Published in Bioinformatics on May 10, 2012
PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees. Nucleic Acids Res (2012) 8.54
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JSBML 1.0: providing a smorgasbord of options to encode systems biology models. Bioinformatics (2015) 0.80
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An algorithm for automated layout of process description maps drawn in SBGN. Bioinformatics (2015) 0.75
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A fully featured COMBINE archive of a simulation study on syncytial mitotic cycles in Drosophila embryos. F1000Res (2016) 0.75
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A comprehensive pathway map of epidermal growth factor receptor signaling. Mol Syst Biol (2005) 5.68
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Visualization of omics data for systems biology. Nat Methods (2010) 4.59
A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology. Nat Biotechnol (2008) 4.55
VANTED: a system for advanced data analysis and visualization in the context of biological networks. BMC Bioinformatics (2006) 4.38
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Automated network analysis identifies core pathways in glioblastoma. PLoS One (2010) 3.64
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The Edinburgh human metabolic network reconstruction and its functional analysis. Mol Syst Biol (2007) 3.59
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A comprehensive map of the toll-like receptor signaling network. Mol Syst Biol (2006) 2.89
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Novel pharmacological targets for the treatment of Parkinson's disease. Nat Rev Drug Discov (2006) 2.23
Ontology annotation: mapping genomic regions to biological function. Curr Opin Chem Biol (2007) 2.21
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Preventing gene silencing with human replicators. Nat Biotechnol (2006) 1.84
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Exploration of biological network centralities with CentiBiN. BMC Bioinformatics (2006) 1.78
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ChiBE: interactive visualization and manipulation of BioPAX pathway models. Bioinformatics (2009) 1.76
Dynamic exploration and editing of KEGG pathway diagrams. Bioinformatics (2006) 1.75
JSBML: a flexible Java library for working with SBML. Bioinformatics (2011) 1.73
Editing, validating and translating of SBGN maps. Bioinformatics (2010) 1.71
SBMLeditor: effective creation of models in the Systems Biology Markup language (SBML). BMC Bioinformatics (2007) 1.68
A comprehensive map of the mTOR signaling network. Mol Syst Biol (2010) 1.59
Systems biology reveals new strategies for personalizing cancer medicine and confirms the role of PTEN in resistance to trastuzumab. Cancer Res (2009) 1.59
Inhibition of histone deacetylase in cancer cells slows down replication forks, activates dormant origins, and induces DNA damage. Cancer Res (2010) 1.53
MetaCrop: a detailed database of crop plant metabolism. Nucleic Acids Res (2007) 1.53
Apomictic and sexual ovules of Boechera display heterochronic global gene expression patterns. Plant Cell (2010) 1.52
Nonclassic functions of human topoisomerase I: genome-wide and pharmacologic analyses. Cancer Res (2007) 1.51
Bloom's syndrome helicase and Mus81 are required to induce transient double-strand DNA breaks in response to DNA replication stress. J Mol Biol (2007) 1.50
VANTED v2: a framework for systems biology applications. BMC Syst Biol (2012) 1.49
In vivo robustness analysis of cell division cycle genes in Saccharomyces cerevisiae. PLoS Genet (2006) 1.49
Minimum Information About a Simulation Experiment (MIASE). PLoS Comput Biol (2011) 1.48
Integration of CellDesigner and SABIO-RK. In Silico Biol (2007) 1.48
Detection of nuclei in 4D Nomarski DIC microscope images of early Caenorhabditis elegans embryos using local image entropy and object tracking. BMC Bioinformatics (2005) 1.46
Genome-wide depletion of replication initiation events in highly transcribed regions. Genome Res (2011) 1.44
Regulation of yeast oscillatory dynamics. Proc Natl Acad Sci U S A (2007) 1.43
Flux balance analysis of barley seeds: a computational approach to study systemic properties of central metabolism. Plant Physiol (2008) 1.43
Antimony: a modular model definition language. Bioinformatics (2009) 1.41
TinkerCell: modular CAD tool for synthetic biology. J Biol Eng (2009) 1.38
BioModels.net Web Services, a free and integrated toolkit for computational modelling software. Brief Bioinform (2009) 1.38
The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core. J Integr Bioinform (2015) 1.37
Mus81-mediated DNA cleavage resolves replication forks stalled by topoisomerase I-DNA complexes. J Cell Biol (2011) 1.36
Integrating pathways of Parkinson's disease in a molecular interaction map. Mol Neurobiol (2013) 1.34
Cascleave: towards more accurate prediction of caspase substrate cleavage sites. Bioinformatics (2010) 1.34