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Network-based stratification of tumor mutations.

Hofree, Matan Shen, John P Carter, Hannah Gross, Andrew Ideker, Trey

Published in Nature methods

Many forms of cancer have multiple subtypes with different causes and clinical outcomes. Somatic tumor genome sequences provide a rich new source of data for uncovering these subtypes but have proven difficult to compare, as two tumors rarely share the same mutations. Here we introduce network-based stratification (NBS), a method to integrate somat...

A travel guide to Cytoscape plugins.

Saito, Rintaro Smoot, Michael E Ono, Keiichiro Ruscheinski, Johannes Wang, Peng-Liang Lotia, Samad Pico, Alexander R Bader, Gary D Ideker, Trey

Published in Nature methods

Cytoscape is open-source software for integration, visualization and analysis of biological networks. It can be extended through Cytoscape plugins, enabling a broad community of scientists to contribute useful features. This growth has occurred organically through the independent efforts of diverse authors, yielding a powerful but heterogeneous set...

Cost-effective strategies for completing the interactome.

As, Schwartz J, Yu Kr, Gardenour Jr, Finley Rl T, Ideker

Published in Nature Methods

Comprehensive protein-interaction mapping projects are underway for many model species and humans. A key step in these projects is estimating the time, cost and personnel required for obtaining an accurate and complete map. Here we modeled the cost of interaction-map completion for various experimental designs. We showed that current efforts may re...

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