MEMOTE for standardized genome-scale metabolic model testing
暂无分享,去创建一个
Ronan M. T. Fleming | Adam M. Feist | Zachary A. King | Jonathan M. Monk | Frank T. Bergmann | Markus J. Herrgård | José P. Faria | Gregory L. Medlock | Benjamín J. Sánchez | Rahuman S. Malik Sheriff | Joana C. Xavier | J. Vik | I. Nookaew | B. Palsson | N. Price | L. Blank | S. Klamt | R. Fleming | H. Hermjakob | R. Mahadevan | B. Teusink | M. König | E. Klipp | M. Ataman | V. Hatzimanikatis | A. Feist | L. Nielsen | S. Lee | A. Mardinoğlu | N. Lewis | Hongwu Ma | H. Kim | C. Henry | O. Reséndis-Antonio | M. Poolman | B. Olivier | Nikolaus Sonnenschein | D. Machado | K. Patil | I. Rocha | Paulo Vilaça | B. Ebert | Dong-Yup Lee | A. Richelle | J. Nielsen | P. Schaap | C. Diener | Meiyappan Lakshmanan | M. Beber | S. Shoaie | Kevin Correia | Georgios Fengos | Juan Nogales | Filipe Liu | J. Edirisinghe | Beatriz García-Jiménez | Qianqian Yuan | Sunjae Lee | P. Babaei | J. Bartell | Christian Lieven | M. Zakhartsev | Siddharth M. Chauhan | Andreas Dräger | J. Papin | Cheng Zhang | Wout van Helvoirt | J. Wodke | A. Kaafarani | J. Koehorst | M. Lakshmanan | Paulo Maia | Dong‐Yup Lee
[1] Minoru Kanehisa,et al. Toward understanding the origin and evolution of cellular organisms , 2019, Protein science : a publication of the Protein Society.
[2] Anne Richelle,et al. Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0 , 2019, Nature Protocols.
[3] Antje Chang,et al. BRENDA in 2019: a European ELIXIR core data resource , 2018, Nucleic Acids Res..
[4] Charlie Hodgman,et al. Gsmodutils: a python based framework for test-driven genome scale metabolic model development , 2018, bioRxiv.
[5] Ronan M. T. Fleming,et al. Reply to "Challenges in modeling the human gut microbiome" , 2018, Nature Biotechnology.
[6] Jens Nielsen,et al. Challenges in modeling the human gut microbiome , 2018, Nature Biotechnology.
[7] Rick L. Stevens,et al. KBase: The United States Department of Energy Systems Biology Knowledgebase , 2018, Nature Biotechnology.
[8] Olivier Dameron,et al. Traceability, reproducibility and wiki-exploration for “à-la-carte” reconstructions of genome-scale metabolic models , 2018, PLoS Comput. Biol..
[9] Frank T. Bergmann,et al. SBML Level 3 Package: Flux Balance Constraints version 2 , 2018, J. Integr. Bioinform..
[10] D. Machado,et al. Fast automated reconstruction of genome-scale metabolic models for microbial species and communities , 2018, bioRxiv.
[11] Lin Wang,et al. Standardizing biomass reactions and ensuring complete mass balance in genome‐scale metabolic models , 2017, Bioinform..
[12] Evan Bolton,et al. Database resources of the National Center for Biotechnology Information , 2017, Nucleic Acids Res..
[13] David S. Wishart,et al. HMDB 4.0: the human metabolome database for 2018 , 2017, Nucleic Acids Res..
[14] Carol J. Bult,et al. The Mouseion at the JAXlibrary , 2022 .
[15] Francisco J. Planes,et al. Creation and analysis of biochemical constraint-based models: the COBRA Toolbox v3.0. , 2017, 1710.04038.
[16] Brett K. Beaulieu-Jones,et al. Reproducibility of computational workflows is automated using continuous analysis , 2017, Nature Biotechnology.
[17] Martin J. Lercher,et al. Erroneous energy-generating cycles in published genome scale metabolic networks: Identification and removal , 2017, PLoS Comput. Biol..
[18] Christoph Thiel,et al. A Comparative Analysis of Drug-Induced Hepatotoxicity in Clinically Relevant Situations , 2017, PLoS Comput. Biol..
[19] I. Goryanin,et al. Pathway-Consensus Approach to Metabolic Network Reconstruction for Pseudomonas putida KT2440 by Systematic Comparison of Published Models , 2017, PloS one.
[20] Ronan M. T. Fleming,et al. Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota , 2016, Nature Biotechnology.
[21] John D. Storey,et al. Systems-level analysis of mechanisms regulating yeast metabolic flux , 2016, Science.
[22] Anne Morgat,et al. Updates in Rhea – an expert curated resource of biochemical reactions , 2016, Nucleic Acids Res..
[23] Katharina Nöh,et al. Current state and challenges for dynamic metabolic modeling. , 2016, Current opinion in microbiology.
[24] Keith Dufault-Thompson,et al. PSAMM: A Portable System for the Analysis of Metabolic Models , 2016, PLoS Comput. Biol..
[25] Olivier Martin,et al. MetaNetX/MNXref – reconciliation of metabolites and biochemical reactions to bring together genome-scale metabolic networks , 2015, Nucleic Acids Res..
