Novel Approach Blocks Amyloid Production in Alzheimer’s Mouse Model

Promises potential early therapeutic intervention —

Offering a potential early intervention for Alzheimer’s disease (AD), researchers at University of California, San Diego School of Medicine and Cenna Biosciences, Inc. have identified compounds that block the production of beta amyloid peptides in mice. The study is reported April 29 in PLOS ONE.

If the results ultimately translate to human treatment, the most promising compound – a peptide dubbed P8 – could be administered to individuals at high risk of developing the disease, long before the tell-tale signs of dementia occur and perhaps with few side effects, due to the compound’s highly specific mode of action. … Read the full story from the UC San Diego Newsroom

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

DELPHI Project Foretells Future of Personalized Population Health

NSF awards $2 million over four years to UC San Diego computer scientists and physicians

Imagine a new type of healthcare app that does it all – it helps you understand your current health status, assists you in making changes in your life to improve your health, and takes into account the perspective of your entire life history, others in your age group–and perhaps even your neighborhood– who share similar characteristics.

That’s the vision put forward by a team of physicians and computer scientists at the University of California, San Diego who are collaborating on a new digital resource that would take advantage of advances in databases, cyberinfrastructure and machine learning to usher in a new era of health and health care…. Read the full story from the UCSD Newsroom


Dr. Lucila Ohno-MachadoLucila Ohno-Machado, MD, PhD, FACMI, is an investigator on the project, whose title is “Data E-platform Leveraged for Patient Empowerment and Population Health Improvement (DELPHI).”

Dr. Ohno-Machado is professor of medicine and founding chief of the Division of Biomedical Informatics. She directs, among other projects, another UCSD biomedical cyberinfrastructure, the Integrating Data for Analysis, Anonymizing and Sharing (iDASH) project. IDASH is a National Center for Biomedical Computing under the auspices of the NIH Roadmap for Bioinformatics and Computational Biology. Under AHRQ funding, she directs the related project Scalable National Network for Effectiveness Research (SCANNER).

Dr. Ohno-Machado’s research specialty is predictive modeling with an emphasis on calibration methods that combine phenotype and genotype/gene expression data for personalized medicine.

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Bringing Power of Prevention, Diagnosis to the People

“A Mercedes Benz isn’t designed to function in the Sahara Desert,” notes Dr. Eliah Aronoff-Spencer of the University of California, San Diego. “So why are we designing medical equipment for developing countries the same way we do for developed ones?”

It’s a question researchers at the new Distributed Health Laboratory in the California Institute for Telecommunications and Information Technology (Calit2) at UC San Diego aim to address, and eventually, to render moot. In collaboration with the UC San Diego School of Medicine and the Universidade Eduardo Mondlane (UEM) in Maputo, Mozambique, Calit2’s DH Lab is designing low-cost medical devices such as microscopes and wireless sensing devices that can be used by virtually anyone anywhere in the world to prevent and even diagnose illness. … Read the full story from the UCSD Newsroom


Co-directing the Distributed Health Laboratory is Eliah Aronoff-Spencer, MD, PhD, fellow in infectious diseases at UCSD and informatics coordinator for the Medical Education Partnership Initiative (MEPI) between UC San Diego and Universidade Eduardo Mondlane (UEM) in Maputo, Mozambique.

Eliah Aronoff-Spencer, MD, PhD with Dr. Manuel TomasThe photo at left shows Dr. Aronoff-Spencer with UEM physician Dr. Manuel Tomás (at right) on a patient ward at Maputo Central Hospital.

Dr. Aronoff-Spencer is also an organizer of the Biomedical Research Informatics for Global Health Training (BRIGHT) program, an international collaboration devoted to training the next generation of informatics researchers in partner countries.

The BRIGHT program, a Division of Biomedical Informatics project, is funded by grant D43TW007015 from the Fogarty International Center of the National Institutes of Health.

A graduate of the UCSD Internal Medicine Residency Program and Physician-Scientist Training Pathway, Dr. Aronoff-Spencer has completed a fellowship in clinical infectious disease and is now a fellow in research in infectious disease, global health informatics and decision making at UCSD. He is also a staff physician in infectious disease at the VA San Diego Healthcare System.

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