A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology
Open accessAbstract
Genomic data allow the large-scale manual or semi-automated assembly of metabolic network reconstructions, which provide highly curated organism-specific knowledge bases. Although several genome-scale network reconstructions describe Saccharomyces cerevisiae metabolism, they differ in scope and content, and use different terminologies to describe the same chemical entities. This makes comparisons between them difficult and underscores the desirability of a consolidated metabolic network that collects and formalizes the 'community knowledge' of yeast metabolism. We describe how we have produced a consensus metabolic network reconstruction for S. cerevisiae. In drafting it, we placed special emphasis on referencing molecules to persistent databases or using database-independent forms, such as SMILES or InChI strings, as this permits their chemical structure to be represented unambiguously and in a manner that permits automated reasoning. The reconstruction is readily available via a publicly accessible database and in the Systems Biology Markup Language (http://www.comp-sys-bio.org/yeastnet). It can be maintained as a resource that serves as a common denominator for studying the systems biology of yeast. Similar strategies should benefit communities studying genome-scale metabolic networks of other organisms.
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
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?
Ignoring most published papers is no longer realistic or necessary in an age of post-genomics, the internet, Web 2.0 and systems biology, and when we are starting to move to integrative models of organisms at a whole organ, genome or whole organism scale.
“This is no longer realistic (nor necessary) in an age of post-genomics, the internet, Web 2.0 and systems biology, and when we are starting to move to integrative (if distributed) models of organisms (including humans) at a whole organ, genome or whole organism scale [118,2135,2407-2416].”
Integration of bibliographic, metabolomic, and genomic data has been used to reconstruct the dynamic range of metabolome flow of organisms, first in Escherichia coli and extended to yeast, mice, and humans.
“For example, the integration of bibliographic, metabolomic, and genomic data have been used to reconstruct the dynamic range of metabolome flow of organisms, first performed in Escherichia coli [35] and since extended to yeast [36, 37] and to individual tissues in mice [38] and humans [39].”
From Multi-omics approaches to disease (2017) · cites this paper as [37]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
Cytoscape: A software Environment for integrated models of biomolecular interaction networks
Shannon, P., Markiel, A., Ozier, O., Baliga, N. S., Wang, J. T., Ramage, D., Amin, N., Schwikowski, B., & Ideker, T. (2003) · Genome Research · doi:10.1101/gr.1239303 · Cited by 51,888 · see citing works
Gene Ontology: tool for the unification of biology
Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D., Butler, H., Cherry, J. M., Davis, A. P., Dolinski, K., Dwight, S. S., Eppig, J. T., et al. (2000) · Nature Genetics · doi:10.1038/75556 · Cited by 43,206 · see citing works
Database resources of the National Center for Biotechnology Information: update
Wheeler, D. L. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkh073 · Cited by 10,691 · see citing works
Network biology: understanding the cell's functional organization
Barabási, A.-L., & Oltvai, Z. N. (2004) · Nature Reviews Genetics · doi:10.1038/nrg1272 · Cited by 7,903 · see citing works
Weininger, D. (1988) · Journal of Chemical Information and Computer Sciences · doi:10.1021/ci00057a005 · Cited by 7,436 · see citing works
Goffeau, A., Barrell, B., Bussey, H., Davis, R. W., Dujon, B., Feldmann, H., Galibert, F., Hoheisel, J., Jacq, C., Johnston, M., et al. (1996) · Science · doi:10.1126/science.274.5287.546 · Cited by 4,420 · see citing works
Self-citationFunctional profiling of the Saccharomyces cerevisiae genome
Giaever, G., Chu, A. M., Ni, L., Connelly, C., Riles, L., Véronneau, S., Dow, S., Lucau-Danila, A., Anderson, K., André, B., et al. (2002) · Nature · doi:10.1038/nature00935 · Cited by 4,316 · see citing works
Winzeler, E. A., Shoemaker, D. D., Astromoff, A., Liang, H., Anderson, K., Andre, B., Bangham, R., Benito, R., Boeke, J. D., Bussey, H., et al. (1999) · Science · doi:10.1126/science.285.5429.901 · Cited by 3,953 · see citing works
The Universal Protein Resource (UniProt)
Bairoch, A. (2004) · Nucleic Acids Research · doi:10.1093/nar/gki070 · Cited by 3,774 · see citing works
Caspi, R., Billington, R., Ferrer, L., Foerster, H., Fulcher, C. A., Keseler, I. M., Kothari, A., Krummenacker, M., Latendresse, M., Mueller, L. A., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkv1164 · Cited by 3,395 · see citing works
Wikinomics: how mass collaboration changes everything
(2007) · Choice Reviews Online · doi:10.5860/choice.44-6933 · Cited by 3,369 · see citing works
HMDB: the Human Metabolome Database
Wishart, D. S., Tzur, D., Knox, C., Eisner, R., Guo, A. C., Young, N., Cheng, D., Jewell, K., Arndt, D., Sawhney, S., et al. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkl923 · Cited by 3,219 · see citing works
From genomics to chemical genomics: new developments in KEGG
Kanehisa, M. I. (2005) · Nucleic Acids Research · doi:10.1093/nar/gkj102 · Cited by 3,126 · see citing works
Hucka, M., Finney, A., Sauro, H. M., Bolouri, H., Doyle, J. C., Kitano, H., Arkin, A. P., Bornstein, B. J., Bray, D., Cornish-Bowden, A., et al. (2003) · Bioinformatics · doi:10.1093/bioinformatics/btg015 · Cited by 3,060 · see citing works
