Published in Bioinformatics on December 01, 2006
Structure and dynamics of molecular networks: a novel paradigm of drug discovery: a comprehensive review. Pharmacol Ther (2013) 2.64
Diverse roles and interactions of the SWI/SNF chromatin remodeling complex revealed using global approaches. PLoS Genet (2011) 2.38
KEGGgraph: a graph approach to KEGG PATHWAY in R and bioconductor. Bioinformatics (2009) 2.31
VisANT 3.0: new modules for pathway visualization, editing, prediction and construction. Nucleic Acids Res (2007) 2.17
Transcriptome sequencing and annotation of the microalgae Dunaliella tertiolecta: pathway description and gene discovery for production of next-generation biofuels. BMC Genomics (2011) 1.55
VANTED v2: a framework for systems biology applications. BMC Syst Biol (2012) 1.49
MetaRoute: fast search for relevant metabolic routes for interactive network navigation and visualization. Bioinformatics (2008) 1.20
Assessment of the Deepwater Horizon oil spill impact on Gulf coast microbial communities. Front Microbiol (2014) 1.17
Entourage: visualizing relationships between biological pathways using contextual subsets. IEEE Trans Vis Comput Graph (2013) 1.14
KEGGconverter: a tool for the in-silico modelling of metabolic networks of the KEGG Pathways database. BMC Bioinformatics (2009) 1.13
Classification and analysis of regulatory pathways using graph property, biochemical and physicochemical property, and functional property. PLoS One (2011) 1.11
Web-based metabolic network visualization with a zooming user interface. BMC Bioinformatics (2011) 1.11
Network integration and graph analysis in mammalian molecular systems biology. IET Syst Biol (2008) 1.03
Genoscape: a Cytoscape plug-in to automate the retrieval and integration of gene expression data and molecular networks. Bioinformatics (2009) 1.02
Extended LineSets: a visualization technique for the interactive inspection of biological pathways. BMC Proc (2015) 1.00
Identifying potential cancer driver genes by genomic data integration. Sci Rep (2013) 0.95
Creating views on integrated multidomain data. Bioinformatics (2011) 0.86
BiNA: a visual analytics tool for biological network data. PLoS One (2014) 0.84
Transcriptome analysis of the oriental melon (Cucumis melo L. var. makuwa) during fruit development. PeerJ (2017) 0.81
RefNetBuilder: a platform for construction of integrated reference gene regulatory networks from expressed sequence tags. BMC Bioinformatics (2011) 0.79
KPP: KEGG Pathway Painter. BMC Syst Biol (2015) 0.77
Transcriptional reprogramming and phenotypic switching associated with the adaptation of Lactobacillus plantarum C2 to plant niches. Sci Rep (2016) 0.76
Metabolomic analysis reveals altered metabolic pathways in a rat model of gastric carcinogenesis. Oncotarget (2016) 0.75
Exploiting publicly available biological and biochemical information for the discovery of novel short linear motifs. PLoS One (2011) 0.75
The Systems Biology Graphical Notation. Nat Biotechnol (2009) 8.53
VANTED: a system for advanced data analysis and visualization in the context of biological networks. BMC Bioinformatics (2006) 4.38
HTPheno: an image analysis pipeline for high-throughput plant phenotyping. BMC Bioinformatics (2011) 1.98
Exploration of biological network centralities with CentiBiN. BMC Bioinformatics (2006) 1.78
Editing, validating and translating of SBGN maps. Bioinformatics (2010) 1.71
Software support for SBGN maps: SBGN-ML and LibSBGN. Bioinformatics (2012) 1.69
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
VANTED v2: a framework for systems biology applications. BMC Syst Biol (2012) 1.49
Flux balance analysis of barley seeds: a computational approach to study systemic properties of central metabolism. Plant Physiol (2008) 1.43
Path2Models: large-scale generation of computational models from biochemical pathway maps. BMC Syst Biol (2013) 1.29
Kavosh: a new algorithm for finding network motifs. BMC Bioinformatics (2009) 1.21
Centrality analysis methods for biological networks and their application to gene regulatory networks. Gene Regul Syst Bio (2008) 1.17
Integration of -omics data and networks for biomedical research with VANTED. J Integr Bioinform (2010) 1.12
Dynamic ¹³C/¹ H NMR imaging uncovers sugar allocation in the living seed. Plant Biotechnol J (2011) 1.10
Combined noninvasive imaging and modeling approaches reveal metabolic compartmentation in the barley endosperm. Plant Cell (2011) 1.06
