The DOI matches its Crossref record; 31 of the 31 references it cites were found in a registry or an index.
MEMOTE for standardized genome-scale metabolic model testing
Open accessPublished version of a preprint
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The cited source says what the claim attributes to it.
In the citing paper
“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]
The cited source says what the claim attributes to it.
In the citing paper
“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]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
A protocol for generating a high-quality genome-scale metabolic reconstruction
Thiele, I., & Palsson, B. Ø. (2010) · Nature Protocols · doi:10.1038/nprot.2009.203 · Cited by 1,789
Self-citationKBase: The United States Department of Energy Systems Biology Knowledgebase
(2018) · doi:10.1038/nbt.4163 · Cited by 1,624
Self-citationCOBRApy: COnstraints-Based Reconstruction and Analysis for Python
Ebrahim, A., Lerman, J. A., Palsson, B. O., & Hyduke, D. R. (2013) · BMC Systems Biology · doi:10.1186/1752-0509-7-74 · Cited by 1,378
Self-citationCreation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0
Heirendt, L., Arreckx, S., Pfau, T., Mendoza, S. N., Richelle, A., Heinken, A., Haraldsdóttir, H. S., Wachowiak, J., Keating, S., Vlasov, V., et al. (2019) · Nature Protocols · doi:10.1038/s41596-018-0098-2 · Cited by 1,222
Self-citationBiGG Models: A platform for integrating, standardizing and sharing genome-scale models
King, Z. A., Lu, J., Dräger, A., Miller, P., Federowicz, S., Lerman, J. A., Ebrahim, A., Palsson, B. O., & Lewis, N. E. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkv1049 · Cited by 938
Self-citationGeneration of genome-scale metabolic reconstructions for 773 members of the human gut microbiota
Magnúsdóttir, S., Heinken, A., Kutt, L., Ravcheev, D. A., Bauer, E., Noronha, A., Greenhalgh, K., Jäger, C., Baginska, J., Wilmes, P., et al. (2017) · Nature Biotechnology · doi:10.1038/nbt.3703 · Cited by 798
Self-citationFast automated reconstruction of genome-scale metabolic models for microbial species and communities
Machado, D., Andrejev, S., Tramontano, M., & Patil, K. R. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky537 · Cited by 754
Self-citationMinimum information requested in the annotation of biochemical models (MIRIAM)
Novère, N. L., Finney, A., Hucka, M., Bhalla, U. S., Campagne, F., Collado-Vides, J., Crampin, E. J., Halstead, M., Klipp, E., Mendes, P., et al. (2005) · Nature Biotechnology · doi:10.1038/nbt1156 · Cited by 622
Self-citationOptFlux: an open-source software platform for in silico metabolic engineering
Rocha, I., Maia, P., Evangelista, P., Vilaça, P., Soares, S., Pinto, J. P., Nielsen, J., Patil, K. R., Ferreira, E. C., & Rocha, M. (2010) · BMC Systems Biology · doi:10.1186/1752-0509-4-45 · Cited by 390
Self-citationLibSBML: an API Library for SBML
Bornstein, B. J., Keating, S. M., Jouraku, A., & Hucka, M. (2008) · Bioinformatics · doi:10.1093/bioinformatics/btn051 · Cited by 373
Cited by
Sorted by citations
Items 501–525 of 525
Corbín-Agustí, P., Álvarez-Herrera, M., Román-Écija, M., Álvarez, P., Tortajada, M., Landa, B. B., & Peretó, J. G. (2026) · Microbiological Research · doi:10.1016/j.micres.2026.128616
Rolle, P., Auricht, H., Marcut, A., López‐Hidalgo, C., Weckwerth, W., & Waldherr, S. (2026) · mSystems · doi:10.1128/msystems.00514-26
Nuñez, D., Krauss, C., Fernandes, M. G., Vlaar, J. M., Cochrane, A., Pérez, J. R., Maass, A., Agosin, E., & Mendoza, S. N. (2026) · Future Foods · doi:10.1016/j.fufo.2026.101132
