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U.S.-Russian Collaboration Develops New Method for Sequencing Dark Matter of Life from a Single Cell

An international team of researchers led by computer scientist Pavel Pevzner, from the University of California, San Diego, have developed a new algorithm to sequence organisms’ genomes from a single cell faster and more accurately. The new algorithm, called SPAdes, can be used to sequence bacteria that can’t be submitted to standard cloning techniques—what researchers refer to as the dark matter of life, from pathogens found in hospitals, to bacteria living deep in ocean or in the human gut.

UC San Diego, Yale Awarded Collaborative NSF Grant for Neuroscience Gateway

The University of California, at San Diego and Yale University have been awarded a collaborative grant by the National Science Foundation (NSF) to develop a Neuroscience Gateway (NSG) that gives neuroscientists broadened access to essential high-performance computing (HPC) and storage resources.

Patterns in Adolescent Brains Could Predict Heavy Alcohol Use

Heavy drinking is known to affect an adolescents’ developing brain, but certain patterns of brain activity may also help predict which teens are at risk of becoming problem drinkers, according to a study by researchers in the University of California, San Diego School of Medicine and VA San Diego Healthcare System. Their results will be published in the September issue of the Journal of Studies on Alcohol and Drugs, online August 8.

Molecular economics: New computer models calculate systems-wide costs of gene expression

Bioengineers at the University of California, San Diego have developed a method of modeling, simultaneously, an organism’s metabolism and its underlying gene expression. In the emerging field of systems biology, scientists model cellular behavior in order to understand how processes such as metabolism and gene expression relate to one another and bring about certain characteristics in the larger organism.

New Drug Successfully Halts Fibrosis in Animal Model of Liver Disease

A study published in the online journal Hepatology reports a potential new NADPH oxidase (NOX) inhibitor therapy for liver fibrosis, a scarring process associated with chronic liver disease that can lead to loss of liver function.

UC San Diego Team Aims to Broaden Researcher Access to Protein Simulation

Using just an upgraded desktop computer equipped with a relatively inexpensive graphics processing card, a team of computer scientists and biochemists at the University of California, San Diego, has developed advanced GPU accelerated software and demonstrated for the first time that this approach can sample biological events that occur on the millisecond timescale.