Self-citation(2004) · Choice Reviews Online · doi:10.5860/choice.42-1645 · Cited by 2,928 · see citing works
COPASI—a COmplex PAthway SImulator
Hoops, S., Sahle, S., Gauges, R., Lee, C., Pahle, J., Simus, N., Singhal, M., Xu, L., Mendes, P., & Kummer, U. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btl485 · Cited by 2,618 · see citing works
Self-citationFunctional Discovery via a Compendium of Expression Profiles
Hughes, T. R., Marton, M. J., Jones, A. R., Roberts, C. J., Stoughton, R. B., Armour, C. D., Bennett, H. A., Coffey, E. M., Dai, H. A., He, Y. D., et al. (2000) · Cell · doi:10.1016/s0092-8674(00)00015-5 · Cited by 2,534 · see citing works
Global Analysis of Protein Activities Using Proteome Chips
Zhu, H., Bilgin, M., Bangham, R., Hall, D., Casamayor, A., Bertone, P., Lan, N., Jansen, R., Bidlingmaier, S., Houfek, T., et al. (2001) · Science · doi:10.1126/science.1062191 · Cited by 1,884 · see citing works
LMSD: LIPID MAPS structure database
Sud, M., Fahy, E., Cotter, D., Brown, A., Dennis, E. A., Glass, C. K., Merrill, A. H., Murphy, R. C., Raetz, C. R. H., Russell, D. W., et al. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl838 · Cited by 1,388 · see citing works
Global reconstruction of the human metabolic network based on genomic and bibliomic data
Duarte, N. C., Becker, S. A., Jamshidi, N., Thiele, I., Mo, M. L., Vo, T. D., Srivas, R., & Palsson, B. Ø. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0610772104 · Cited by 1,374 · see citing works
Self-citationGenome-Scale Reconstruction of the <i>Saccharomyces cerevisiae</i> Metabolic Network
Förster, J., Famili, I., Fu, P., Palsson, B. Ø., & Nielsen, J. (2003) · Genome Research · doi:10.1101/gr.234503 · Cited by 1,069 · see citing works
Self-citationAn expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR)
Reed, J. L., Vo, T. D., Schilling, C. H., & Palsson, B. Ø. (2003) · Genome biology · doi:10.1186/gb-2003-4-9-r54 · Cited by 1,001 · see citing works
Self-citationThe small world inside large metabolic networks
Wagner, A., & Fell, D. A. (2001) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2001.1711 · Cited by 986 · see citing works
The Universal Protein Resource (UniProt)
The UniProt Consortium (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm895 · Cited by 824 · see citing works
The wisdom of crowds : why the many are smarter than the few
Surowiecki, J. (2005) · Cited by 745 · see citing works
Database resources of the National Center for Biotechnology Information
Wheeler, D. L., Barrett, T., Benson, D. A., Bryant, S. H., Canese, K., Chetvernin, V., Church, D. M., DiCuccio, M., Edgar, R., Federhen, S., et al. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkl1031 · Cited by 734 · see citing works
Systems biology properties of reconstructed networks
Palsson, B. Ø. (2006) · Cited by 684 · see citing works
Self-citationDuarte, N. C., Herrgård, M. J., & Palsson, B. Ø. (2004) · Genome Research · doi:10.1101/gr.2250904 · Cited by 639 · see citing works
Self-citationCellDesigner: a process diagram editor for gene-regulatory and biochemical networks
Funahashi, A., Morohashi, M., Kitano, H., & Tanimura, N. (2003) · BIOSILICO · doi:10.1016/s1478-5382(03)02370-9 · Cited by 631 · see citing works
Minimum 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 · see citing works
Self-citationMetaCyc: a multiorganism database of metabolic pathways and enzymes
Caspi, R. R. (2005) · Nucleic Acids Research · doi:10.1093/nar/gkj128 · Cited by 620 · see citing works
Systems Biology: Properties of Reconstructed Networks
Palsson, B. Ø. (2006) · doi:10.1017/cbo9780511790515 · Cited by 617 · see citing works
Self-citationCaspi, R. R., Foerster, H., Fulcher, C., Kaipa, P., Krummenacker, M., Latendresse, M., Paley, S., Rhee, S. Y., Shearer, A. G., Tissier, C. P., et al. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm900 · Cited by 580 · see citing works
High-throughput classification of yeast mutants for functional genomics using metabolic footprinting
Allen, J., Davey, H. M., Broadhurst, D., Heald, J. K., Rowland, J. J., Oliver, S. G., & Kell, D. B. (2003) · Nature Biotechnology · doi:10.1038/nbt823 · Cited by 538 · see citing works
Self-citationThe Edinburgh human metabolic network reconstruction and its functional analysis
Ma, H., Sorokin, A., Mazein, A., Selkov, A., Selkov, E., Demin, O., & Goryanin, I. (2007) · Molecular Systems Biology · doi:10.1038/msb4100177 · Cited by 435 · see citing works
Metabolic Profiling: Its Role in Biomarker Discovery and Gene Function Analysis
(2003) · Springer eBooks · doi:10.1007/978-1-4615-0333-0 · Cited by 390 · see citing works
LibSBML: 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 · see citing works
Self-citationText mining and its potential applications in systems biology
Ananiadou, S., Kell, D. B., & Tsujii, J. (2006) · Trends in biotechnology · doi:10.1016/j.tibtech.2006.10.002 · Cited by 324 · see citing works
Self-citationBlank, L. M., Kuepfer, L., & Sauer, U. (2005) · Genome biology · doi:10.1186/gb-2005-6-6-r49 · Cited by 318 · see citing works
Self-citationSystems biology, metabolic modelling and metabolomics in drug discovery and development
Kell, D. B. (2006) · Drug Discovery Today · doi:10.1016/j.drudis.2006.10.004 · Cited by 297 · see citing works
Self-citationPutative regulatory sites unraveled by network‐embedded thermodynamic analysis of metabolome data
Kümmel, A., Panke, S., & Heinemann, M. (2006) · Molecular Systems Biology · doi:10.1038/msb4100074 · Cited by 290 · see citing works
Self-citationGrowth control of the eukaryote cell: a systems biology study in yeast
Castrillo, J. I., Zeef, L. A., Hoyle, D. C., Zhang, N., Hayes, A., Gardner, D. C., Cornell, M. J., Petty, J., Hakes, L., Wardleworth, L., et al. (2007) · Journal of Biology · doi:10.1186/jbiol54 · Cited by 263 · see citing works
