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.

Lower Vitamin D Level in Blood Linked to Higher Premature Death Rate

Researchers at the University of California, San Diego School of Medicine have found that persons with lower blood levels of vitamin D were twice as likely to die prematurely as people with higher blood levels of vitamin D. … Read the full story from the UC San Diego Newsroom

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:

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.

Powerful Approach to the Analysis of Protein Motions

DXMS analysis provides novel tool for studying how movements allow proteins to perform their functions as molecular machines

Researchers at the University of California, San Diego School of Medicine and the University of Texas Medical Branch (UTMB) in Galveston have concluded a study that offers a new understanding of the role that motions, or dynamics, play in the functioning of the protein Epac2. Their work provides information likely to help scientists design drugs to battle major diseases in which Epac2 plays a role, such as diabetes and cancer. … Read the full story from the UCSD Newsroom

Virgil L. Woods, Jr., MD

The study’s UC San Diego principal investigator is Virgil L. Woods, Jr., MD, Professor of Medicine in the Division of Rheumatology, Allergy and Immunology (pictured). First author Sheng Li, PhD, is chief scientist in the UCSD DXMS Proteomics Resource.