Four Department of Medicine Faculty Members Are on 2015 Thomson Reuters Highly Cited Researchers List

Dr. William Sandborn

William Sandborn, MD

Four UC San Diego Department of Medicine researchers are among the most influential researchers in the world, according to the 2015 Thomson Reuters Highly Cited Researchers list.

They are , William Sandborn, MDDon W. Cleveland, PhD, Lewis J. Rubin, MD, and Sergei L. Kosakovsky Pond, PhD.

Dr. Don W. Cleveland

Don W. Cleveland, PhD

Dr. Sandborn is Professor and Chief of the Division of Gastroenterology & Hepatology.

Dr. Cleveland is Chair of the Department of Cellular and Molecular Medicine and Distinguished Professor of Medicine, Cellular and Molecular Medicine, and Neurosciences.

Sergei L. Kosakovsky Pond, PhD

Sergei L. Kosakovsky Pond, PhD

Dr. Pond, Associate Professor of Medicine, is a specialist in infectious disease with a focus on developing software models of evolving pathogens such as HIV and hepatitis C virus.

Dr. Rubin, whose research addresses pulmonary vascular disease and pulmonary arterial hypertension, is Professor of Medicine, Emeritus, in the Division of Pulmonary, Critical Care & Sleep Medicine.

Lewis Rubin, MD

Lewis Rubin, MD

With 165 faculty members on the latest edition of the list, the UC System ranks first in the world on the list of highly cited researchers.

Each year, Thomson Reuters uses citation analysis to identify the world’s most influential contemporary scientists. The 2015 list, encompassing publications from 2003 to 2013, contains more than 3,100 names.

More on the UC System’s achievement from the UC Office of the President

See the names of all UC System faculty members on the list

More about the list and the methodology from Thomson Reuters

View a searchable database of the researchers

Jill P. Mesirov Appointed Associate Vice Chancellor for Computational Health Sciences

UC San Diego School of Medicine recruits world leader in computational biology —

Leading computational biologist Jill P. Mesirov, PhD, has been appointed associate vice chancellor for computational health sciences and professor of medicine at University of California, San Diego School of Medicine and Moores Cancer Center. Mesirov most recently served as associate director and chief informatics officer at the Broad Institute of MIT and Harvard, where she directed the Computational Biology and Bioinformatics Program. … Read the full story from the UC San Diego Newsroom


Dr. Mesirov joins the Department of Medicine as a professor in the Division of Medical Genetics.

Clinical Trial Launched to Assess Safety and Efficacy of Autism Drug Treatment

UC San Diego researchers open first study of suramin in children with autism —

Researchers at the University of California, San Diego School of Medicine have launched a clinical trial to investigate the safety and efficacy of an unprecedented drug therapy for autism.

The phase 1 clinical trial, which is recruiting 20 qualifying participants, will evaluate suramin – a century-old drug still used for African sleeping sickness – as a novel treatment for children with a diagnosis of Autism Spectrum Disorder (ASD). Previous published research by Robert K. Naviaux, MD, PhD, professor of medicine, pediatrics and pathology at UC San Diego School of Medicine, and colleagues reported that a single injection of suramin reversed symptoms of ASD in mouse models. …Read the full story from the UC San Diego Newsroom


Robert Naviaux, MD, PhD, is professor of medicine in the Division of Medical Genetics and professor in the departments of pediatrics and pathology.

He co-directs the Mitochondrial and Metabolic Disease Center at UC San Diego.

More about research in the Naviaux laboratory

Clinical Trial Launched to Assess Safety and Efficacy of Autism Drug Treatment

UC San Diego researchers open first study of suramin in children with autism —

Researchers at the University of California, San Diego School of Medicine have launched a clinical trial to investigate the safety and efficacy of an unprecedented drug therapy for autism.