Self-citationMetabolic functions of duplicate genes in Saccharomyces cerevisiaePreprint
Kuepfer, L., Sauer, U., & Blank, L. M. (2005) · Genome Research · doi:10.1101/gr.3992505 · Cited by 238 · see citing works
Self-citationYeast as a model for medical and medicinal research
Mager, W. H., & Winderickx, J. (2005) · Trends in Pharmacological Sciences · doi:10.1016/j.tips.2005.03.004 · Cited by 217 · see citing works
Nookaew, I., Jewett, M. C., Meechai, A., Thammarongtham, C., Laoteng, K., Cheevadhanarak, S., Nielsen, J., & Bhumiratana, S. (2008) · BMC Systems Biology · doi:10.1186/1752-0509-2-71 · Cited by 185 · see citing works
Self-citationKell, D. B. (2006) · FEBS Journal · doi:10.1111/j.1742-4658.2006.05136.x · Cited by 147 · see citing works
Self-citationLarge-Scale Evaluation of In Silico Gene Deletions in Saccharomyces cerevisiae
Förster, J., Famili, I., Palsson, B. Ø., & Nielsen, J. (2003) · OMICS A Journal of Integrative Biology · doi:10.1089/153623103322246584 · Cited by 140 · see citing works
Self-citationWu, J., Zhang, N., Hayes, A., Panoutsopoulou, K., & Oliver, S. G. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0308321100 · Cited by 139 · see citing works
Self-citationIntegration of metabolome data with metabolic networks reveals reporter reactions
Çakır, T., Patil, K. R., Önsan, Z. I., Ülgen, K. Ö., Kırdar, B., & Nielsen, J. (2006) · Molecular Systems Biology · doi:10.1038/msb4100085 · Cited by 138 · see citing works
Self-citationA network approach to the systematic analysis of yeast gene function
Oliver, S. G. (1996) · Trends in Genetics · doi:10.1016/0168-9525(96)30053-x · Cited by 133 · see citing works
Self-citationTarO: a target optimisation system for structural biology
Overton, I. M., van Niekerk, C. A. J., Carter, L. G., Dawson, A., Martin, D. M. A., Cameron, S., McMahon, S. A., White, M. F., Hunter, W. N., Naismith, J. H., et al. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn141 · Cited by 113 · see citing works
The European Bioinformatics Institute's data resources: towards systems biology
Brooksbank, C. (2004) · Nucleic Acids Research · doi:10.1093/nar/gki026 · Cited by 103 · see citing works
Delneri, D., Hoyle, D. C., Gkargkas, K., Cross, E. J. M., Rash, B. M., Zeef, L. A. H., Leong, H. S., Davey, H. M., Hayes, A., Kell, D. B., et al. (2007) · Nature Genetics · doi:10.1038/ng.2007.49 · Cited by 95 · see citing works
Self-citationYeast-based functional genomics and proteomics technologies: the first 15 years and beyond
Suter, B., Auerbach, D., & Štagljar, I. (2006) · BioTechniques · doi:10.2144/000112151 · Cited by 92 · see citing works
Enhancement of the chemical semantic web through the use of InChI identifiers
Coles, S. J., Day, N. E., Murray‐Rust, P., Rzepa, H. S., & Zhang, Y. (2005) · Organic & Biomolecular Chemistry · doi:10.1039/b502828k · Cited by 85 · see citing works
Expanded protein information at SGD: new pages and proteome browser
Nash, R. S., Weng, S., Hitz, B. C., Balakrishnan, R., Christie, K., Costanzo, M. C., Dwight, S. S., Engel, S. R., Fisk, D. G., Hirschman, J., et al. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl931 · Cited by 79 · see citing works
Conservation analysis of large biochemical networks
Vallabhajosyula, R. R., Chickarmane, V. S., & Sauro, H. M. (2005) · Bioinformatics · doi:10.1093/bioinformatics/bti800 · Cited by 78 · see citing works
Internet-based tools for communication and collaboration in chemistry
Williams, A. J. (2008) · Drug Discovery Today · doi:10.1016/j.drudis.2008.03.015 · Cited by 78 · see citing works
A perspective of publicly accessible/open-access chemistry databases
Williams, A. J. (2008) · Drug Discovery Today · doi:10.1016/j.drudis.2008.03.017 · Cited by 69 · see citing works
Two-dimensional annotation of genomes
Palsson, B. Ø. (2004) · Nature Biotechnology · doi:10.1038/nbt1004-1218 · Cited by 65 · see citing works
Self-citationChallenges to be faced in the reconstruction of metabolic networks from public databases
Poolman, M. G., Bonde, B. K., Gevorgyan, A., Patel, H., & Fell, D. A. (2006) · Systems Biology · doi:10.1049/ip-syb:20060012 · Cited by 58 · see citing works
GEM System: automatic prototyping of cell-wide metabolic pathway models from genomes
Arakawa, K., Yamada, Y., Shinoda, K., Nakayama, Y., & Tomita, M. (2006) · BMC Bioinformatics · doi:10.1186/1471-2105-7-168 · Cited by 54 · see citing works
An improved tetO promoter replacement system for regulating the expression of yeast genes
Yen, K., Gitsham, P., Wishart, J. A., Oliver, S. G., & Zhang, N. (2003) · Yeast · doi:10.1002/yea.1037 · Cited by 42 · see citing works
Self-citationSpasić, ., Schober, D., Sansone, S., Rebholz‐Schuhmann, D., Kell, D. B., & Paton, N. W. (2008) · BMC Bioinformatics · doi:10.1186/1471-2105-9-s5-s5 · Cited by 41 · see citing works
Self-citationAutomated manipulation of systems biology models using libSBML within Taverna workflows
Li, P., Oinn, T., Soiland‐Reyes, S., & Kell, D. B. (2007) · Bioinformatics · doi:10.1093/bioinformatics/btm578 · Cited by 35 · see citing works
Self-citationUsing a logical model to predict the growth of yeast
Whelan, K. E., & King, R. D. (2008) · BMC Bioinformatics · doi:10.1186/1471-2105-9-97 · Cited by 24 · see citing works
The Montagues and the Capulets
Goble, C., & Wroe, C. (2004) · Comparative and Functional Genomics · doi:10.1002/cfg.442 · Cited by 18 · see citing works
Databases and Visualization for Metabolomics
Li, X., Brazhnik, O., Kamal, A. H., Guo, D., Lee, C., Hoops, S., & Mendes, P. (2003) · Springer eBooks · doi:10.1007/978-1-4615-0333-0_16 · Cited by 10 · see citing works
Self-citation
Flagged first, then by citations
1 of the 69 references couldn’t be matched to a known paper.
