Published in Nat Biotechnol on December 01, 2005
Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project. Nat Biotechnol (2008) 12.96
BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems. Nucleic Acids Res (2006) 9.49
BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol (2010) 5.75
LibSBML: an API library for SBML. Bioinformatics (2008) 5.61
A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology. Nat Biotechnol (2008) 4.55
A community-driven global reconstruction of human metabolism. Nat Biotechnol (2013) 3.89
Web services at the European Bioinformatics Institute-2009. Nucleic Acids Res (2009) 3.78
MIFlowCyt: the minimum information about a Flow Cytometry Experiment. Cytometry A (2008) 3.33
cPath: open source software for collecting, storing, and querying biological pathways. BMC Bioinformatics (2006) 3.24
Controlled vocabularies and semantics in systems biology. Mol Syst Biol (2011) 2.79
MIRIAM Resources: tools to generate and resolve robust cross-references in Systems Biology. BMC Syst Biol (2007) 2.56
Identifiers.org and MIRIAM Registry: community resources to provide persistent identification. Nucleic Acids Res (2011) 2.48
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The 2010 Nucleic Acids Research Database Issue and online Database Collection: a community of data resources. Nucleic Acids Res (2009) 2.42
Iron behaving badly: inappropriate iron chelation as a major contributor to the aetiology of vascular and other progressive inflammatory and degenerative diseases. BMC Med Genomics (2009) 2.36
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Model storage, exchange and integration. BMC Neurosci (2006) 2.13
Towards reproducible descriptions of neuronal network models. PLoS Comput Biol (2009) 2.11
The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services. BMC Bioinformatics (2010) 2.03
The RAVEN toolbox and its use for generating a genome-scale metabolic model for Penicillium chrysogenum. PLoS Comput Biol (2013) 2.00
Genome-scale models of bacterial metabolism: reconstruction and applications. FEMS Microbiol Rev (2008) 1.97
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Current progress in patient-specific modeling. Brief Bioinform (2009) 1.91
PyMOOSE: Interoperable Scripting in Python for MOOSE. Front Neuroinform (2008) 1.80
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Programming with models: modularity and abstraction provide powerful capabilities for systems biology. J R Soc Interface (2009) 1.69
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SBMLeditor: effective creation of models in the Systems Biology Markup language (SBML). BMC Bioinformatics (2007) 1.68
SABIO-RK--database for biochemical reaction kinetics. Nucleic Acids Res (2011) 1.63
A comprehensive modular map of molecular interactions in RB/E2F pathway. Mol Syst Biol (2008) 1.61
The metabolic network of Synechocystis sp. PCC 6803: systemic properties of autotrophic growth. Plant Physiol (2010) 1.61
The RICORDO approach to semantic interoperability for biomedical data and models: strategy, standards and solutions. BMC Res Notes (2011) 1.59
CellML metadata standards, associated tools and repositories. Philos Trans A Math Phys Eng Sci (2009) 1.59
Minimum Information About a Simulation Experiment (MIASE). PLoS Comput Biol (2011) 1.48
KEGGtranslator: visualizing and converting the KEGG PATHWAY database to various formats. Bioinformatics (2011) 1.46
Integration of metabolic databases for the reconstruction of genome-scale metabolic networks. BMC Syst Biol (2010) 1.44
BioModels: ten-year anniversary. Nucleic Acids Res (2014) 1.41
BioModels.net Web Services, a free and integrated toolkit for computational modelling software. Brief Bioinform (2009) 1.38
Meeting Report from the Second "Minimum Information for Biological and Biomedical Investigations" (MIBBI) workshop. Stand Genomic Sci (2010) 1.35
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SEEK: a systems biology data and model management platform. BMC Syst Biol (2015) 1.30
Quantitative and logic modelling of molecular and gene networks. Nat Rev Genet (2015) 1.30
Path2Models: large-scale generation of computational models from biochemical pathway maps. BMC Syst Biol (2013) 1.29
libAnnotationSBML: a library for exploiting SBML annotations. Bioinformatics (2009) 1.29
Bridging biological ontologies and biosimulation: the ontology of physics for biology. AMIA Annu Symp Proc (2008) 1.26
Multiscale models of angiogenesis. IEEE Eng Med Biol Mag (2009) 1.26
Standards and ontologies in computational systems biology. Essays Biochem (2008) 1.25
Multiple ontologies in action: composite annotations for biosimulation models. J Biomed Inform (2010) 1.25