The phase 1 clinical trial, which is recruiting 20 qualifying participants, will evaluate suramin – a century-old drug still used for African sleeping sickness – as a novel treatment for children with a diagnosis of Autism Spectrum Disorder (ASD). Previous published research by Robert K. Naviaux, MD, PhD, professor of medicine, pediatrics and pathology at UC San Diego School of Medicine, and colleagues reported that a single injection of suramin reversed symptoms of ASD in mouse models. …Read the full story from the UC San Diego Newsroom


Senior author Robert K. Naviaux, MD, PhD, is professor of medicine in the Division of Medical Genetics. He co-directs the Mitochondrial and Metabolic Disease Center at UC San Diego.

Visit the Naviaux Laboratory website

UC San Diego, UC San Francisco Launch New Cancer Cell Mapping Initiative

Researchers from the University of California, San Diego School of Medicine and University of California, San Francisco, with support from a diverse team of collaborators, have launched an ambitious new project – dubbed the Cancer Cell Map Initiative or CCMI – to determine how all of the components of a cancer cell interact.

“We’re going to draw the complete wiring diagram of a cancer cell,” said Nevan Krogan, PhD, director of the UC San Francisco division of QB3, a life science research institute and accelerator, an investigator at Gladstone Institutes and co-director of CCMI with Trey Ideker, PhD, chief of medical genetics in the UC San Diego Department of Medicine and founder of the UC San Diego Center for Computational Biology & Bioinformatics. … Read the full story from the UC San Diego Newsroom

 


Trey Ideker, PhD

Trey Ideker, PhD

Trey Ideker, PhD, is professor of bioengineering and professor of medicine in the Division of Medical Genetics. He was recently named a fellow of the American Association for the Advancement of Science (AAAS).

Dr. Ideker’s Laboratory Website

Dr. Trey Ideker Named AAAS Fellow

Trey Ideker, PhD

Trey Ideker, PhD

Trey Ideker, PhD, professor of medicine in the Division of Medical Genetics and professor of bioengineering, is one of three UC San Diego faculty members to be named Fellow of the American Association for the Advancement of Science (AAAS) this year. …Read the full story from the UC San Diego Newsroom.

 

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

 

“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)

More Information:

Potential Nutritional Therapy for Childhood Neurodegenerative Disease

Researchers at the University of California, San Diego School of Medicine have identified the gene mutation responsible for a particularly severe form of pontocerebellar hypoplasia, a currently incurable neurodegenerative disease affecting children. Based on results in cultured cells, they are hopeful that a nutritional supplement may one day be able to prevent or reverse the condition…. Read the full story from the UCSD Newsroom


Robert K. Naviaux, MD, PhD, is a coauthor of the study. He is professor of medicine in the Division of Medical Genetics and professor in the departments of pediatrics and pathology.

Naviaux leads a medical genetics research laboratory whose two major areas of study are the mitochondrial mechanisms of disease and development and evolutionary systems biology and marine metagenomics. He is founder and co-director of the UC San Diego Mitochondrial and Metabolic Disease Center.

Citation for the report:  Naiara Akizu, Vincent Cantagrel, Jana Schroth, Na Cai, Keith Vaux, Douglas McCloskey, Robert K. Naviaux, Jeremy Van Vleet, Ali G. Fenstermaker, Jennifer L. Silhavy, Judith S. Scheliga, Keiko Toyama, Hiroko Morisaki, Fatma M. Sonmez, Figen Celep, Azza Oraby, Maha S. Zaki, Raidah Al-Baradie, Eissa A. Faqeih, Mohammed A.M. Saleh, Emily Spencer, Rasim Ozgur Rosti, Eric Scott, Elizabeth Nickerson, Stacey Gabriel, Takayuki Morisaki, Edward W. Holmes, Joseph G. Gleeson. AMPD2 Regulates GTP Synthesis and Is Mutated in a Potentially Treatable Neurodegenerative Brainstem Disorder. Cell, Volume 154, Issue 3, 1 August 2013, Pages 505–517 http://dx.doi.org/10.1016/j.cell.2013.07.005  Read the report

Related Stories:

Drug Treatment Corrects Autism Symptoms in Mouse Model – March 14, 2013

$5.9 Million Grant to UC San Diego for Paradigm-Shifting Diabetes Research – October 3, 2011

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