GenomeSpace “Recipes” Help Biologists Interpret Genomic Data

Data analysis platform will enlist the user community to streamline use of multiple bioinformatics tools —

Many biomedical researchers are striving to make sense of the flood of data that has followed recent advances in genomic sequencing technologies. In particular, researchers are often limited by the challenge of getting multiple bioinformatics tools to “talk” to one another. To help address this need, researchers at University of California, San Diego School of Medicine, in collaboration with labs at the Broad Institute of MIT and Harvard, Stanford University, Weizmann Institute and Pennsylvania State University, developed GenomeSpace, a cloud-based, biologist-friendly platform that connects more than 20 bioinformatics software packages and resources for genomic data analysis.

The team is now developing and crowdsourcing “recipes” — step-by-step workflows — to better enable non-programming researchers to interpret their genomic data … Read the full story from the UC San Diego Newsroom


Dr. Jill Mesirov

Dr. Jill Mesirov

Jill Mesirov, PhD, is senior investigator on the GenomeSpace project. Dr. Mesirov joined UC San Diego in 2015 as Associate Vice Chancellor for Computational Health Sciences and Professor of Medicine in the Division of Medical Genetics.

Trey Ideker, PhD, Professor of Medicine, is a coauthor.

The article citation: Qu K, Garamszegi S, Wu F, et al. Nature Methods. 2016 Jan 18. doi: 10.1038/nmeth.3732.

Grant Gives New Breath to Patients Suffering from Severe Pulmonary Hypertension

Nearly $8 million grant helps launch a nationwide patient registry to improve CTEPH practices

Imagine trying to take a deep breath, but feeling like you’re sucking air through a straw. That’s how some patients with chronic thromboembolic pulmonary hypertension (CTEPH) describe living with the condition, which is estimated to affect several thousand Americans yearly but is commonly misdiagnosed. UC San Diego Health System is a world leader in CTEPH, and now with a $7.6 million grant, has helped launch the first national CTEPH registry to improve best practices and patient care. … Read the full story from the UC San Diego Newsroom


Dr. Kim KerrPrincipal Investigator of the project is Kim Kerr, MD, professor of clinical medicine in the Division of Pulmonary and Critical Care Medicine. She directs the Medical Intensive Care Unit at UC San Diego Health System’s Thornton Hospital in La Jolla.

Dr. Michael MadaniCardiac surgeon Michael Madani, MD, co-investigator, is chief of cardiothoracic surgery and director of UC San Diego Sulpizio Cardiovascular Center – Surgery.

UC San Diego-Human Longevity Inc. Agreement Seeks to Accelerate Medical Science

Thousands of patient genomes expected to fuel diverse medical research, beginning with cancer

The new collaborative research agreement between Human Longevity Inc. (HLI) and the University of California, San Diego, announced today, represents a significant and necessary step in efforts to research and translate the potential of the human genome into novel and real treatments and therapies able to change and improve the human condition.

“This agreement brings together the resources of two entities that, in combination, may ultimately help improve countless lives,” said David A. Brenner, MD, vice chancellor of health sciences at UC San Diego and dean of the UC San Diego School of Medicine. “HLI aims to bring leading-edge thinking in genomics technologies. UC San Diego boasts some of the world’s finest researchers and physicians working at places like the Moores Cancer Center. Together, we will collaborate to marshal the people, the tools and the resources to really make a difference in human health.” … Read the full story from the UC San Diego News Center

University of California Launches its First Tool for Data Sharing Among Medical Centers with UC Research eXchange

Announcement for UC Investigators

Gary S. Firestein, MD
Chair, University of California Biomedical Research
Acceleration, Integration and Development (UCBRAID)
Professor of Medicine
Dean and Associate Vice Chancellor, Translational Medicine
Director, Clinical and Translational Research Institute
UC San Diego

Dr. Gary Firestein

Dr. Gary Firestein, UC BRAID Chair

The University of California Biomedical Research Acceleration, Integration and Development (UC BRAID; ucbraid.org) is pleased to announce the launch of the UC Research eXchange (UC ReX) and the UC ReX Data Explorer tool. This system enables exploration of a combined population of over 12 million patients from medical center databases at UC Los Angeles, UC Irvine, UC Davis, UC San Diego, and UC San Francisco.

UC ReX Data Explorer gives researchers and quality specialists access to cohort counts derived from de-identified clinical data collected at the point of care to improve medical care and advance research.