Cited by
Sorted by citations
Multi-omics approaches to disease
Hasin, Y., Seldin, M., & Lusis, A. (2017) · Genome Biology · doi:10.1186/s13059-017-1215-1 · Cited by 2,953 · see citing works
ChEBI in 2016: Improved services and an expanding collection of metabolites
Hastings, J., Owen, G., Dekker, A., Ennis, M., Kale, N., Muthukrishnan, V., Turner, S., Swainston, N., Mendes, P., & Steinbeck, C. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkv1031 · Cited by 1,083 · see citing works
Self-citationA community-driven global reconstruction of human metabolism
Thiele, I., Swainston, N., Fleming, R. M. T., Hoppe, A., Sahoo, S., Aurich, M. K., Haraldsdottir, H., Mo, M. L., Rolfsson, O., Stobbe, M. D., et al. (2013) · Nature Biotechnology · doi:10.1038/nbt.2488 · Cited by 1,019 · see citing works
Self-citationProtein Phylogenetic Analysis of Ca2+/cation Antiporters and Insights into their Evolution in Plants
Emery, L. R., Whelan, S., Hirschi, K. D., & Pittman, J. K. (2012) · Frontiers in Plant Science · doi:10.3389/fpls.2012.00001 · Cited by 930 · see citing works
Structure and dynamics of molecular networks: A novel paradigm of drug discovery
Csermely, P., Korcsmáros, T., Kiss, H., London, G., & Nussinov, R. (2013) · Pharmacology & Therapeutics · doi:10.1016/j.pharmthera.2013.01.016 · Cited by 889 · see citing works
Dunn, W. B., Broadhurst, D., Atherton, H. J., Goodacre, R., & Griffin, J. L. (2010) · Chemical Society Reviews · doi:10.1039/b906712b · Cited by 870 · see citing works
Self-citationApplications of genome‐scale metabolic reconstructions
Oberhardt, M., Palsson, B. Ø., & Papin, J. A. (2009) · Molecular Systems Biology · doi:10.1038/msb.2009.77 · Cited by 820 · see citing works
Self-citationGreenblum, S., Turnbaugh, P. J., & Borenstein, E. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1116053109 · Cited by 821 · see citing works
Current status and applications of genome-scale metabolic models
Gu, C., Kim, G. B., Kim, W. J., Kim, H. U., & Lee, S. Y. (2019) · Genome biology · doi:10.1186/s13059-019-1730-3 · Cited by 765 · see citing works
Systems biology and multi-omics integration: viewpoints from the metabolomics research community
Pinu, F. R., Beale, D. J., Paten, A. M., Kouremenos, K., Swarup, S., Schirra, H. J., & Wishart, D. (2019) · Metabolites · doi:10.3390/metabo9040076 · Cited by 723 · see citing works
King, R. D., Rowland, J., Oliver, S. G., Young, M., Aubrey, W., Byrne, E., Liakata, M., Markham, M., Pir, P., Soldatova, L. N., et al. (2009) · Science · doi:10.1126/science.1165620 · Cited by 679 · see citing works
Self-citationSingle-Cell Metabolomics: Analytical and Biological Perspectives
Zenobi, R. (2013) · Science · doi:10.1126/science.1243259 · Cited by 659 · see citing works
Perspectives and Challenges of Microbial Application for Crop Improvement
Timmusk, S., Behers, L., Muthoni, J., Muraya, A. M., & Aronsson, A.-C. (2017) · Frontiers in Plant Science · doi:10.3389/fpls.2017.00049 · Cited by 593 · see citing works
BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions
Schellenberger, J., Park, J. O., Conrad, T. M., & Palsson, B. Ø. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-213 · Cited by 585 · see citing works
Self-citationMass appeal: metabolite identification in mass spectrometry-focused untargeted metabolomics
Dunn, W. B., Erban, A., Weber, R. J. M., Creek, D. J., Brown, M., Rainer Breitling, A., Hankemeier, T., Goodacre, R., Neumann, S., Kopka, J., et al. (2012) · Metabolomics · doi:10.1007/s11306-012-0434-4 · Cited by 560 · see citing works
Self-citationKell, D. B. (2009) · BMC Medical Genomics · doi:10.1186/1755-8794-2-2 · Cited by 554 · see citing works
Self-citation13C-based metabolic flux analysis
Zamboni, N., Fendt, S., Rühl, M., & Sauer, U. (2009) · Nature Protocols · doi:10.1038/nprot.2009.58 · Cited by 549 · see citing works
Self-citationLight-driven fine chemical production in yeast biohybrids
Guo, J., Suástegui, M., Sakimoto, K. K., Moody, V. M., Xiao, G., Nocera, D. G., & Joshi, N. S. (2018) · Science · doi:10.1126/science.aat9777 · Cited by 460 · see citing works
Connecting extracellular metabolomic measurements to intracellular flux states in yeast
Mo, M. L., Palsson, B. Ø., & Herrgård, M. J. (2009) · BMC Systems Biology · doi:10.1186/1752-0509-3-37 · Cited by 452 · see citing works
Self-citationÅgren, R., Liu, L., Shoaie, S., Vongsangnak, W., Nookaew, I., & Nielsen, J. (2013) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002980 · Cited by 418 · see citing works
Self-citationRegulation of amino acid metabolic enzymes and transporters in plants
Pratelli, R., & Pilot, G. (2014) · Journal of Experimental Botany · doi:10.1093/jxb/eru320 · Cited by 410 · see citing works
Currin, A., Swainston, N., Day, P. J., & Kell, D. B. (2014) · Chemical Society Reviews · doi:10.1039/c4cs00351a · Cited by 383 · see citing works
Self-citationKell, D. B. (2010) · Archives of Toxicology · doi:10.1007/s00204-010-0577-x · Cited by 361 · see citing works
Self-citationProduction of recombinant proteins by yeast cells
Çelik, E., & Çalı́k, P. (2011) · Biotechnology Advances · doi:10.1016/j.biotechadv.2011.09.011 · Cited by 338 · see citing works
Environments that Induce Synthetic Microbial Ecosystems
