Livermore, CA - February 14, 2013 - The Fannie and John Hertz Foundation announces its finalists for the 2013-2014 Hertz Fellowship. From among more than 700 applicants, 50 are chosen as finalists to receive the Hertz Fellowship. The new Fellows will be announced by April 1st. Considered to be the Nation’s most generous support for graduate education in the applied physical, biological and engineering sciences, the Hertz Fellowship has been awarded to over 1100 individuals. Valued at more than a quarter million dollars per student, this support lasts for up to five years.
Department News
February 10, 2013
Learning Natural Selection from the Site Frequency Spectrum.
Roy Ronen, Nitin Udpa, Eran Halperin, and Vineet Bafna.
Abstract: Genetic adaptation to external stimuli occurs through the combined action of mutation and selection. A central problem in genetics is to identify loci responsive to specific selective constraints. Over the last two decades, many tests have been proposed to identify genomic signatures of natural selection. However, the power of these tests changes unpredictably from one dataset to another, with no single dominant method. We build upon recent work that connects many of these tests in a common framework, by describing how positive selection strongly impacts the observed site frequency spectrum (SFS). Many of the proposed tests quantify the skew in SFS to predict selection. Here, we show that the skew depends on many parameters, including the selection coefficient, and time since selection. Moreover, for each of the different regimes of positive selection, informative features of the scaled SFS can be learned from simulated data and applied to population-scale variation data. Using support vector machines, we develop a test that is effective over all selection regimes. On simulated data, our test outperforms existing ones over the entire parameter space. We apply our test to variation data from Drosophila melanogaster populations adapted to hypoxia, and identify loci that were missed by previous approaches, strengthening the role of the Notch pathway in hypoxia tolerance. We further apply our test to human variation data, and identify several regions that are in agreement with earlier studies, as well as many novel regions.
UCSD coauthors are Bioinformatics and Systems Biology graduate students Roy Ronen and Nitin Udpa, and Prof. Vineet Bafna.
September 4, 2012
A study led by researchers at the UC San Diego Stem Cell Research program and funded by the California Institute for Regenerative Medicine (CIRM) looks at an important RNA binding protein called LIN28, which is implicated in pluripotency and reprogramming as well as in cancer and other diseases. According to the researchers, their study – published in the September 6 online issue of Molecular Cell – will change how scientists view this protein and its impact on human disease.
Studying embryonic stem cells and somatic cells stably expressing LIN28, the researchers defined discrete binding sites of LIN28 in 25 percent of human transcripts. In addition, splicing-sensitive microarrays demonstrated that LIN28 expression causes widespread downstream alternative splicing changes – variations in gene products that can result in cancer or other diseases.
Bioinformatics and Systems Biology Graduate Program coauthors are Ph.D. candidate Stephanie Huelga, alumnus Kasey R. Hutt, and Prof. Gene Yeo.
May 1, 2012
The National Academy of Sciences today elected three professors at the University of California, San Diego to membership in the prestigious National Academy of Sciences, one of the highest honors bestowed on U.S. scientists and engineers. Roberto Malinow, Ruth Williams and William Young were among the 84 new members and 21 foreign associates elected to the academy today “in recognition of their distinguished and continuing achievements in original research.” Ruth Williams, a professor in the Department of Mathematics, is a member of the Graduate Program in Bioinformatics and Systems Biology.
U.S.-Russian Collaboration Develops New Method for Sequencing Dark Matter of Life from a Single Cell
August 9, 2012
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. Ultimately, the researchers hope to apply this algorithm to cancer cells to monitor early stages of the disease when normal cells first turn into malignant ones. Pevzner and colleagues published their findings in the May issue of the Journal of Computational Biology.
September 19, 2011
Researchers have developed a new method to sequence and analyze the dark matter of life—the genomes of thousands of bacteria species previously beyond scientists’ reach, from microorganisms that produce antibiotics and biofuels to microbes living in the human body.
Scientists from UC San Diego, the J. Craig Venter Institute and Illumina Inc., published their findings in the Sept. 18 online issue of the journal Nature Biotechnology. The breakthrough will enable researchers to assemble virtually complete genomes from DNA extracted from a single bacterial cell. By contrast, traditional sequencing methods require at least a billion identical cells, grown in cultures in the lab. The study opens the door to the sequencing of bacteria that cannot be cultured—the lion’s share of bacterial species living on the planet.
The UC San Diego coauthors are computer science postdoctoral researcher Hamidreza Chitsaz; mathematics professor Glenn Tesler; and computer science professor Pavel Pevzner.
August 7, 2012
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.
In addition to serving as a platform for investigating fundamental biological questions, this technology enables far more detailed calculations of the total cost of synthesizing many different chemicals, including biofuels. Their method accounts, in molecular detail, for the material and energy required to keep a cell growing, the research team reported in the journal Nature Communications.
“With this new method, it is now possible to perform computer simulations of systems-level molecular biology to formulate questions about fundamental life processes, the cellular impacts of genetic manipulation or to quantitatively analyze gene expression data,” said Joshua Lerman, a Ph.D. candidate in Bernhard Palsson’s Systems Biology Research Group.
October 15, 2012
The Program and everyone who knew him was saddened today by the news of the passing of Professor Virgil Woods, an innovator of mass spectrometry and structural bioinformatics, and an engaging colleague, advisor and committee member to several of the Program students.
May 13, 2011
The National Academy of Sciences today elected three professors at the University of California, San Diego to membership in the National Academy of Sciences, one of the highest honors bestowed on U.S. scientists and engineers.
Andrew McCammon, the Joseph E. Mayer Chair of Theoretical Chemistry, Howard Hughes Medical Institute investigator and distinguished professor of chemistry and biochemistry, and pharmacology, and faculty in the Bioinformatics and Systems Biology Graduate Program, has invented theoretical methods for accurately predicting and interpreting how molecules interact with one another, methods that play a growing role in the design of new drugs and other materials.
December 22, 2011
In eukaryotes – the group of organisms that include humans – a key to survival is the ability of certain proteins to quickly and accurately repair genetic errors that occur when DNA is replicated to make new cells.
In a paper published in the December 23, 2011 issue of the journal Science, researchers at the Ludwig Institute for Cancer Research and the University of California, San Diego School of Medicine have solved part of the mystery of how these proteins do their job, a process called DNA mismatch repair (MMR).
Using Saccharomyces cerevisiae, or baker’s yeast, as their model organism, the researchers, led by Richard D. Kolodner, PhD, Ludwig Institute investigator and UCSD professor of medicine and cellular and molecular medicine, discovered that newly replicated DNA produces a temporary signal for 10 to 15 minutes after replication which helps identify it as new – and thus a potential subject for MMR.