SBML2L(A)T(E)X: conversion of SBML files into human-readable reports. Bioinformatics (2009) 1.24
Designing and encoding models for synthetic biology. J R Soc Interface (2009) 1.23
Sensitivity analysis of intracellular signaling pathway kinetics predicts targets for stem cell fate control. PLoS Comput Biol (2007) 1.22
PathText: a text mining integrator for biological pathway visualizations. Bioinformatics (2010) 1.20
Further developments towards a genome-scale metabolic model of yeast. BMC Syst Biol (2010) 1.20
Advances in semantic representation for multiscale biosimulation: a case study in merging models. Pac Symp Biocomput (2009) 1.20
The signaling petri net-based simulator: a non-parametric strategy for characterizing the dynamics of cell-specific signaling networks. PLoS Comput Biol (2008) 1.19
Integrated multilaboratory systems biology reveals differences in protein metabolism between two reference yeast strains. Nat Commun (2010) 1.18
Integrating systems biology models and biomedical ontologies. BMC Syst Biol (2011) 1.16
Simulating plant metabolic pathways with enzyme-kinetic models. Plant Physiol (2010) 1.16
Computational biology of cardiac myocytes: proposed standards for the physiome. J Exp Biol (2007) 1.16
Programming biological models in Python using PySB. Mol Syst Biol (2013) 1.15
Mathematical modeling of intracellular signaling pathways. BMC Neurosci (2006) 1.14
Systematic integration of experimental data and models in systems biology. BMC Bioinformatics (2010) 1.13
KEGGconverter: a tool for the in-silico modelling of metabolic networks of the KEGG Pathways database. BMC Bioinformatics (2009) 1.13
Improving collaboration by standardization efforts in systems biology. Front Bioeng Biotechnol (2014) 1.12
Saint: a lightweight integration environment for model annotation. Bioinformatics (2009) 1.12
How to deal with large models? Mol Syst Biol (2009) 1.12
Precise generation of systems biology models from KEGG pathways. BMC Syst Biol (2013) 1.11
Version 6 of the consensus yeast metabolic network refines biochemical coverage and improves model performance. Database (Oxford) (2013) 1.09
A comprehensive molecular interaction map of the budding yeast cell cycle. Mol Syst Biol (2010) 1.06
Annotation of SBML models through rule-based semantic integration. J Biomed Semantics (2010) 1.05
Minimal information: an urgent need to assess the functional reliability of recombinant proteins used in biological experiments. Microb Cell Fact (2008) 1.04
A metabolic model of the mitochondrion and its use in modelling diseases of the tricarboxylic acid cycle. BMC Syst Biol (2011) 1.04
Rule-based modeling: a computational approach for studying biomolecular site dynamics in cell signaling systems. Wiley Interdiscip Rev Syst Biol Med (2013) 1.04
Cell size at S phase initiation: an emergent property of the G1/S network. PLoS Comput Biol (2007) 1.03
Payao: a community platform for SBML pathway model curation. Bioinformatics (2010) 1.02
CytoSolve: A Scalable Computational Method for Dynamic Integration of Multiple Molecular Pathway Models. Cell Mol Bioeng (2010) 1.02
In silico models of cancer. Wiley Interdiscip Rev Syst Biol Med (2010) 1.01
PathCase-SB architecture and database design. BMC Syst Biol (2011) 1.00
Harnessing Big Data for Systems Pharmacology. Annu Rev Pharmacol Toxicol (2016) 0.99
Retrieval, alignment, and clustering of computational models based on semantic annotations. Mol Syst Biol (2011) 0.99
The model repository of the models of infectious disease agent study. IEEE Trans Inf Technol Biomed (2008) 0.99
Qualitative translation of relations from BioPAX to SBML qual. Bioinformatics (2012) 0.98
A model of yeast glycolysis based on a consistent kinetic characterisation of all its enzymes. FEBS Lett (2013) 0.97
Reconstruction and validation of a genome-scale metabolic model for the filamentous fungus Neurospora crassa using FARM. PLoS Comput Biol (2013) 0.95
COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project. BMC Bioinformatics (2014) 0.95
BioModels: Content, Features, Functionality, and Use. CPT Pharmacometrics Syst Pharmacol (2015) 0.94
The challenges of informatics in synthetic biology: from biomolecular networks to artificial organisms. Brief Bioinform (2009) 0.94
A comprehensive map of the influenza A virus replication cycle. BMC Syst Biol (2013) 0.93
A framework for different levels of integration of computational models into web-based virtual patients. J Med Internet Res (2014) 0.93
MEMOSys: Bioinformatics platform for genome-scale metabolic models. BMC Syst Biol (2011) 0.93
Dupuytren's: a systems biology disease. Arthritis Res Ther (2011) 0.91