Klitgord, N., & Segrè, D. (2010) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1001002 · Cited by 331 · see citing works
Kell, D. B. (2012) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2011.0244 · Cited by 317 · see citing works
Self-citationKinetic models in industrial biotechnology – Improving cell factory performance
Almquist, J. O., Cvijović, M., Vassily Hatzimanikatis, A., Nielsen, J., & Jirstrand, M. (2014) · Metabolic Engineering · doi:10.1016/j.ymben.2014.03.007 · Cited by 291 · see citing works
Self-citationRecon 2.2: from reconstruction to model of human metabolism
Swainston, N., Smallbone, K., Hefzi, H., Dobson, P. D., Brewer, J., Hanscho, M., Zielinski, D. C., Ang, K. S., Gardiner, N. J., Gutierrez, J. M., et al. (2016) · Metabolomics · doi:10.1007/s11306-016-1051-4 · Cited by 285 · see citing works
Self-citationYeast Systems Biology: Model Organism and Cell Factory
Nielsen, J. (2019) · Biotechnology Journal · doi:10.1002/biot.201800421 · Cited by 283 · see citing works
Self-citationBrown, M., Dunn, W. B., Dobson, P. D., Patel, Y., Winder, C. L., Francis‐McIntyre, S., Begley, P., Carroll, K. M., Broadhurst, D., Tseng, A., et al. (2009) · The Analyst · doi:10.1039/b901179j · Cited by 270 · see citing works
Self-citationGrowth-limiting Intracellular Metabolites in Yeast Growing under Diverse Nutrient Limitations
Boer, V. M., Crutchfield, C. A., Bradley, P. H., Botstein, D., & Rabinowitz, J. D. (2009) · Molecular Biology of the Cell · doi:10.1091/mbc.e09-07-0597 · Cited by 260 · see citing works
Software for systems biology: from tools to integrated platforms
Ghosh, S., Matsuoka, Y., Asai, Y., Hsin, K., & Kitano, H. (2011) · Nature Reviews Genetics · doi:10.1038/nrg3096 · Cited by 258 · see citing works
Evolution of biomolecular networks — lessons from metabolic and protein interactions
Yamada, T., & Peer Bork, B. (2009) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm2787 · Cited by 253 · see citing works
Nielsen, J. (2017) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-061516-044757 · Cited by 252 · see citing works
Self-citationFueling the future with fungal genomics
Grigoriev, I. V., Cullen, D., Goodwin, S. B., Hibbett, D., Jeffries, T. W., Kubicek, C. P., Kuske, C., Magnuson, J. K., Martin, F., Spatafora, J. W., et al. (2011) · Mycology · doi:10.1080/21501203.2011.584577 · Cited by 250 · see citing works
“(Herrgard et al. 2008; Andersen et al. 2008) to predict genes whose deletion or overexpression”
Computational Metabolomics: A Framework for the Million Metabolome
Uppal, K., Walker, D. I., Liu, K., Li, S., Go, Y., & Jones, D. P. (2016) · Chemical Research in Toxicology · doi:10.1021/acs.chemrestox.6b00179 · Cited by 241 · see citing works
Weckwerth, W. (2011) · Journal of Proteomics · doi:10.1016/j.jprot.2011.07.010 · Cited by 243 · see citing works
Extensive In Vivo Metabolite-Protein Interactions Revealed by Large-Scale Systematic Analyses
Li, X., Gianoulis, T. A., Yip, K. Y., Gerstein, M., & Snyder, M. (2010) · Cell · doi:10.1016/j.cell.2010.09.048 · Cited by 237 · see citing works
Event extraction for systems biology by text mining the literature
Ananiadou, S., Pyysalo, S., Tsujii, J., & Kell, D. B. (2010) · Trends in biotechnology · doi:10.1016/j.tibtech.2010.04.005 · Cited by 235 · see citing works
Self-citationOptimizing genome-scale network reconstructions
Monk, J. M., Nogales, J., & Palsson, B. Ø. (2014) · Nature Biotechnology · doi:10.1038/nbt.2870 · Cited by 200 · see citing works
Self-citationThe Metabolic Network of Synechocystis sp. PCC 6803: Systemic Properties of Autotrophic Growth
Knoop, H., Zilliges, Y., Lockau, W., & Steuer, R. (2010) · PLANT PHYSIOLOGY · doi:10.1104/pp.110.157198 · Cited by 195 · see citing works
Membrane transporter engineering in industrial biotechnology and whole cell biocatalysis
Kell, D. B., Swainston, N., Pir, P., & Oliver, S. G. (2015) · Trends in biotechnology · doi:10.1016/j.tibtech.2015.02.001 · Cited by 195 · see citing works
Self-citationYMDB: the Yeast Metabolome Database
Jewison, T., Knox, C., Neveu, V., Djoumbou, Y., Guo, A. C., Lee, J., Liu, P., Mandal, R., Krishnamurthy, R., Sinelnikov, I., et al. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr916 · Cited by 194 · see citing works
Pathway databases and tools for their exploitation: benefits, current limitations and challenges
Bauer‐Mehren, A., Furlong, L. I., & Sanz, F. (2009) · Molecular Systems Biology · doi:10.1038/msb.2009.47 · Cited by 193 · see citing works
Modeling cancer metabolism on a genome scale
Yizhak, K., Chaneton, B., Gottlieb, E., & Ruppin, E. (2015) · Molecular Systems Biology · doi:10.15252/msb.20145307 · Cited by 182 · see citing works
Algorithms and tools for the preprocessing of LC–MS metabolomics data
Castillo, S., Gopalacharyulu, P. V., Yetukuri, L., & Orešič, M. (2011) · Chemometrics and Intelligent Laboratory Systems · doi:10.1016/j.chemolab.2011.03.010 · Cited by 175 · see citing works
Path2Models: large-scale generation of computational models from biochemical pathway maps
Büchel, F., Rodríguez, N., Swainston, N., Wrzodek, C., Czauderna, T., Keller, R., Mittag, F., Schubert, M., Glont, M., Golebiewski, M., et al. (2013) · BMC Systems Biology · doi:10.1186/1752-0509-7-116 · Cited by 173 · see citing works
