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.

UC San Diego Part of New Effort to Fight Autoimmune Disorders

Major multi-year partnership will focus first on rheumatoid arthritis and lupus

The Division of Rheumatology, Allergy and Immunology at University of California, San Diego School of Medicine has been named a key site in a national, multi-institution, multi-year $41.6 million program to speed drug discovery, development, diagnostics and therapies for patients with autoimmune disorders, primarily rheumatoid arthritis (RA) and lupus erythematosus, which affect millions of Americans. …Read the full story from the UC San Diego Newsroom

Molecular Tumor Board Helps in Advanced Cancer Cases

With accelerating development of personalized cancer treatments matched to a patient’s DNA sequencing, proponents say frontline physicians increasingly need help to maneuver through the complex genomic landscape to find the most effective, individualized therapy.

In a paper published in the May 5 online issue of The Oncologist, researchers at the University of California, San Diego School of Medicine and Moores Cancer Center detail their experience evaluating 34 patients between December 2012 and June 2013 using a molecular tumor board – a new type of advisory group comprised of multidisciplinary experts, including those in the fields of tumor genetics, basic science and bioinformatics. … Read the full story from the UC San Diego Newsroom

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

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.

Schizophrenia Gene Mutation Found; Target for New Drugs

In a major advance for schizophrenia research, an international team of scientists, led by Jonathan Sebat, PhD, assistant professor of psychiatry and cellular and molecular medicine at the University of California, San Diego School of Medicine, has identified a gene mutation strongly linked to the brain disorder – and a signaling pathway that may be treatable with existing compounds. … Read the full story from the UCSD Newsroom

One of the co-authors of the study report is Marie Dell’Aquila, Ph.D., Clinical Professor of Medicine in the Division of Medical Genetics and Director of the Cytogenetics Laboratory for the UC San Diego Health System.

In the Media: Dr. Ajit Varki

Dr. Ajit Varki is one of a team of researchers whose recent study is described in the Wired article, “Rare Gene Glitch a Clue to Genomics Mystery.”

Ajit Varki, M.D., is Professor of Medicine in the Division of Hematology-Oncology and Professor in the Department of Cellular and Molecular Medicine. He co-directs the UC San Diego Glycobiology Research and Training Center and the UC San Diego/Salk Center for Academic Research and Training in Anthropogeny (CARTA). He is Associate Dean of the Physician-Scientist Training Program.