Biographer: web-based editing and rendering of SBGN compliant biochemical networks. Bioinformatics (2013) 0.91
An analysis of a 'community-driven' reconstruction of the human metabolic network. Metabolomics (2013) 0.90
A systems biology approach identifies the biochemical mechanisms regulating monoterpenoid essential oil composition in peppermint. Proc Natl Acad Sci U S A (2008) 0.90
Dry work in a wet world: computation in systems biology. Mol Syst Biol (2006) 0.90
Ranked retrieval of Computational Biology models. BMC Bioinformatics (2010) 0.90
Combining computational models, semantic annotations and simulation experiments in a graph database. Database (Oxford) (2015) 0.89
Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol Syst Biol (2006) 40.15
EcoCyc: a comprehensive database resource for Escherichia coli. Nucleic Acids Res (2005) 11.01
COPASI--a COmplex PAthway SImulator. Bioinformatics (2006) 10.57
The EcoCyc Database. Nucleic Acids Res (2002) 10.42
BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems. Nucleic Acids Res (2006) 9.49
The BioPAX community standard for pathway data sharing. Nat Biotechnol (2010) 9.19
The Systems Biology Graphical Notation. Nat Biotechnol (2009) 8.53
Escherichia coli K-12: a cooperatively developed annotation snapshot--2005. Nucleic Acids Res (2006) 7.93
RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation. Nucleic Acids Res (2007) 7.64
The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models. Nat Biotechnol (2010) 7.08
EcoCyc: a comprehensive view of Escherichia coli biology. Nucleic Acids Res (2008) 7.05
DNA methylation signatures identify biologically distinct subtypes in acute myeloid leukemia. Cancer Cell (2010) 6.72
BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol (2010) 5.75
RegulonDB (version 4.0): transcriptional regulation, operon organization and growth conditions in Escherichia coli K-12. Nucleic Acids Res (2004) 5.73
LibSBML: an API library for SBML. Bioinformatics (2008) 5.61
RegulonDB (version 5.0): Escherichia coli K-12 transcriptional regulatory network, operon organization, and growth conditions. Nucleic Acids Res (2006) 5.57
Parameter estimation in biochemical pathways: a comparison of global optimization methods. Genome Res (2003) 5.50
EcoCyc: fusing model organism databases with systems biology. Nucleic Acids Res (2012) 5.30
Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110. Mol Syst Biol (2006) 5.20
EcoCyc: a comprehensive database of Escherichia coli biology. Nucleic Acids Res (2010) 4.68
A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology. Nat Biotechnol (2008) 4.55
Identifying global regulators in transcriptional regulatory networks in bacteria. Curr Opin Microbiol (2003) 4.51
Condition-dependent transcriptome reveals high-level regulatory architecture in Bacillus subtilis. Science (2012) 4.41
Potential of metabolomics as a functional genomics tool. Trends Plant Sci (2004) 4.10
Molecular memory of prior infections activates the CRISPR/Cas adaptive bacterial immunity system. Nat Commun (2012) 4.04
Web-based kinetic modelling using JWS Online. Bioinformatics (2004) 4.03
A community-driven global reconstruction of human metabolism. Nat Biotechnol (2013) 3.89
Rules for modeling signal-transduction systems. Sci STKE (2006) 3.86
RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more. Nucleic Acids Res (2012) 3.83
RegulonDB version 7.0: transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units). Nucleic Acids Res (2010) 3.76
Phenotype microarray analysis of Escherichia coli K-12 mutants with deletions of all two-component systems. J Bacteriol (2003) 3.74
Discovery of meaningful associations in genomic data using partial correlation coefficients. Bioinformatics (2004) 3.74
Transcriptome analysis of all two-component regulatory system mutants of Escherichia coli K-12. Mol Microbiol (2002) 3.68
Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions. J Integr Bioinform (2015) 3.61
Next generation simulation tools: the Systems Biology Workbench and BioSPICE integration. OMICS (2003) 3.38
GPCRDB information system for G protein-coupled receptors. Nucleic Acids Res (2003) 3.34
Multidimensional annotation of the Escherichia coli K-12 genome. Nucleic Acids Res (2007) 3.34
A proposed framework for the description of plant metabolomics experiments and their results. Nat Biotechnol (2004) 3.32
Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals. J Mol Biol (2003) 3.23
A powerful non-homology method for the prediction of operons in prokaryotes. Bioinformatics (2002) 3.17
High-throughput, quantitative analyses of genetic interactions in E. coli. Nat Methods (2008) 3.17
