New Bioinformatic Analysis Reveals Role of Proteins in Diabetic Kidney Disease

MDM2 emerges as key; Software could expose metabolomic information of other diseases —

A new bioinformatic framework developed by researchers at University of California San Diego School of Medicine has identified key proteins significantly altered at the gene-expression level in biopsied tissue from patients with diabetic kidney disease, a result that may reveal new therapeutic targets. … Read the Full Story from the UC San Diego Newsroom


Kumar Sharma, MD, FAHADr. Kumar Sharma is lead investigator of the team that published the study report in JCI Insights.Kumar Sharma, MD, is Professor of Medicine in the Division of Nephrology and Hypertension.

He directs the Institute for Metabolomic Medicine and the Center for Renal Translational Medicine at UC San Diego School of Medicine.

Study Report (full text UC San Diego only)

What Makes A Bacterial Species Able to Cause Human Disease?

Global effort produces first cross-species genomic analysis of Leptospira, a bacterium that can cause disease – and death – in targeted mammals, including humans —

An international team of scientists, led by researchers at University of California, San Diego School of Medicine and the J. Craig Venter Institute (JCVI), have created the first comprehensive, cross-species genomic comparison of all 20 known species of Leptospira, a bacterial genus that can cause disease and death in livestock and other domesticated mammals, wildlife and humans. … Read the Full Story from the UC San Diego Newsroom


Dr. Joseph Vinetz

Dr. Joseph Vinetz

Joseph M. Vinetz, MD, senior author of the study, is Professor of Medicine in the Division of Infectious Diseases and Director of the UC San Diego Center for Tropical Medicine and Travelers Health.

Fellow UC San Diego Division of Infectious Diseases faculty members Michael A. Matthias, PhD, and Douglas E. Berg, PhD, are the other Department of Medicine investigators in the international multi-center leptospirosis project. Dr. Berg is Professor of Medicine and Professor of Genetics, and Dr. Matthias is Assistant Professor of Medicine.

Dr. Vinetz conducts his research in tropical infectious disease in laboratories at UC San Diego and at Instituto de Medicina “Alexander von Humboldt,” Universidad Peruana Cayetano Heredia in Lima, Peru.  He focuses his work on malaria and leptospirosis.

Read the article in PLOS Neglected Tropical Diseases (Open Access)

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.

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