Self-citationDraper, J., Enot, D. P., Parker, D., Beckmann, M., Snowdon, S., Lin, W., & Zubair, H. (2009) · BMC Bioinformatics · doi:10.1186/1471-2105-10-227 · Cited by 169 · see citing works
Aung, H. W., Henry, S. A., & Walker, L. P. (2013) · Industrial Biotechnology · doi:10.1089/ind.2013.0013 · Cited by 156 · see citing works
Towards a genome-scale kinetic model of cellular metabolism
B, K. S. A., Simeonidis, E., Swainston, N., & Mendes, P. (2010) · BMC Systems Biology · doi:10.1186/1752-0509-4-6 · Cited by 171 · see citing works
Self-citationIndustrial Systems Biology of Saccharomyces cerevisiae Enables Novel Succinic Acid Cell Factory
Otero, J. M., Cimini, D., Patil, K. R., Poulsen, S. G., Lisbeth Olsson, A., & Nielsen, J. (2013) · PLoS ONE · doi:10.1371/journal.pone.0054144 · Cited by 167 · see citing works
Self-citationKell, D. B., & Goodacre, R. (2013) · Drug Discovery Today · doi:10.1016/j.drudis.2013.07.014 · Cited by 169 · see citing works
Self-citationSynthetic biology tools for engineering Yarrowia lipolytica
Larroude, M., Rossignol, T., Nicaud, J., & Ledesma‐Amaro, R. (2018) · Biotechnology Advances · doi:10.1016/j.biotechadv.2018.10.004 · Cited by 163 · see citing works
Production of 2,3-butanediol in Saccharomyces cerevisiae by in silico aided metabolic engineering
Ng, C. Y., Jung, M.-Y., Lee, J., & Oh, M. (2012) · Microbial Cell Factories · doi:10.1186/1475-2859-11-68 · Cited by 159 · see citing works
Matsuda, F., Ishii, J., Kondo, T., Ida, K., Tezuka, H., & Kondo, A. (2013) · Microbial Cell Factories · doi:10.1186/1475-2859-12-119 · Cited by 159 · see citing works
Synergies between synthetic biology and metabolic engineering
Nielsen, J., & Keasling, J. D. (2011) · Nature Biotechnology · doi:10.1038/nbt.1937 · Cited by 156 · see citing works
Self-citationKell, D. B., & Oliver, S. G. (2014) · Frontiers in Pharmacology · doi:10.3389/fphar.2014.00231 · Cited by 155 · see citing works
Self-citationAn introduction to biological nuclear magnetic resonance spectroscopy
Bothwell, J. H. F., & Griffin, J. L. (2010) · Biological reviews/Biological reviews of the Cambridge Philosophical Society · doi:10.1111/j.1469-185x.2010.00157.x · Cited by 156 · see citing works
A detailed genome-wide reconstruction of mouse metabolism based on human Recon 1
Sigurdsson, M. I., Jamshidi, N., Steingrimsson, E., Thiele, I., & Palsson, B. Ø. (2010) · BMC Systems Biology · doi:10.1186/1752-0509-4-140 · Cited by 154 · see citing works
Self-citationOtero, J. M., & Nielsen, J. (2009) · Biotechnology and Bioengineering · doi:10.1002/bit.22592 · Cited by 154 · see citing works
Self-citationAssessing the impact of transcriptomics, proteomics and metabolomics on fungal phytopathology
Tan, K., IPCHO, S. V. S., Trengove, R. D., Oliver, R. P., & Solomon, P. S. (2009) · Molecular Plant Pathology · doi:10.1111/j.1364-3703.2009.00565.x · Cited by 152 · see citing works
The application of flux balance analysis in systems biology
Gianchandani, E. P., Chavali, A. K., & Papin, J. A. (2009) · WIREs Systems Biology and Medicine · doi:10.1002/wsbm.60 · Cited by 149 · see citing works
A model of yeast glycolysis based on a consistent kinetic characterisation of all its enzymes
Smallbone, K., Messiha, H. L., Carroll, K. M., Winder, C. L., Malys, N., Dunn, W. B., Murabito, E., Swainston, N., Dada, J. O., Khan, F., et al. (2013) · FEBS Letters · doi:10.1016/j.febslet.2013.06.043 · Cited by 147 · see citing works
Self-citationMicrokinetic modeling in homogeneous catalysis
Besora, M., & Maseras, F. (2018) · Wiley Interdisciplinary Reviews Computational Molecular Science · doi:10.1002/wcms.1372 · Cited by 146 · see citing works
Improving metabolic flux predictions using absolute gene expression data
Lee, D. C. H., B, K. S. A., Dunn, W. B., Murabito, E., Winder, C. L., Kell, D. B., Mendes, P., & Swainston, N. (2012) · BMC Systems Biology · doi:10.1186/1752-0509-6-73 · Cited by 145 · see citing works
Self-citationExpanding the chemical palate of cells by combining systems biology and metabolic engineering
Curran, K. A., & Alper, H. S. (2012) · Metabolic Engineering · doi:10.1016/j.ymben.2012.04.006 · Cited by 143 · see citing works
Kell, D. B., Dobson, P. D., Bilsland, E., & Oliver, S. G. (2012) · Drug Discovery Today · doi:10.1016/j.drudis.2012.11.008 · Cited by 141 · see citing works
Self-citationYeast 5 – an expanded reconstruction of the Saccharomyces cerevisiae metabolic network
Heavner, B., B, K. S. A., Barker, B., Mendes, P., & Walker, L. P. (2012) · BMC Systems Biology · doi:10.1186/1752-0509-6-55 · Cited by 142 · see citing works
Self-citationMahadevan, R., Palsson, B. Ø., & Lovley, D. R. (2010) · Nature Reviews Microbiology · doi:10.1038/nrmicro2456 · Cited by 140 · see citing works
Self-citationGenome‐scale metabolic networks
Terzer, M., Maynard, N. D., Covert, M. W., & Stelling, J. (2009) · WIREs Systems Biology and Medicine · doi:10.1002/wsbm.37 · Cited by 138 · see citing works
Thiele, I., Hyduke, D. R., Steeb, B., Fankam, G., Allen, D. K., Bazzani, S., Charusanti, P., Chen, F., Fleming, R. M. T., Hsiung, C. A., et al. (2011) · BMC Systems Biology · doi:10.1186/1752-0509-5-8 · Cited by 141 · see citing works