Transcription, processing and function of CRISPR cassettes in Escherichia coli. Mol Microbiol (2010) 3.05
eSGA: E. coli synthetic genetic array analysis. Nat Methods (2008) 3.01
SNOSID, a proteomic method for identification of cysteine S-nitrosylation sites in complex protein mixtures. Proc Natl Acad Sci U S A (2006) 2.89
The Database of Quantitative Cellular Signaling: management and analysis of chemical kinetic models of signaling networks. Bioinformatics (2003) 2.88
Plant metabolomics: large-scale phytochemistry in the functional genomics era. Phytochemistry (2003) 2.84
Controlled vocabularies and semantics in systems biology. Mol Syst Biol (2011) 2.79
Dynamic rerouting of the carbohydrate flux is key to counteracting oxidative stress. J Biol (2007) 2.70
The pathogen-associated iroA gene cluster mediates bacterial evasion of lipocalin 2. Proc Natl Acad Sci U S A (2006) 2.63
A polymorphism in CALHM1 influences Ca2+ homeostasis, Abeta levels, and Alzheimer's disease risk. Cell (2008) 2.55
The metabolomics standards initiative. Nat Biotechnol (2007) 2.54
Interoperability of neuroscience modeling software: current status and future directions. Neuroinformatics (2007) 2.54
Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli. PLoS One (2009) 2.48
NeuroML: a language for describing data driven models of neurons and networks with a high degree of biological detail. PLoS Comput Biol (2010) 2.45
The partitioned Rhizobium etli genome: genetic and metabolic redundancy in seven interacting replicons. Proc Natl Acad Sci U S A (2006) 2.44
A hybrid approach for efficient and robust parameter estimation in biochemical pathways. Biosystems (2005) 2.43
Reproducible computational biology experiments with SED-ML--the Simulation Experiment Description Markup Language. BMC Syst Biol (2011) 2.40
The phosphate regulon and bacterial virulence: a regulatory network connecting phosphate homeostasis and pathogenesis. FEMS Microbiol Rev (2008) 2.39
Global network reorganization during dynamic adaptations of Bacillus subtilis metabolism. Science (2012) 2.38
Regulatory network of Escherichia coli: consistency between literature knowledge and microarray profiles. Genome Res (2003) 2.37
myo-inositol oxygenase offers a possible entry point into plant ascorbate biosynthesis. Plant Physiol (2004) 2.25
Update on the Keio collection of Escherichia coli single-gene deletion mutants. Mol Syst Biol (2009) 2.11
Systems biology standards--the community speaks. Nat Biotechnol (2007) 2.09
Global regulation by the seven-component Pi signaling system. Curr Opin Microbiol (2010) 2.07
Bacterial regulatory networks are extremely flexible in evolution. Nucleic Acids Res (2006) 2.04
Metabolic profiling of Medicago truncatula cell cultures reveals the effects of biotic and abiotic elicitors on metabolism. J Exp Bot (2004) 2.04
What do aquaporin knockout studies tell us about fluid transport in epithelia? J Membr Biol (2013) 2.03
Non-redundant odor coding by sister mitral cells revealed by light addressable glomeruli in the mouse. Nat Neurosci (2010) 1.86
SBMLToolbox: an SBML toolbox for MATLAB users. Bioinformatics (2006) 1.86
Gene networks: how to put the function in genomics. Trends Biotechnol (2002) 1.84
The emerging world of wikis. Science (2008) 1.84
The glycolytic flux in Escherichia coli is controlled by the demand for ATP. J Bacteriol (2002) 1.83
Linking the genes: inferring quantitative gene networks from microarray data. Trends Genet (2002) 1.83
Modular analysis of the transcriptional regulatory network of E. coli. Trends Genet (2005) 1.83
PyMOOSE: Interoperable Scripting in Python for MOOSE. Front Neuroinform (2008) 1.80
Automatic reconstruction of a bacterial regulatory network using Natural Language Processing. BMC Bioinformatics (2007) 1.79
JSBML: a flexible Java library for working with SBML. Bioinformatics (2011) 1.73
Alternative pathways as mechanism for the negative effects associated with overexpression of superoxide dismutase. J Theor Biol (2005) 1.71
Genome-scale identification of conditionally essential genes in E. coli by DNA microarrays. Biochem Biophys Res Commun (2004) 1.69
Internal-sensing machinery directs the activity of the regulatory network in Escherichia coli. Trends Microbiol (2005) 1.68
Run-time interoperability between neuronal network simulators based on the MUSIC framework. Neuroinformatics (2010) 1.66
Modelling the dynamics of the yeast pheromone pathway. Yeast (2004) 1.65
Variability in DNA methylation defines novel epigenetic subgroups of DLBCL associated with different clinical outcomes. Blood (2014) 1.64
Triple-negative breast cancer: present challenges and new perspectives. Mol Oncol (2010) 1.63