UC San Diego Center for Microbiome Innovation names Dr. Andrew Bartko, a veteran research leader from Battelle Memorial Institute, as its new Executive Director. Bartko embarks on new role as founding executive director Dr. Sandrine Miller-Montgomery departs to lead Micronoma, a San Diego-based startup spawned out of the Center.
Researchers at the University of California San Diego have been applying their high-performance computing expertise by porting the popular UniFrac microbiome tool to graphic processing units (GPUs) in a bid to increase the acceleration and accuracy of scientific discovery, including urgently needed COVID-19 research.
“Our initial results exceeded our most optimistic expectations,” said Igor Sfiligoi, lead scientific software developer for high-throughput computing at the San Diego Supercomputer Center (SDSC) at UC San Diego. “As a test we selected a computational challenge that we previously measured as requiring some 900 hours of time using server class CPUs, or about 13,000 CPU core hours. We found that it could be finished in just 8 hours on a single NVIDIA Tesla V100 GPU, or about 30 minutes if using 16 GPUs, which could reduce analysis runtimes by several orders of magnitude. A workstation-class NVIDIA RTX 2080TI would finish it in about 12 hours.”
The University of California San Diego and IBM are building on the existing AI for Healthy Living (AIHL) collaboration in order to help tackle the COVID-19 pandemic. AI for Healthy Living is a multi-year partnership leveraging a unique, pre-existing cohort of adults in a senior living facility to study healthy aging and the human microbiome as part of IBM's AI Horizons Network of university partners.
The Microsetta Initiative, a crowdsourced research effort based at the University of California San Diego School of Medicine, has expanded its capabilities to now allow citizen-scientists around the world to help collect crucial information about SARS-CoV-2, the novel coronavirus causing a COVID-19 pandemic.
“We are now positioned to collect data that will help drive epidemiological studies of where the virus is and isn’t, and help researchers determine who is at greatest risk, who is already immune, how the virus is transmitted and how it spreads through a population,” said Rob Knight, professor and director of the Center for Microbiome Innovation and co-founder of The Microsetta Initiative, which is run by his research lab at UC San Diego School of Medicine under Scientific Director Daniel McDonald.
In a new paper published in mSystems, researchers at the University of California San Diego in partnership with Danone Nutricia Research have found that the gut microbiome of people who regularly consume fermented foods is associated with certain microbes derived directly from these foods, and their microbiomes are subtly yet significantly different from the gut microbiome of those not eating fermented food.
Unlock The Secrets Of Your Gut! New Research Project Offers 800 Participants Opportunity To Map Their Gut Health Free Of Charge.
The Microsetta Initiative, a research project led by a team at the University of California, San Diego in partnership with Danone Nutricia Research — the research and innovation division of Danone North America's global parent company, Danone S.A. — is recruiting hundreds of U.S. citizen scientists to map their gut microbiome. Participants in the program will have the opportunity to get their microbiome sequenced, at no personal charge, and will receive a free report. This is the first phase of an unprecedented program to map the gut microbiome of people around the world.
A widespread, fast-growing plant called Chlamydomonas reinhardtii is famous in scientific laboratories due to its position as the world’s most exhaustively studied algae. Researchers at the University of California San Diego recently completed the first study examining the effects of consuming C. reinhardtii and demonstrated that the algae improves human gastrointestinal issues associated with irritable bowel syndrome (IBS) such as diarrhea, gas and bloating. Results of the project are published in the Journal of Functional Foods.
Scientists at the University of California San Diego have reported in the latest publication of Nature Biotechnology on a new type of tool to easily search for mass spectrometry (MS) data instead. This new web-enabled small-molecule MS search engine, called MASST - short for Mass Spectrometry Search Tool, is a starting point for enabling data-driven discovery of mass spectrometry data in the public domain and enables the reuse of public data and its related knowledge.
A paper in Cell Systems by leading co-authors Dr. Pavel Pevzner and his graduate student, Bahar Behsaz, alongside collaborators from around the world, presents the new CycloNovo algorithm that identifies cyclopeptide spectra in a haystack of all peptides (a vast majority of peptides are linear) and decodes them by analyzing large MS datasets.
To further increase the understanding of the microbiome’s impact on human health and to accelerate the development of innovative nutritional solutions promoting health and wellbeing, Nestlé has entered into a partnership with the University of California San Diego Center for Microbiome Innovation (CMI).