRF-2012M1A2A2026556, NRF-2012M1A2A2026556 and NRF-2012M1A2A2026557)
- Agency for Science, Technology and Research
- Deutsche Forschungsgemeinschaft (EXC 2124, GM119850)
- Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung
- Universiteit Leiden
- University of Queensland
- Vrije Universiteit Amsterdam
- Eberhard Karls Universität Tübingen
- Bundesministerium für Bildung und Forschung (FKZ 031A303A, 031L0054, 031A303A)
- Chinese Academy of Sciences
- Sungkyunkwan University
- Chalmers Tekniska Högskola
- University of Toronto
- Rural Development Administration (PJ01334605)
- Universidad Politécnica de Madrid
- Knut och Alice Wallenbergs Stiftelse (NNF10CC1016517)
- Novo Nordisk (NNF10CC1016517)
- Kungliga Tekniska Högskolan
- Danmarks Tekniske Universitet (R35 GM119850, NNF10CC1016517)
- Norges Forskningsråd (248810, 244164, 248792)
- Universidade Nova de Lisboa
- Humboldt-Universität zu Berlin
- Korea Advanced Institute of Science and Technology
- RWTH Aachen University
- Norges Miljø- og Biovitenskapelige Universitet
- Universidade do Minho
- Science for Life Laboratory
- Novo Nordisk Fonden (NNF10CC1016517)
- Hanzehogeschool Groningen
- Ministry of Science and ICT, South Korea (NRF2012M1A2A2026557, NRF2012M1A2A2026556)
- German Network for Bioinformatics Infrastructure
- National Institutes of Health (NNF10CC1016517)
- Directorate for Biological Sciences
- University of California, San Diego
- Biotechnology and Biological Sciences Research Council (BB/N019482/1)
- Consejo Superior de Investigaciones Científicas
- Wageningen University and Research
- Coordinación de la Investigación Científica
- Max Planck Institute for Dynamics of Complex Technical Systems Magdeburg
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa
- National Cancer Institute (P30CA023100)
- National Institute of General Medical Sciences (GM119850, R01GM108501, R01GM070923, NNF10CC1016517, P20GM125503, R35GM119850)
- U.S. National Library of Medicine (T32LM012416)
- Advanced Scientific Computing Research
- Biological and Environmental Research (DE-SC0010429)
- National Center for Complementary and Integrative Health (R01AT010253)
- School of Medicine, University of California, San Diego
- Centro Nacional de Biotecnología
- Argonne National Laboratory
- H2020 European Research Council (666053)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Microbial Metabolic Engineering and Bioproduction
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Keywords
- genome-scale metabolic models, test suite, model metadata, interoperability, provenance tracking, metabolic network reconstruction
- MeSH terms
- Models, Biological, Genome, Computational Biology, Metabolic Networks and Pathways, Workflow, Molecular Sequence Annotation
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
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