Tumor Suppressor Mutations Alone Don’t Explain Deadly Cancer

Biomarker for head and neck cancers identified

Although mutations in a gene dubbed “the guardian of the genome” are widely recognized as being associated with more aggressive forms of cancer, researchers at the University of California, San Diego School of Medicine have found evidence suggesting that the deleterious health effects of the mutated gene may in large part be due to other genetic abnormalities, at least in squamous cell head and neck cancers. … Read the full story from the UCSD Newsroom


Trey Ideker, PhD

Trey Ideker, PhD, professor and chief in the Division of Medical Genetics and professor of bioengineering, is one of the study’s co-senior authors.

Other Department of Medicine faculty authors include Hannah Carter, PhD, assistant professor; and Scott M. Lippman, MD, professor of medicine and director of the UC San Diego Moores Cancer Center.

Hannah Carter, PhD Dr. Scott M. Lippman

“Wildly Heterogeneous Genes”

New approach subtypes cancers by shared genetic effects; a step toward personalized medicine

Cancer tumors almost never share the exact same genetic mutations, a fact that has confounded scientific efforts to better categorize cancer types and develop more targeted, effective treatments.

In a paper published in the September 15 advanced online edition of Nature Methods, researchers at the University of California, San Diego propose a new approach called network-based stratification (NBS), which identifies cancer subtypes not by the singular mutations of individual patients, but by how those mutations affect shared genetic networks or systems. … Read the full story from the UCSD Newsroom


Trey Ideker, PhDLead investigator in the study is Trey Ideker, PhD, professor of medicine and bioengineering and chief of the Division of Medical Genetics in the Department of Medicine.

Postdoctoral researcher Hannah K. Carter and hematology/oncology fellow John P. Shen are the other Department of Medicine coauthors.

Citation for the study report:  Matan Hofree, John P Shen, Hannah Carter, Andrew Gross, Trey Ideker. Network-based stratification of tumor mutations. Nature Methods (2013) doi:10.1038/nmeth.2651. |  Full text (UCSD only)

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Trey Ideker and Collaborators Release Cytoscape v3

Visualizing Complex Networks using New Cytoscape v3

On April 22, 2013, computational biologists and computer scientists at UC San Diego released version 3 of Cytoscape for general availability. Cytoscape is the leading open source visualization software platform supporting systems biology; it enables researchers to visualize molecular interaction networks and biological pathways and integrate them with annotations, gene expression profiles and other state and process data.

Cytoscape was developed in the early 2000s to meet the need for an analytical tool that would allow researchers to organize, view and interpret large-scale biological data in a unified conceptual framework.

Approximately 1,600 scientific papers have cited the software to date, with approximately 300-400 new papers each year.

The Cytoscape-generated image below is a visualization of a data set composed of molecular and genetic interactions within cells in the human body.

A Cytoscape visualization of a data set composed of molecular and genetic interactions within cells

Although it was originally designed for biological research, Cytoscape is now a general platform for complex network analysis and visualization, with additional applications in software engineering and the study of social networks.

Features new in Cytoscape v3 include edge bending and bundling visualizations (see image below), network annotations, advanced searching, node grouping and associated tutorials.

Cytoscape v3 also incorporates a new App Store, which enables Cytoscape users to access and use a large and growing pool of community-published visualization and analytics modules, thereby driving and enabling Cytoscape’s use both in biology and in diverse research environments.

The Cytoscape core application is open source and is distributed under a Library GNU Public License; each app carries an independent software license. Cytoscape’s open application programmer interface is based on Java™ technology.

Trey Ideker, PhDCytoscape project principal investigator Trey Ideker, PhD (left), said, “Cytoscape v3 is an important milestone in the support of systems biology, enabling deep insights into complex biologic relationships and processes.

“From a biological perspective, it will enable multiscale, dynamic, and ontological studies. From a systems perspective, it will enable collaborative workflows and better, more intensive use of existing and future computing resources.”

Ideker is professor of bioengineering and professor and chief of the Division of Medical Genetics in the Department of Medicine.Barry Demchak

The Ideker laboratory offers Cytoscape and a number of other software packages and tools for download. (http://idekerlab.ucsd.edu/software).

There are approximately 6,000 Cytoscape downloads each month, Ideker said.

Lead Cytoscape software architect Barry Demchak, PhD, pictured above right, said Cytoscape v3 represents a major redesign to boost the program’s performance, improve the user interface, and make the software more extensible and stable.

Cytoscape 3 visualization image.

New feature in Cytoscape 3: Automatic edge bundling consolidates multiple edges to de-clutter dense network views.

Cytoscape v3 is the culmination of two years’ work conducted by the National Institutes of Health-funded Cytoscape Consortium, which includes collaborators at UC San Diego, UC San Francisco, the University of Toronto, the Pasteur Institute, the Broad Institute, the Memorial Sloan-Kettering Cancer Center, and the Institute for Systems Biology.

Cytoscape is available for free download at http://cytoscape.org.

User support, education and new initiatives for Cytoscape are supported by the National Resource for Network Biology under award numbers P41 RR031228 and GM103504.   |  Watch Trey Ideker’s video introduction to NRNB

For further information, contact Barry Demchak (bdemchak@ucsd.edu or 858-452-8700) at UC San Diego.

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Other News Releases about Ideker’s Work

Biomarking Time

Methylome modifications offer new measure of our “biological” age

Women live longer than men. Individuals can appear or feel years younger – or older – than their chronological age. Diseases can affect our aging process. When it comes to biology, our clocks clearly tick differently.

In a new study, researchers at the University of California, San Diego School of Medicine, with colleagues elsewhere, describe markers and a model that quantify how aging occurs at the level of genes and molecules, providing not just a more precise way to determine how old someone is, but also perhaps anticipate or treat ailments and diseases that come with the passage of time. … Read the full story from the UCSD Newsroom


Trey Ideker, PhDTrey Ideker, PhD, is co-senior author of the study report. He is professor of medicine and chief of the Division of Medical Genetics, professor of bioengineering and faculty investigator in the UCSD Institute for Genomic Medicine.The overall goal of Ideker’s work is to map and model molecular networks of cellular processes in health and disease, particularly in cancer and the response to genotoxic stress.

Coauthors of the study report include Rob DeConde, a graduate student in Ideker’s laboratory.

Read the abstract of the study report in PubMed

Citation: Hannum G, Guinney J, Zhao L, Zhang L, Hughes G, Sadda S, Klotzle B, Bibikova M, Fan J-B, Gao Y, Deconde R, Chen M, Rajapakse I, Friend S, Ideker T, Zhang K: Genome-wide Methylation Profiles Reveal Quantitative Views of Human Aging Rates. Molecular cell doi:10.1016/j.molcel.2012.10.016. PMID: 23177740

New Center Looks at How Human Systems Function or Fail

A new center called the National Resource for Network Biology (NRNB), based at the University of California, San Diego School of Medicine, will help clinicians analyze an ever-growing wealth of complex biological data and apply that knowledge to real problems and diseases… Read the full story from the UCSD Newsroom

Dr. Trey Ideker

Lead investigator of the study is Trey Ideker, Ph.D., Professor and Chief of the Division of Medical Genetics in the Department of Medicine and Professor of Bioengineering (pictured above).

Among the Department of Medicine project collaborators is James H. Fowler, Ph.D., Professor of Medicine and Political Science.

Read the abstract of the project.