BiNA: A Visual Analytics Tool for Biological Network Data

NetworkTrail--a web service for identifying and visualizing deregulated subnetworks

(2013) D. Stockel et al.   BIOINFORMATICS

miRTrail - a comprehensive webserver for analyzing gene and miRNA patterns to enhance the understanding of regulatory mechanisms in diseases

(2012) Cedric Laczny et al.   BMC BIOINFORMATICS

The mzIdentML Data Standard for Mass Spectrometry-Based Proteomics Results

(2012) Andrew R. Jones et al.   MOLECULAR & CELLULAR PROTEOMICS

NCBI GEO: archive for functional genomics data sets—update

(2012) Tanya Barrett et al.   NUCLEIC ACIDS RESEARCH

An integer linear programming approach for finding deregulated subgraphs in regulatory networks

(2011) Christina Backes et al.   NUCLEIC ACIDS RESEARCH

KEGG for integration and interpretation of large-scale molecular data sets

(2011) M. Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Cytoscape Web: an interactive web-based network browser

(2010) Christian T. Lopes et al.   BIOINFORMATICS

Visualizing biological data—now and in the future

(2010) Seán I O'Donoghue et al.   NATURE METHODS

Visualization of omics data for systems biology

(2010) Nils Gehlenborg et al.   NATURE METHODS

A novel algorithm for detecting differentially regulated paths based on gene set enrichment analysis

(2009) Andreas Keller et al.   BIOINFORMATICS

Infrastructure for the life sciences: design and implementation of the UniProt website

(2009) Eric Jain et al.   BMC BIOINFORMATICS

The Systems Biology Graphical Notation

(2009) Nicolas Le Novère et al.   NATURE BIOTECHNOLOGY

VisANT 3.5: multi-scale network visualization, analysis and inference based on the gene ontology

(2009) Zhenjun Hu et al.   NUCLEIC ACIDS RESEARCH

The Universal Protein Resource (UniProt) in 2010

(2009)   NUCLEIC ACIDS RESEARCH

GeneTrailExpress: a web-based pipeline for the statistical evaluation of microarray experiments

(2008) Andreas Keller et al.   BMC BIOINFORMATICS

Using Atom Mapping Rules for an Improved Detection of Relevant Routes in Weighted Metabolic Networks

(2008) Torsten Blum et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

CellDesigner 3.5: A Versatile Modeling Tool for Biochemical Networks

(2008) A. Funahashi et al.   PROCEEDINGS OF THE IEEE

A survey of visualization tools for biological network analysis

(2008) Georgios A Pavlopoulos et al.   BioData Mining