Multiscale metabolic modeling: dynamic flux balance analysis on a whole-plant scale. Plant Physiol (2013) 1.04
MODA: an efficient algorithm for network motif discovery in biological networks. Genes Genet Syst (2009) 1.03
An engineer's view on regulation of seed development. Trends Plant Sci (2010) 0.99
Evidence of a key role for photosynthetic oxygen release in oil storage in developing soybean seeds. New Phytol (2005) 0.97
Modularization of biochemical networks based on classification of Petri net t-invariants. BMC Bioinformatics (2008) 0.96
FBA-SimVis: interactive visualization of constraint-based metabolic models. Bioinformatics (2009) 0.95
Creating interactive, web-based and data-enriched maps with the Systems Biology Graphical Notation. Nat Protoc (2012) 0.95
Meta-All: a system for managing metabolic pathway information. BMC Bioinformatics (2006) 0.94
Integrating data from biological experiments into metabolic networks with the DBE information system. In Silico Biol (2005) 0.93
Controllability in cancer metabolic networks according to drug targets as driver nodes. PLoS One (2013) 0.91
Ranking of network elements based on functional substructures. J Theor Biol (2007) 0.90
OPTIMAS-DW: a comprehensive transcriptomics, metabolomics, ionomics, proteomics and phenomics data resource for maize. BMC Plant Biol (2012) 0.90
Bioinformatics strategies for the analysis of lipids. Methods Mol Biol (2009) 0.90
Visualisation and navigation methods for typed protein-protein interaction networks. Appl Bioinformatics (2003) 0.88
FluxMap: a VANTED add-on for the visual exploration of flux distributions in biological networks. BMC Syst Biol (2012) 0.88
Fast multi-core based multimodal registration of 2D cross-sections and 3D datasets. BMC Bioinformatics (2010) 0.86
Creating views on integrated multidomain data. Bioinformatics (2011) 0.86
Structural analysis of metabolic networks based on flux centrality. J Theor Biol (2010) 0.85
Systems Biology Graphical Notation: Activity Flow language Level 1 Version 1.2. J Integr Bioinform (2015) 0.84
Novel developments of the MetaCrop information system for facilitating systems biological approaches. J Integr Bioinform (2010) 0.82
An improved constraint filtering technique for inferring hidden states and parameters of a biological model. Bioinformatics (2013) 0.82
The system architecture of the BioPath system. In Silico Biol (2002) 0.82
Lessons from GNE-deficient embryonic stem cells: sialic acid biosynthesis is involved in proliferation and gene expression. Glycobiology (2009) 0.81
Exploration of networks using overview+detail with constraint-based cooperative layout. IEEE Trans Vis Comput Graph (2008) 0.81
CentiLib: comprehensive analysis and exploration of network centralities. Bioinformatics (2012) 0.81
Wiring diagrams in biology: towards the standardized representation of biological information. Trends Biotechnol (2012) 0.80
Systems Biology Graphical Notation: Entity Relationship language Level 1 Version 2. J Integr Bioinform (2015) 0.79
Translation of SBGN maps: Process Description to Activity Flow. BMC Syst Biol (2013) 0.78
Visual analysis of transcriptome data in the context of anatomical structures and biological networks. Front Plant Sci (2012) 0.78
DBE2 - management of experimental data for the VANTED system. J Integr Bioinform (2011) 0.78
Specifications of Standards in Systems and Synthetic Biology. J Integr Bioinform (2015) 0.77
Toward Community Standards and Software for Whole-Cell Modeling. IEEE Trans Biomed Eng (2016) 0.77
2.5D visualisation of overlapping biological networks. J Integr Bioinform (2008) 0.77
Elementary flux modes, flux balance analysis, and their application to plant metabolism. Methods Mol Biol (2014) 0.76
Why integrate InfoVis and SciVis?: An example from systems biology. IEEE Comput Graph Appl (2014) 0.76
Conversion of KEGG metabolic pathways to SBGN maps including automatic layout. BMC Bioinformatics (2013) 0.76
Flux visualization using VANTED/FluxMap. Methods Mol Biol (2014) 0.75
Flux balance analysis as an alternative method to estimate fluxes without labeling. Methods Mol Biol (2014) 0.75
IDPredictor: predict database links in biomedical database. J Integr Bioinform (2012) 0.75
Nutrilyzer: a tool for deciphering atomic stoichiometry of differentially expressed paralogous proteins. J Integr Bioinform (2012) 0.75
Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2016. J Integr Bioinform (2016) 0.75