Self-citationMetRxn: a knowledgebase of metabolites and reactions spanning metabolic models and databases
Kumar, A., Suthers, P. F., & Maranas, C. D. (2012) · BMC Bioinformatics · doi:10.1186/1471-2105-13-6 · Cited by 141 · see citing works
‘Metabolite-likeness’ as a criterion in the design and selection of pharmaceutical drug libraries
Dobson, P. D., Patel, Y., & Kell, D. B. (2008) · Drug Discovery Today · doi:10.1016/j.drudis.2008.10.011 · Cited by 138 · see citing works
Self-citationAnalytical Challenges of Microbial Biofilms on Medical Devices
Vértes, Á., Hitchins, V. M., & Phillips, K. S. (2012) · Analytical Chemistry · doi:10.1021/ac2029997 · Cited by 137 · see citing works
Advances in plant disease and pest management
Lucas, J. (2010) · The Journal of Agricultural Science · doi:10.1017/s0021859610000997 · Cited by 140 · see citing works
Systems metabolic engineering: Genome‐scale models and beyond
Blazeck, J., & Alper, H. S. (2010) · Biotechnology Journal · doi:10.1002/biot.200900247 · Cited by 132 · see citing works
A genome-scale metabolic model of the lipid-accumulating yeast Yarrowia lipolytica
Loira, N., Dulermo, T., Nicaud, J., & Sherman, D. J. (2012) · BMC Systems Biology · doi:10.1186/1752-0509-6-35 · Cited by 131 · see citing works
Reconciliation of Genome-Scale Metabolic Reconstructions for Comparative Systems Analysis
Oberhardt, M., Puchałka, J., dos Santos, V. A. P. M., & Papin, J. A. (2011) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1001116 · Cited by 129 · see citing works
Lambert, N. D., Ovsyannikova, I. G., Pankratz, V. S., Jacobson, R. M., & Poland, G. A. (2012) · Expert Review of Vaccines · doi:10.1586/erv.12.61 · Cited by 127 · see citing works
Edelman, L. B., Eddy, J. A., & Price, N. D. (2009) · WIREs Systems Biology and Medicine · doi:10.1002/wsbm.75 · Cited by 127 · see citing works
The metabolome 18 years on: a concept comes of age
Kell, D. B., & Oliver, S. G. (2016) · Metabolomics · doi:10.1007/s11306-016-1108-4 · Cited by 127 · see citing works
Self-citationMapping condition-dependent regulation of metabolism in yeast through genome-scale modeling
Österlund, T., Nookaew, I., Bordel, S., & Nielsen, J. (2013) · BMC Systems Biology · doi:10.1186/1752-0509-7-36 · Cited by 125 · see citing works
Self-citationTowards genome-scale signalling-network reconstructions
Hyduke, D. R., & Palsson, B. Ø. (2010) · Nature Reviews Genetics · doi:10.1038/nrg2750 · Cited by 125 · see citing works
Self-citationAn appeal to magic? The discovery of a non-enzymatic metabolism and its role in the origins of life
Ralser, M. (2018) · Biochemical Journal · doi:10.1042/bcj20160866 · Cited by 117 · see citing works
Systems biology of lipid metabolism: From yeast to human
Nielsen, J. (2009) · FEBS Letters · doi:10.1016/j.febslet.2009.10.054 · Cited by 119 · see citing works
Self-citationKell, D. B. (2013) · FEBS Journal · doi:10.1111/febs.12268 · Cited by 120 · see citing works
Self-citationCaspeta, L., Shoaie, S., Ågren, R., Nookaew, I., & Nielsen, J. (2012) · BMC Systems Biology · doi:10.1186/1752-0509-6-24 · Cited by 120 · see citing works
Self-citationNetwork Reconstruction from Random Phase Resetting
Levnajić, Z., & PIKOVSKY, A. S. (2011) · Physical Review Letters · doi:10.1103/physrevlett.107.034101 · Cited by 119 · see citing works
Fifteen years of large scale metabolic modeling of yeast: Developments and impacts
Österlund, T., Nookaew, I., & Nielsen, J. (2011) · Biotechnology Advances · doi:10.1016/j.biotechadv.2011.07.021 · Cited by 117 · see citing works
Self-citationUsing the reconstructed genome-scale human metabolic network to study physiology and pathology
Bordbar, A., & Palsson, B. O. (2012) · Journal of Internal Medicine · doi:10.1111/j.1365-2796.2011.02494.x · Cited by 115 · see citing works
Self-citationPitkänen, E., Jouhten, P., Hou, J., Syed, M. F., Blomberg, P., Kludas, J., Oja, M., Holm, L., Penttilä, M. E., Rousu, J., et al. (2014) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003465 · Cited by 116 · see citing works
Self-citationComprehensive two-dimensional gas chromatography in metabolomics
Almstetter, M. F., Oefner, P. J., & Dettmer, K. (2012) · Analytical and Bioanalytical Chemistry · doi:10.1007/s00216-011-5630-y · Cited by 116 · see citing works
Metabolic Profiling Uncovers a Phenotypic Signature of Small for Gestational Age in Early Pregnancy
Horgan, R., Broadhurst, D., Walsh, S. K., Dunn, W. B., Brown, M., Roberts, C. T., North, R. A., McCowan, L. M. E., Kell, D. B., Baker, P. N., et al. (2011) · Journal of Proteome Research · doi:10.1021/pr2002897 · Cited by 115 · see citing works
Self-citationCostenoble, R., Picotti, P., Reiter, L., Stallmach, R., Heinemann, M., Sauer, U., & Aebersold, R. H. (2011) · Molecular Systems Biology · doi:10.1038/msb.2010.122 · Cited by 112 · see citing works
Self-citationMetaNetX.org: a website and repository for accessing, analysing and manipulating metabolic networks
Ganter, M., Bernard, T., Moretti, S., Stelling, J., & Pagni, M. (2013) · Bioinformatics · doi:10.1093/bioinformatics/btt036 · Cited by 113 · see citing works
Genome-scale modeling for metabolic engineering
