Active Genetics Goes Global

Tata Trusts & University of California San Diego partner to establish Tata Institute for Active Genetics and Society (TIAGS) —

UC San Diego has received a $70 million commitment from the India-based philanthropic Tata Trusts, which includes the Sir Dorabji Tata Trust, the Sir Ratan Tata Trust and the Tata Education and Development Trust, to establish the Tata Institute for Active Genetics and Society (TIAGS), a collaborative partnership between the university and research operations in India. UC San Diego, which will be home to the lead unit of the institute (TIAGS-UC San Diego), will receive $35 million in funding, while the remainder of the committed funds is anticipated to support a complementary research enterprise in India (TIAGS-India). … Read the Full Story from the UC San Diego Newsroom


Anita Raj, PhD

Anita Raj, PhD

Anita Raj, PhD, Professor of Medicine in the Division of Global Public Health, is one of the UC San Diego researchers who will contribute to the TIAGS.

Division of Regenerative Medicine Holds First Research Symposium

Catriona H. M. Jamieson, MD, PhD

Dr. Catriona Jamieson

On Friday, January 30, the Division of Regenerative Medicine presented its inaugural symposium on novel research and technologies in regenerative medicine.

The meeting featured scientific presentations by world-renowned academic investigators and industry leaders as well as a discussion panel including keynote speakers Dr. Hans Clevers, Dr. Derrick Rossi, Dr. Carl June and Dr. Wolfgang Dillmann.

Division Chief Catriona Jamieson, MD, PhD, presented the mission and milestones of the new Division of Regenerative Medicine after introductions from UC San Diego Chancellor Pradeep Khosla; Vice Chancellor Health Sciences and Dean of UC San Diego School of Medicine Dr. David Brenner; and Chief Executive Officer of UC San Diego Health System and Associate Vice Chancellor of UC San Diego Health Sciences Paul Viviano.

UC San Diego Moores Cancer Center

UC San Diego Moores Cancer Center

Catriona Jamieson, MD, PhD, is associate professor in the Division of Hematology-Oncology, deputy director of the Sanford Stem Cell Clinical Center, chief of the Division of Regenerative Medicine and director of stem cell research at the Moores Cancer Center.

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

 

Richard Garfein and Kevin Patrick Named M2M Pioneers

Applying Machine-to-Machine (M2M) Technology to Verify Compliance with Tuberculosis Treatment Regimen

Dr. Richard Garfein

Dr. Richard Garfein

UC San Diego’s Richard Garfein and Kevin Patrick have been named M2M Pioneers for 2013 for their Video Directly Observed Therapy (VDOT) Program for tuberculosis.

The honor comes from Connected World magazine, which presents the M2M Pioneer awards to a small number of outstanding innovators in machine-to-machine technology each year.

The VDOT program uses smartphone video to verify that tuberculosis patients comply with the painstaking six-month regimen of antibiotics required for a cure. Incomplete treatment fails to cure the TB and raises the risk that antibiotic-resistant strains of TB will develop.

Richard Garfein, PhD, MPH, an infectious disease epidemiologist, is professor of medicine in the Division of Global Public Health. The inspiration for the VDOT program came to him as he watched his children use smartphones to send videos to their friends.

Dr. Kevin Patrick

Dr. Kevin Patrick

Kevin Patrick, MD, MS, is director of the Center for Wireless and Population Health Systems at the Qualcomm Institute (the San Diego division of Calit2) and professor of family and preventive medicine in the Division of Preventive Medicine.

In their NIH-funded pilot study in San Diego and Tijuana in 2011-2012, Garfein and Patrick demonstrated that the VDOT program was an effective tool for ensuring that patients adhered to their treatment regimens.

They also showed that VDOT could reduce costs for the local public health agency; in the pilot study, the San Diego County Health and Human Services Agency. The agency’s only previous option had been to send health workers to patients’ homes to watch them take their medications.

Garfein and Patrick reported their results in an mHealth Summit Meeting abstract published in the Journal of Mobile Technology in Medicine.

Now, Garfein and colleagues are working on implementing the program on a larger scale through a public/private partnership with the Verizon Foundation, which provides funding and in-kind assistance.

The Garfein-Patrick team included other faculty and staff of the Global Public Health division and a number of specialists from the Qualcomm Institute.

Steffanie Strathdee, PhD

Dr. Steffanie Strathdee. Image ©International AIDS Society/Marcus Rose/Workers’ Photos. Used with permission.

“Congratulations to them both, and to Ramesh Rao and their team from the Qualcomm Institute, for this fantastic achievement and excellent teamwork,” said Steffanie Strathdee, PhD, Harold Simon Professor, Associate Dean of Global Health Sciences and chief of the Division of Global Public Health.

Ramesh Rao, PhD, director of the San Diego division of the Qualcomm Institute, holds the QUALCOMM Endowed Chair in Telecommunications and Information Technology. He is professor of electrical and computer engineering in the Jacobs School of Engineering at UC San Diego.

Said Garfein, “Working with Kevin and collaborating with the expert programmers at the Qualcomm Institute has been one of the highlights of my academic career.

“Although they are not included in the article because of the magazine’s information technology focus, we wouldn’t have been as successful if it weren’t for all the hard work by Jazmine Cuevas-Mota, Kelly Collins, and Fatima Muñoz in the Division of Global Public Health, and the dedicated employees of the San Diego County TB Control Program led by Dr. Kathleen Moser,” he said.

In the Division of Global Public Health, Cuevas-Mota is a project coordinator for Garfein, Collins is an assistant project coordinator and Muñoz is a postdoctoral fellow on the project.

“This has been a terrific project and it’s been a true pleasure to work with Richard and his team on it,” said Patrick.