UC ReX was initiated by UC BRAID in 2011 with a 5-year grant of $5 million from the UC Office of the President (UCOP) and developed through a collaboration of the medical campuses and their Chief Information Officers and CTSAs.

An important part of UC BRAID’s mission is to improve UC collaborative research opportunities. UC ReX is a great example of how UC BRAID facilitates integration of research programs, clinical informatics, technology, and resources across University of California campuses.

To start exploring UC ReX with Data Explorer, please go to ucrex.org for more information.  |  See UC ReX Flier

Access UC-ReX via UC San Diego Clinical and Translational Research Institute

 

IDASH Projects: Protecting Privacy and Patient Rights in the Name of Scientific Progress

In the years since the best-selling book “The Immortal Life of Henrietta Lacks” made the issue of informed consent and patient privacy a national topic of conversation, scientists and clinicians have continued to struggle to develop a comprehensive methodology for collecting and sharing data from patients and research subjects without jeopardizing their rights.

The University of California, San Diego’s iDASH project aims to address some of these fundamental challenges to research progress with its most recent series of “Driving Biological Projects” (DBPs) … Read the full story from the UCSD Newsroom


Dr. Lucila Ohno-MachadoLead investigator in the iDASH project is Lucila Ohno-Machado, MD, MBA, PhD, professor of medicine, founding chief of the Division of Biomedical Informatics and associate dean for informatics and technology at UC San Diego.

Among other research and education projects directed by Dr. Ohno-Machado are the Biomedical Research Informatics for Global Health training program and the biomedical informatics component of the UC San Diego – Universidade Eduardo Mondlane Medical Education Partnership Initiative.  |  See all DBMI research projects

Dr. Ohno-Machado joined the UC San Diego faculty from Harvard Medical School in 2009. She was elected to the American Society for Clinical Investigation in 2010.

More Information:

UC San Diego Named 15th Best Research University in the World for Scientific Impact

Geisel Library, UC San Diego

Geisel Library, UC San Diego

In a global ranking designed to provide highly accurate measurements of the scientific impact of universities and their contributions to scientific collaboration, the University of California, San Diego is ranked the 15th best research university in the world. … Read the full story from the UCSD 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.

More Information:

Other News Releases about Ideker’s Work

Toward a New Model of the Cell

Everything You Always Wanted to Know About Genes

Turning vast amounts of genomic data into meaningful information about the cell is the great challenge of bioinformatics, with major implications for human biology and medicine. Researchers at the University of California, San Diego School of Medicine and colleagues have proposed a new method that creates a computational model of the cell from large networks of gene and protein interactions, discovering how genes and proteins connect to form higher-level cellular machinery. …Read the full story from the UCSD Newsroom


Trey Ideker, PhDThe new approach comes from the medical genetics laboratory of Trey Ideker, PhD, in the departments of bioengineering and medicine. Postdoctoral fellow Janusz Dutkowski, PhD, is lead author and Michael Kramer, PhD, a coauthor of the study report in Nature Biotechnology.

Ideker, senior author, is professor of bioengineering and medicine and chief of the Division of Medical Genetics in the Department of Medicine.

Citation for the report:  Dutkowski J, Kramer M, Surma MA, Balakrishnan R, Cherry JM, Krogan NJ, Ideker T. A gene ontology inferred from molecular networks. Nature Biotechnology (2012) doi:10.1038/nbt.2463. Published online 16 December 2012  Read the abstract

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.

More Information:

SDSC’s “Big Data” Expertise Aiding Genomics Research

Focus on Genomics Medicine is Growing, says SDSC’s Norman

The San Diego Supercomputer Center (SDSC) at the University of California, San Diego, has in the last three years undergone a major reboot, remaking itself into a center of expertise on all aspects of “big data” research including genomics, one of the fastest growing areas of scientific study. …. Read the full story from the UCSD Newsroom

Dr. Lucila Ohno-Machado
Among the current “big data” genomics projects at the San Diego Supercomputer Center is the Integrating Data for Analysis, Anonymization, and Sharing (iDASH) center, led by Lucila Ohno-Machado, MD, PhD, pictured above.

Ohno-Machado is professor of medicine, founding chief of the Division of Biomedical Informatics and associate dean for informatics and technology at UC San Diego.

iDASH is supported by the National Institutes of Health through the NIH Roadmap for Medical Research.  |  Read iDASH project abstract  |  Visit iDASH website  |   Visit San Diego Supercomputer Center website
Photo of Dr. Ohno-Machado: John Hanacek, Calit2 UC San Diego.