Simeonidis, E., & Price, N. D. (2015) · Journal of Industrial Microbiology & Biotechnology · doi:10.1007/s10295-014-1576-3 · Cited by 112 · see citing works
Self-citationFurther developments towards a genome-scale metabolic model of yeast
Dobson, P. D., B, K. S. A., Jameson, D., Simeonidis, E., Lanthaler, K., Pir, P., Lü, C., Swainston, N., Dunn, W. B., Fisher, P., et al. (2010) · BMC Systems Biology · doi:10.1186/1752-0509-4-145 · Cited by 110 · see citing works
Self-citationConstraint-based stoichiometric modelling from single organisms to microbial communities
Gottstein, W., Olivier, B. G., Bruggeman, F. J., & Teusink, B. (2016) · Journal of The Royal Society Interface · doi:10.1098/rsif.2016.0627 · Cited by 109 · see citing works
Metabolic flux analysis and pharmaceutical production
Boghigian, B. A., Seth, G., Kiss, R., & Pfeifer, B. A. (2009) · Metabolic Engineering · doi:10.1016/j.ymben.2009.10.004 · Cited by 112 · see citing works
Systematic Construction of Kinetic Models from Genome-Scale Metabolic Networks
Stanford, N., Lubitz, T., B, K. S. A., Klipp, E., Mendes, P., & Liebermeister, W. (2013) · PLoS ONE · doi:10.1371/journal.pone.0079195 · Cited by 109 · see citing works
Self-citation
- Authors
- Herrgård, M. J., Swainston, N., Dobson, P., Dunn, W. B., Arga, K. Y., Arvas, M., Blüthgen, N., Borger, S., Costenoble, R., Heinemann, M., Hucka, M., Le Novère, N., Li, P., Liebermeister, W., Mo, M. L., Oliveira, A. P., Petranovic, D., Pettifer, S., Simeonidis, E., Smallbone, K., Spasié, I., Weichart, D., Brent, R., Broomhead, D. S., Westerhoff, H. V., Kürdar, B., Penttilä, M., Klipp, E., Palsson, B. Ø., Sauer, U., Oliver, S. G., Mendes, P., Nielsen, J., & Kell, D. B.
- Affiliations
- University of California System (US)
- University of Manchester (GB)
- VTT Technical Research Centre of Finland (FI)
- Max Planck Institute for Molecular Genetics (DE)
- University of Zurich (CH)
- California Institute of Technology (US)
- Technical University of Denmark (DK)
- Molecular Sciences Institute (US)
- Boğaziçi University (TR)
- University of Cambridge (GB)
- Chalmers University of Technology (SE)
- Corresponding author
- Kell, Douglas B
- ORCID
- Herrgård, Markus J
- Swainston, Neil
- Dobson, Paul
- Dunn, Warwick B
- Arvas, Mikko
- Blüthgen, Nils
- Heinemann, Matthias
- Hucka, Michael
- Li, Peter
- Liebermeister, Wolfram
- Oliveira, Ana Paula
- Brent, Roger
- Westerhoff, Hans V
- Penttilä, Merja
- Klipp, Edda
- Palsson, Bernhard Ø
- Sauer, Uwe
- Oliver, Stephen G
- Mendes, Pedro
- Nielsen, Jens
- Kell, Douglas B
- Venue
- Nature Biotechnology
- Published
- 2008-10
- Volume
- 26
- Issue
- 10
- Pages
- 1155-1160
- ISSN
- 0733-222X (ISSN-L)
- 1087-0156
- 1546-1696
- PMC
- PMC4018421
- OpenAlex
- W2047632644
- Cited by
- 588
- References
- 69
- Citations by year
- 2026: 12 · 2025: 7 · 2024: 10 · 2023: 13 · 2022: 12 · 2021: 19 · 2020: 22 · 2019: 27 · 2018: 17 · 2017: 24 · 2016: 43 · 2015: 42 · 2014: 56 · 2013: 59 · 2012: 55
- FWCI
- 23.29
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- other-oa
- www.springer.com/tdm (tdm)
- Locations
- Nature Biotechnology (publishedVersion, other-oa)
- PubMed (publishedVersion)
- Research Explorer (The University of Manchester) (publishedVersion)
- University of Groningen research database (University of Groningen / Centre for Information Technology) (publishedVersion, other-oa)
- MIMS EPrints (University of Southampton) (acceptedVersion, other-oa)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Chalmers Publication Library (Chalmers University of Technology) (acceptedVersion)
- CaltechAUTHORS (California Institute of Technology) (submittedVersion, cc-by-sa)
- Max Planck Institute for Plasma Physics (submittedVersion)
- University of Birmingham Research Portal (University of Birmingham) (submittedVersion)
- Technical University of Denmark, DTU Orbit (Technical University of Denmark, DTU) (submittedVersion)
- Chalmers Research (Chalmers University of Technology) (submittedVersion)
- VU Research Portal (submittedVersion, other-oa)
- University of Groningen research database (University of Groningen / Centre for Information Technology) (submittedVersion, other-oa)
- Data Archiving and Networked Services (DANS) (submittedVersion, other-oa)
- Funders
- National Institutes of Health (NIH-R01)
- Directorate for Biological Sciences
- University of California, San Diego
- Engineering and Physical Sciences Research Council
- Biotechnology and Biological Sciences Research Council (BB/F010516/1, BB/C008219/1, BB/E016065/1, BB/E006248/1)
- National Institute of General Medical Sciences (R01GM071808, R01GM097479)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Microbial Metabolic Engineering and Bioproduction
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
- Keywords
- Saccharomyces cerevisiae, metabolic network reconstruction, consensus networks, genome-scale metabolic networks, community knowledge, chemical structure representation, SMILES, InChI, SBML
- MeSH terms
- Computer Simulation, Models, Biological, Saccharomyces cerevisiae, Signal Transduction, Information Storage and Retrieval, Systems Integration, Saccharomyces cerevisiae Proteins, Databases, Protein, Systems Biology
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