“With a bit of luck, this could have world-wide impact on the health of the public. When all is said and done, this is why we are in this game.”

“This is very exciting and well deserved,” said Susan Taylor, PhD, UC San Diego professor of chemistry and biochemistry and pharmacology. She is a Howard Hughes Medical Institute investigator in biophysics and structural biology.

“It has been so much fun for me to watch these amazing things unfold and to realize how much we can achieve by working together and building bridges across the boundaries of our campus. This is much of what makes UCSD so special.

UC San Diego Health Sciences Video: VDOT Technology Eases Monitoring for Patients with Tuberculosis

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California’s First Robotically Assisted Coronary Stenting Procedure Performed at UC San Diego Sulpizio Cardiovascular Center

Technology Improves Accuracy of Device Placement and Patient Outcomes

The interventional cardiology team led by Ehtisham Mahmud, MD, FACC, at UC San Diego Sulpizio Cardiovascular Center (SCVC) has successfully completed the first two robotically-assisted coronary angioplasty/stent procedures in California. Patients with coronary artery disease (CAD) now have access to this new technology that puts the precision of a robot in the hands of interventional cardiologists during procedures to open clogged heart arteries. … 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

 

UC Medical Campus Consortium Named Designated Center to Translate Innovations into Improved Health

A consortium of the five University of California medical campuses at UC San Diego, UC Davis, UC Irvine, UCLA and UC San Francisco has been designated a Center for Accelerated Innovations by the National Heart, Lung and Blood Institute (NHLBI). The designation, among the first of its kind from NHLBI, recognizes the University of California’s potential to translate its leading-edge discoveries into innovative products that benefit patients. … Read the full story from the UCSD Newsroom


Dr. Gary FiresteinGary S. Firestein, MD, chair of the UC BRAID consortium that will oversee the new UC Center for Accelerated Innovations, is dean and associate vice chancellor of translational medicine at UC San Diego Health Sciences

He led UC San Diego’s successful effort to win a Clinical and Translational Science Award in 2010 and is the founding director of the UC San Diego Clinical and Translational Research Institute.

Firestein is professor of medicine and former chief of the Division of Rheumatology, Allergy & Immunology at UC San Diego. He served as division chief from 1998 until he stepped down in 2010 to devote full time to his activities as dean of translational medicine.

In 2011, philanthropists Lisa and Steve Altman made a major gift to the planned Clinical and Translational Research building on the La Jolla campus of UC San Diego Health System. Construction started in early 2013 and the building, named the Altman Clinical and Translational Research Institute, is scheduled to open in 2016.

UC San Diego Health System Video: The Altman Clinical and Translational Research Institute

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Progress: the UC San Diego – Universidade Eduardo Mondlane Medical Education Partnership Initiative

In this official video, Dr. Emilia Noormahomed describes the goals and progress of the UC San Diego—Universidade Eduardo Mondlane (UEM) Medical Education Partnership Initiative (MEPI) program in Mozambique.

Map of Africa showing location of MozambiqueEmilia Noormahomed, MD, PhD, is UEM principal investigator of the MEPI project, which is intended to strengthen Mozambique’s medical education system by building infrastructure to support medical training, research and technology.

Noormahomed is associate professor in the Parasitology Section, Department of Microbiology, at UEM and associate professor of medicine at UC San Diego.

In their partnership, UEM receives the bulk of the grant funding and UC San Diego provides partners and mentors to help UEM meet its goals.  |  More about UC San Diego’s role

The UC San Diego Internal Medicine Residency Training Program offers a global medicine elective in which residents rotate to the UEM’s Maputo Central Hospital in Mozambique for a four-week period.  |  More about the elective

MEPI is a joint initiative of the United States National Institutes of Health and the President’s Emergency Plan for AIDS Relief (PEPFAR).

More Information:

Internal Medicine Residency Training Program

Medical Education Partnership Initiative

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

UC San Diego Health System and Qualcomm Life Join Forces to Improve Care Remotely

2net™ Platform provides physicians with state-of-the-art patient monitoring platform

UC San Diego Health System is collaborating with Qualcomm Life, a wholly owned subsidiary of Qualcomm Technologies, Inc. to pilot the 2net Platform and Hub for remote patient monitoring. Qualcomm Life’s innovative 2net™ technology collects patients’ clinical information from wireless medical devices and transmits it to UC San Diego Health System physicians, to supplement information already available. This system provides a rapid, automated way to collect patient data in near real-time, analyze the readings, and suggest follow up actions with the patient, if needed.. … Read the full story from the UCSD Newsroom


Marlene Millen, MDQuoted in the UCSD Newsroom story is Marlene Millen, MD, clinical service chief of the Internal Medicine Group and medical director of the Internal Medicine Group Hillcrest for UC San Diego Health System.

Dr. Millen and Dr. Deanna Hill, both primary care physicians in the Fourth & Lewis Medical Offices, are overseeing the pilot project. With the help of the clinic’s nurse case manager, they are reviewing the real-time data online and providing medical follow up with patients if needed.

While this is just a pilot project at present, Drs. Millen and Hill are hopeful that such monitoring will become a reality in patient care in the future.

Dr. Millen, pictured above left, is associate clinical professor in the Division of General Internal Medicine. She trained in internal medicine here at UCSD and was chief medical resident in 2004-2005.

In 2012, Dr. Millen was named on the “San Diego’s Top Doctors” list for the third straight year.

Dr. Deanna HillDr. Hill (left), a new member of the UC San Diego Health System faculty, is assistant clinical professor in the Division of General Internal Medicine. She is accepting new patients.

After her internship and residency training in internal medicine at UCLA, she spent two years at Yale-New Haven Hospital’s Primary Care Center before coming to UCSD.