[26] Philip Miller,et al. BiGG Models: A platform for integrating, standardizing and sharing genome-scale models , 2015, Nucleic Acids Res..
[27] Peter D. Karp,et al. Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology , 2015, Briefings Bioinform..
[28] Christoph Steinbeck,et al. ChEBI in 2016: Improved services and an expanding collection of metabolites , 2015, Nucleic Acids Res..
[29] Nikos Sidiropoulos,et al. SinaPlot: an enhanced chart for simple and truthful representation of single observations over multiple classes , 2015, bioRxiv.
[30] Ronan M. T. Fleming,et al. Do genome-scale models need exact solvers or clearer standards? , 2015, Molecular systems biology.
[31] Nathan D Price,et al. Transparency in metabolic network reconstruction enables scalable biological discovery. , 2015, Current opinion in biotechnology.
[32] M. Keller,et al. The widespread role of non-enzymatic reactions in cellular metabolism , 2015, Current opinion in biotechnology.
[33] Isabel Rocha,et al. Integration of Biomass Formulations of Genome-Scale Metabolic Models with Experimental Data Reveals Universally Essential Cofactors in Prokaryotes , 2015, Metabolic engineering.
[34] Karthik Raman,et al. Critical assessment of genome-scale metabolic networks: the need for a unified standard , 2015, Briefings Bioinform..
[35] B. Palsson. Systems Biology: Constraint-based Reconstruction and Analysis , 2015 .
[36] Nicolas Le Novère,et al. COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project , 2014, BMC Bioinformatics.
[37] Yangyang Zhao,et al. BioModels: ten-year anniversary , 2014, Nucleic Acids Res..
[38] Bernhard O. Palsson,et al. Optimizing genome-scale network reconstructions , 2014, Nature Biotechnology.
[39] Gilles Louppe,et al. Understanding variable importances in forests of randomized trees , 2013, NIPS.
[40] Henning Hermjakob,et al. The Reactome pathway knowledgebase , 2013, Nucleic Acids Res..
[41] Edward J. O'Brien,et al. Genome-scale models of metabolism and gene expression extend and refine growth phenotype prediction , 2013, Molecular systems biology.
[42] Joshua A. Lerman,et al. COBRApy: COnstraints-Based Reconstruction and Analysis for Python , 2013, BMC Systems Biology.
[43] Andreas Zell,et al. Path2Models: large-scale generation of computational models from biochemical pathway maps , 2013, BMC Systems Biology.
[44] Intawat Nookaew,et al. The RAVEN Toolbox and Its Use for Generating a Genome-scale Metabolic Model for Penicillium chrysogenum , 2013, PLoS Comput. Biol..
[45] Jindan Zhou,et al. EcoGene 3.0 , 2012, Nucleic Acids Res..
[46] E. Ruppin,et al. Predicting Drug Targets and Biomarkers of Cancer via Genome-Scale Metabolic Modeling , 2012, Clinical Cancer Research.
[47] Jacky L. Snoep,et al. Reproducible computational biology experiments with SED-ML - The Simulation Experiment Description Markup Language , 2011, BMC Systems Biology.
[48] Suzanne M. Paley,et al. The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases , 2011, Nucleic Acids Res..
[49] Michel Dumontier,et al. Controlled vocabularies and semantics in systems biology , 2011, Molecular systems biology.
[50] Rick L. Stevens,et al. High-throughput generation, optimization and analysis of genome-scale metabolic models , 2010, Nature Biotechnology.
[51] Melanie I. Stefan,et al. BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models , 2010, BMC Systems Biology.
[52] Miguel Rocha,et al. OptFlux: an open-source software platform for in silico metabolic engineering , 2010, BMC Systems Biology.
[53] Sandhya Rani,et al. Human Protein Reference Database—2009 update , 2008, Nucleic Acids Res..
[54] Andrew G. McDonald,et al. ExplorEnz: the primary source of the IUBMB enzyme list , 2008, Nucleic Acids Res..
[55] Michael Hucka,et al. LibSBML: an API Library for SBML , 2008, Bioinform..
[56] Jacky L. Snoep,et al. BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems , 2005, Nucleic Acids Res..
[57] Hugh D. Spence,et al. Minimum information requested in the annotation of biochemical models (MIRIAM) , 2005, Nature Biotechnology.
[58] S. Heller,et al. An Open Standard for Chemical Structure Representation: The IUPAC Chemical Identifier , 2003 .
[59] Dagmar Waltemath,et al. A call for virtual experiments: accelerating the scientific process. , 2015, Progress in biophysics and molecular biology.
[60] B. Palsson,et al. A protocol for generating a high-quality genome-scale metabolic reconstruction , 2010, Nature Protocols.
[61] Cathy H. Wu,et al. UniProt: the Universal Protein knowledgebase , 2004, Nucleic Acids Res..
[62] L. Breiman. Random Forests , 2001, Machine Learning.
[63] Michael K. Gilson,et al. ASAP, a systematic annotation package for community analysis of genomes , 2003, Nucleic Acids Res..
[64] I. Thiele,et al. Bioinformatics Applications Note Systems Biology Rbionet: a Cobra Toolbox Extension for Reconstructing High-quality Biochemical Networks , 2022 .