ePlant and the 3D Data Display Initiative: Integrative Systems Biology on the World Wide Web

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

Prequips--an extensible software platform for integration, visualization and analysis of LC-MS/MS proteomics data

(2009) N. Gehlenborg et al.   BIOINFORMATICS

Simultaneous analysis of distinct Omics data sets with integration of biological knowledge: Multiple Factor Analysis approach.

(2009) Marie de Tayrac et al.   BMC GENOMICS

FORG3D: Force-directed 3D graph editor for visualization of integrated genome scale data

(2009) Jussi Paananen et al.   BMC Systems Biology

Protein Sectors: Evolutionary Units of Three-Dimensional Structure

(2009) Najeeb Halabi et al.   CELL

ProPhylER: A curated online resource for protein function and structure based on evolutionary constraint analyses

(2009) J. Binkley et al.   GENOME RESEARCH

How to visually interpret biological data using networks

(2009) Daniele Merico et al.   NATURE BIOTECHNOLOGY

Protein structure prediction on the Web: a case study using the Phyre server

(2009) Lawrence A Kelley et al.   Nature Protocols

Network visualization and analysis of gene expression data using BioLayout Express3D

(2009) Athanasios Theocharidis et al.   Nature Protocols

Web-Queryable Large-Scale Data Sets for Hypothesis Generation in Plant Biology

(2009) S. M. Brady et al.   PLANT CELL

Gene expression map of the Arabidopsis shoot apical meristem stem cell niche

(2009) R. K. Yadav et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Penetration of the Stigma and Style Elicits a Novel Transcriptome in Pollen Tubes, Pointing to Genes Critical for Growth in a Pistil

(2009) Yuan Qin et al.   PLoS Genetics

The 1001 Genomes Project for Arabidopsis thaliana

(2009) Detlef Weigel et al.   GENOME BIOLOGY

Exploration and visualization of gene expression with neuroanatomy in the adult mouse brain

(2008) Christopher Lau et al.   BMC BIOINFORMATICS

Arena3D: visualization of biological networks in 3D

(2008) Georgios A Pavlopoulos et al.   BMC Systems Biology

Life Sciences and the web: a new era for collaboration

(2008) Jonathan A Sagotsky et al.   Molecular Systems Biology

CDD: specific functional annotation with the Conserved Domain Database

(2008) A. Marchler-Bauer et al.   NUCLEIC ACIDS RESEARCH

Reactome knowledgebase of human biological pathways and processes

(2008) L. Matthews et al.   NUCLEIC ACIDS RESEARCH

InterPro: the integrative protein signature database

(2008) S. Hunter et al.   NUCLEIC ACIDS RESEARCH

Arabidopsis Reactome: A Foundation Knowledgebase for Plant Systems Biology

(2008) N. Tsesmetzis et al.   PLANT CELL

The AtGenExpress hormone and chemical treatment data set: experimental design, data evaluation, model data analysis and data access

(2008) Hideki Goda et al.   PLANT JOURNAL

Isolation of a strong Arabidopsis guard cell promoter and its potential as a research tool

(2008) Yingzhen Yang et al.   Plant Methods

Evolutionary Diversification of Plant Shikimate Kinase Gene Duplicates

(2008) Geoffrey Fucile et al.   PLoS Genetics

GeneMANIA: a real-time multiple association network integration algorithm for predicting gene function

(2008) Sara Mostafavi et al.   GENOME BIOLOGY