Jiang, G., Yin, Y., Tian, L., Lu, J., Cai, X., Deng, T., Cao, Y., Wang, S. W., Tang, Y., Morel, J., et al. (2026) · Journal of Hazardous Materials · doi:10.1016/j.jhazmat.2026.143053
Proteus: an executable, statically-checked language for biological reaction modelsPreprint
Deprez, F. (2026) · SSRN Electronic Journal · doi:10.2139/ssrn.7324287
BioEMMA: Automated Generation of Model-Specific Escher-Compatible Maps from KEGG Pathways
Kachnov, V. A., Esembaeva, M. A., Melikhova, E. V., & Kulyashov, M. A. (2026) · Biology · doi:10.3390/biology15171493
Aguirre, I. C., Priya, M., Garza-Garcı́a, A., de Carvalho, L. P. S., de Jong, H., & Ropers, D. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.09.02.748904
Hu, C., Luan, A., Yang, Y., Wang, L., Wang, H., Wang, N., He, G., Yang, Y., Noor, R., Hussain, J., et al. (2026) · BMEMat · doi:10.1002/bmm2.70135
A metadata-managed FAIR end-to-end workflow for microbial community omics data analysis
Ke, C., Koehorst, J. J., Nijsse, B., Scott, W. T., & Schaap, P. J. (2026) · Scientific Data · doi:10.1038/s41597-026-08224-w
Self-citationMuigano, M. N. (2026) · Research Square · doi:10.21203/rs.3.rs-10989479/v1
Pan-Genome-Scale Metabolic Reconstruction Reveals Conserved Metabolic Functions in Candida albicans
Meng, Y., Zhang, Y., & Zhang, L. (2026) · Journal of Fungi · doi:10.3390/jof12090697
Canto-Encalada, G., Hajama, H., Saldivar, A., Ademikanra, A. F., Willkeen, G. A., Segall, A. M., & Zúñiga, C. (2026) · Research Square · doi:10.21203/rs.3.rs-10656614/v1
Xu, S.-S., Ding, J., Chen, S., Li, Y.-C., Wan, J.-Y., Mo, L., Liu, H., & Xu, Q. (2026) · Biotechnology Advances · doi:10.1016/j.biotechadv.2026.109069
Muzahid, N. H., Patel, A., Raymond, M., Egidi, T., Nguyen, N., & Zúñiga, C. (2026) · Infection and Immunity · doi:10.1128/iai.00435-26
Kocabaş, P. (2026) · Biotechnology and Bioengineering · doi:10.1002/bit.70402
Scott, W. T., Jácome, L. A. P., Nijsse, B., Wang, J., Stouten, G. R., Koehorst, J. J., Smidt, H., Edwards, E. A., Schaap, P. J., & Kleerebezem, R. (2026) · Water Research · doi:10.1016/j.watres.2026.127036
Self-citationAnalysis of metabolic interactions in an artificial consortium including butyrogenic gut microbes
Torres-Miranda, A., Guron, G. K. P., Renye, J. A., Hotchkiss, A. T., & Garrido, D. A. (2026) · mSystems · doi:10.1128/msystems.00612-26
Pentjuss, A., Koļesovs, S., Grūbe, M., Ščerbaka, R., Shvirksts, K., Stalidzāns, E., Vīgants, A., Smetana, S. M., & Pleißner, D. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.10.15.759342
High-light correlates with adaptive dominance of comammox Nitrospira clade B in alpine rivers
Wu, X., Cai, H., Zhang, X., Li, B., Chen, Q., & Ni, J. (2026) · Water Research · doi:10.1016/j.watres.2026.127173
Host-like temperature unlocks glucose uptake and metabolism in pathogenic Leptospira
Ozuru, R., Yoshimura, M., Powers, D. A., Sonoda, T., Papin, J. A., Obata, F., Kolling, G. L., & Hiromatsu, K. (2026) · mBio · doi:10.1128/mbio.01814-26
Self-citationMicrobial resistance from genotype to metabolic phenotype
Clasen, F., Jin, Y., Brett, J., García-Guevara, F., Ehrlich, S. D., & Shoaie, S. (2026) · Trends in Microbiology · doi:10.1016/j.tim.2026.09.009
Self-citationFAIRsharing record for: Metabolic Atlas
FAIRsharing Team, McQuilton, P., & Mihail (2018) · FAIRsharing.org · doi:10.25504/fairsharing.7jcjd0
Wei, J., & Lin, W. (2026) · Briefings in Bioinformatics · doi:10.1093/bib/bbag344
Aerobic microbial conversion of carbon monoxide to value-added products: progress and challenges
Zhang, Z., Weng, C., Han, Y., & Peng, X. (2026) · Engineering Microbiology · doi:10.1016/j.engmic.2026.100313
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.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
