Hannah Carter Receives NIH Early Independence Award

CTRI Helps Launch Career of Bioengineer Hannah Carter

November 22, 2013 – With support from UC San Diego’s Clinical and Translational Research Institute (CTRI), bioengineer Hannah Carter, PhD, received the highly prestigious NIH Early Independence Award and recently began began her transition to a junior faculty position at UC San Diego.

Presently she is acquiring a research team and computational resources to delve into her project: Network approaches to identify cancer drivers from high-dimensional tumor data. … Read the full story from CTRI News & Events


Hannah Carter, PhDHannah Carter, PhD, is assistant professor of medicine in the Division of Medical Genetics. Her project is Network Approaches to Identify Cancer Drivers from High-Dimensional Tumor Data.

She is now recruiting postdoctoral fellows for her project, which is funded for five years.

Carter Laboratory website

 

HIV Transmission Networks Mapped to Reduce Infection Rate

Researchers at the University of California, San Diego School of Medicine have mapped the transmission network of human immunodeficiency virus (HIV) in San Diego. The mapping of HIV infections, which used genetic sequencing, allowed researchers to predictively model the likelihood of new HIV transmissions and identify persons at greatest risk for transmitting the virus. … Read the full story from the UC San Diego Newsroom

$5.6 Million Grant Renewal Expands Research in Kidney Failure

The National Institute of Diabetes and Digestive and Kidney Diseases (NIDDKD) – part of the National Institutes of Health – has renewed a grant shared by the University of California, San Diego and the University of Alabama at Birmingham Schools of Medicine. The five-year, $5.64 million renewal will extend and expand research into acute kidney failure, or acute kidney injury, which kills 70 to 80 percent of patients in intensive care units who develop the disease.Read the full story from the UCSD Newsroom


Dr. Ravindra MehtaRavindra L. Mehta, MD, FACP, UC San Diego professor of clinical medicine and vice chair for clinical research in the Department of Medicine, is associate director of the UC San Diego – University of Alabama at Birmingham O’Brien Center for Acute Kidney Injury Research.

He directs the O’Brien Center’s clinical studies core with co-director Daniel O’Connor, MD. O’Connor is professor of medicine and pharmacology and co-director, UCSD Center for Human Genetics and Genomics.

UC San Diego nephrology faculty members Roland Blantz, MD, and Volker Vallon, MD, are co-directors of the pre-clinical studies core of the O’Brien Center. Blantz is distinguished professor of medicine emeritus and former chief of the Division of Nephrology-Hypertension; Vallon is professor of medicine and pharmacology.

UC San Diego nephrologist Satish RamachandraRao, PhD, assistant professor of medicine, is a co-director of the Bioanalytical Resource Core.

Ravindra L. Mehta is Director of Dialysis Programs and Clinical Nephrology for UC San Diego Health System. In the UC San Diego School of Medicine, Mehta directs the Clinical Research Enhancement through Supplemental Training (CREST) and Master’s Degree in Clinical Research programs.

In 2011, Mehta received the International Society of Nephrology (ISN) Shire Bywaters Award for his lifetime achievements in acute kidney injury.

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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

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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Scientists Map Changes in Genetic Networks Caused By DNA Damage

Using a new technology called “differential epistasis maps,” an international team of scientists, led by researchers at the University of California, San Diego School of Medicine, has documented for the first time how a cellular genetic network completely rewires itself in response to stress by DNA-damaging agents… Read the full story from the UCSD Newsroom


Dr. Trey Ideker

Senior author 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).  Department of Medicine faculty coauthors include Richard D. Kolodner, Ph.D., Professor in the Division of Hematology-Oncology.

Read the abstract of the article in the December 3 issue of Science.

Researchers Create Atlas of Transcription Factor Combinations

Trey Ideker, Ph.D., Associate Professor of Medicine and Bioengineering and Chief of the Division of Medical Genetics, is principal investigator of the project described in the UCSD Newsroom story, “Researchers Create Atlas of Transcription Factor Combinations.”  |  Read the story