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News Releases from 2016

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Big data for chemistry: new method helps identify antibiotics in mass spectrometry datasets

An international team of computer scientists has for the first time developed a method to find antibiotics hidden in huge but still unexplored mass spectrometry datasets. They detailed their new method, called DEREPLICATOR, in the Oct. 31 issue of Nature Chemical Biology.   Full Story

What Molecules You Leave on Your Phone Reveal About Your Lifestyle

We leave behind trace chemicals, molecules and microbes on every object we touch. By sampling the molecules on cell phones, UC San Diego researchers constructed lifestyle sketches for each phone’s owner, including diet, preferred hygiene products, health status and locations visited. This proof-of-concept study could have a number of applications, including environmental exposure studies, medication adherence monitoring, clinical trial participant stratification, criminal profiling and airport screening. Full Story

Dog Poop Microbiome Predicts Canine Inflammatory Bowel Disease

Our gut microbiomes — the varieties of microbes living in our digestive tracts — may play a role in inflammatory bowel disease (IBD). UC San Diego researchers analyzed microbiome information in fecal samples from dogs to predict which dogs had IBD and which did not. This is part of a larger research effort on campus to improve human health, at the level of individuals and communities, through microbiome science.   Full Story

Crowdsourcing the Transformation of Mass Spectrometry Big Data into Scientific Living Data

In a landmark paper published in the August issue of Nature Biotechnology, 127 scientists from a consortium of universities and research labs in the U.S. and worldwide report for the first time on the establishment of an online, crowdsourced knowledge base and workbench that could be a game-changer for the study of natural products that could potentially be useful in the development of the next antibiotic, better pesticides, or more effective cancer drugs. Full Story

Machine Learning Method Differentiates Between Healthy Male, Female Microbiomes

The week-long International Conference on Machine Learning (ICML) ended June 24, and the last day included the 2016 ICML Workshop on Computational Biology.  CSE professors Larry Smarr and Rob Knight as well as Qualcomm Institute data scientist Mehrdad Yazdani were represented in a poster presentation and paper on “Using Topological Data Analysis to find discrimination between microbial states in human microbiome data.” Borrowing a statistical method originally from topology, the co-authors applied Topological Data Analysis (TDA) as an “unsupervised learning and data exploration tool to identify changes in microbial states.” Full Story

Bioengineering professor Bernhard Palsson receives 2016 International Metabolic Engineering Award

Bernhard Palsson, Galletti Professor of Bioengineering and Professor of Pediatrics at the University of California, San Diego, has been named the recipient of the 2016 International Metabolic Engineering Award. The award, presented every two years by the International Metabolic Engineering Society (IMES), recognizes an outstanding career contributor to the field of metabolic engineering. Palsson is being honored for developing genome-scale metabolic modeling and simulation strategies for better understanding large metabolic and gene regulatory networks and for demonstrating application methods. The Metabolic Engineering Award and an associated lecture by Palsson will be presented on June 29, 2016 at the IMES-sponsored Metabolic Engineering 11 conference, which will take place June 26–30 in Awaji Island, Japan. Full Story

American Gut Project Expands to Asia

University of California San Diego School of Medicine researchers are expanding the American Gut Project into Asia. The goal of American Gut, the world’s largest crowdfunded citizen science project, is to sequence as many human microbiomes — the unique collection of bacteria and other microbes that live in and on us — as possible.American Gut Project participants are “citizen scientists.” They learn how many of which types of bacteria inhabit their bodies, and in doing so also contribute valuable data to researchers around the world who want to know how microbiomes influence human and environmental health. Full Story

No. 1 From the Start

Bioengineers at the University of California San Diego have helped us understand why atherosclerosis develops and how it is impacted by blood flow. They have pioneered the development of very thin, small and flexible sensors that stick to the skin and monitor vital signs, such as the brain activity of a newborn. They also developed injectable hydrogels that can help muscle tissues heal after a heart attack. Researchers celebrated their achievements over the past five decades and looked to the future during a three-day 50th anniversary celebration May 19 to 21. Full Story

Bioengineering: Research landmarks

The faculty of the UC San Diego bioengineering department boast a number of achievements in a wide range of fields, gravitating around diagnostic tools and treatment and prevention, genomics, and regenerative medicine.  Full Story

UC San Diego to Participate in White House's National Microbiome Initiative

On May 13, the White House Office of Science and Technology Policy (OSTP) announced a new National Microbiome Initiative, a coordinated effort to better understand microbiomes and to develop tools to protect and restore healthy microbiome function. UC San Diego is a leader in microbiome science. The Jacobs School of Engineering runs the Center for Microbiome Innovation.  Full Story

Fermentation Festival Leads to Rapid Response System at UC San Diego Center for Microbiome Innovation

The personalized collections of microorganisms and molecules found in, on and around us — known as our microbiome and metabolome, respectively — are increasingly recognized for their influences on everything from allergies to obesity. While advances in genetic sequencing and computing power have made it easier to map the minutiae of our bodies and environments, these types of studies typically take months or years — too long for that data to be medically useful. Researchers at the University of California San Diego Center for Microbiome Innovation used a study with the 2016 San Diego Fermentation Festival as a test case for a first-of-its-kind rapid response system. In the study, published April 26 in mSystems, the team collected human and environmental samples, analyzed microbiome and metabolome data, and reported conclusions in an unprecedented 48 hours. Full Story

In an effort to understand microbial communities, a UC San Diego biology professor has turned cheese into her 'lab rat'

UC San Diego professor of Biological Sciences Rachel Dutton examines the communities of bacteria and fungi that produce different kinds of hand-crafted artisanal cheese in order to better understand how microbial communities form and work together. Full Story

UC San Diego Scientists Receive $9.5 Million NIH Grant to Combat Antibiotic Resistance

Physicians and bioengineers at University of California, San Diego, have received a five-year, $9.5-million award from the National Institute of Allergy and Infectious Diseases at the National Institutes of Health (NIH) to establish an interdisciplinary center to define the systems biology of antibiotic resistance. The program will be led by Bernhard Palsson, Distinguished Professor of Bioengineering and Pediatrics, and Dr. Victor Nizet, professor of pediatrics and pharmacy at UC San Diego.  Full Story

New Research Centers and 200+ Graduate Student Posters to be Highlighted at Research Expo 2016

Advances coming out of new industry-focused research centers at the University of California, San Diego Jacobs School of Engineering will be highlighted in faculty talks and in some of the more than 200+ graduate student posters that will be presented on April 14, 2016 at Research Expo. Full Story

A new method to dramatically improve the sequencing of metagenomes

An international team of computer scientists developed a method that greatly improves researchers’ ability to sequence the DNA of organisms that can’t be cultured in the lab, such as microbes living in the human gut or bacteria living in the depths of the ocean.  They published their work in the Feb. 1 issue of Nature Methods.  Full Story

Vaginal Microbes Can be Partially Restored to C-Section Babies

In a small pilot study, UC San Diego and Icahn School of Medicine at Mount Sinai researchers determined that a simple swab to transfer vaginal microbes from a mother to her C-section-delivered newborn can alter the baby's microbial makeup (microbiome) in a way that more closely resembles the microbiome of a vaginally delivered baby.  Full Story

Jacobs School Researchers Cited Among 'World's Most Influential Scientific Minds'

Four researchers at the Jacobs School of Engineering at UC San Diego were included on the 2015 listing of “The World’s Most Influential Scientific Minds,” an annual compendium of “Highly Cited Researchers” by Thomson Reuters, a multinational mass media and information company. Full Story

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