iCAVE: an open source tool for visualizing biomolecular networks in 3D, stereoscopic 3D and immersive 3D

Visualizing genome and systems biology: technologies, tools, implementation techniques and trends, past, present and future

(2015) Georgios A. Pavlopoulos et al.   GigaScience

BiNA: A Visual Analytics Tool for Biological Network Data

(2014) Andreas Gerasch et al.   PLoS One

CR1 and the “Vanishing Amyloid” Hypothesis of Alzheimer’s Disease

(2013) Sam Gandy et al.   BIOLOGICAL PSYCHIATRY

3DScapeCS: application of three dimensional, parallel, dynamic network visualization in Cytoscape

(2013) Qi Wang et al.   BMC BIOINFORMATICS

Integrative Annotation of Variants from 1092 Humans: Application to Cancer Genomics

(2013) Ekta Khurana et al.   SCIENCE

Interpretation of Genomic Variants Using a Unified Biological Network Approach

(2013) Ekta Khurana et al.   PLoS Computational Biology

Network Medicine Strikes a Blow against Breast Cancer

(2012) Janine T. Erler et al.   CELL

Architecture of the human regulatory network derived from ENCODE data

(2012) Mark B. Gerstein et al.   NATURE

A century of Gestalt psychology in visual perception: I. Perceptual grouping and figure–ground organization.

(2012) Johan Wagemans et al.   PSYCHOLOGICAL BULLETIN

Gaussian graphical modeling reconstructs pathway reactions from high-throughput metabolomics data

(2011) Jan Krumsiek et al.   BMC Systems Biology

Visualization of omics data for systems biology

(2010) Nils Gehlenborg et al.   NATURE METHODS

Computational solutions to large-scale data management and analysis

(2010) Eric E. Schadt et al.   NATURE REVIEWS GENETICS

Automated Network Analysis Identifies Core Pathways in Glioblastoma

(2010) Ethan Cerami et al.   PLoS One

Force-Directed Edge Bundling for Graph Visualization

(2009) Danny Holten et al.   COMPUTER GRAPHICS FORUM

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

Protein kinase Cε: an oncogene and emerging tumor biomarker

(2009) Michael A Gorin et al.   Molecular Cancer

Dynamic modularity in protein interaction networks predicts breast cancer outcome

(2009) Ian W Taylor et al.   NATURE BIOTECHNOLOGY

CO-EXPRESSION AMONG CONSTITUENTS OF A MOTIF IN THE PROTEIN–PROTEIN INTERACTION NETWORK

(2009) NITIN BHARDWAJ et al.   Journal of Bioinformatics and Computational Biology

Visualizing graphs in three dimensions

(2008) Colin Ware et al.   ACM Transactions on Applied Perception

Arena3D: visualization of biological networks in 3D

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

Novel Breast Cancer Biomarkers Identified by Integrative Proteomic and Gene Expression Mapping

(2008) Keli Ou et al.   JOURNAL OF PROTEOME RESEARCH

The Knowledge-Integrated Network Biomarkers Discovery for Major Adverse Cardiac Events

(2008) Guangxu Jin et al.   JOURNAL OF PROTEOME RESEARCH

Organization of modular networks

(2008) S. N. Dorogovtsev et al.   PHYSICAL REVIEW E