The National Science Foundation has awarded Graduate Research Fellowships to Ph.D. students Gabriel Pratt and Kunal Bhutani in the Bioinformatics Graduate Program.
News
February 14, 2013
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.
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.
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.
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.
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.
Upcoming Events
Wednesday, May 29th
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Ph.D. Defense: Marcus Kinsella
- Start time: 10:00am
- End date: Thursday, May 30th
- End time: 12:00pm
- Where: Fung Auditorium, PFBH
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Description:
UCSD Bioinformatics and Systems Biology Graduate Program
Ph.D. Dissertation Defense AnnouncementMarcus Kinsella
"Computational Tools to Investigate Structural Variation"
Wednesday, May 29, 2013
10:00 AM
Location: Fung Auditorium
Powell-Focht Bioengineering Hall
Dissertation Committee:
Chair: Vineet Bafna
Co-Chair: Kelly A. FrazerAbstract:
The importance of structural variation as a source of phenotypic variation has become more and more apparent in recent years. At the same time, tools and techniques that detect structural variation using high-throughput data have proliferated. These trends have spurred interest in making increasingly sophisticated inferences about structural variation, including identifying complex or difficult to observe variants and elucidating the biological mechanisms that produce structural variants.In this talk, we identify several challenging problems in the investigation of structural variation and discuss computational techniques that solve them. First, we examine the discovery of fusion genes in the transcriptome using paired-end reads, a task complicated by reads that have multiple mappings. We demonstrate a method to resolve these ambiguous mappings and increase the sensitivity of fusion gene detection. Second, we investigate whether the breakage-fusion-bridge mechanism leaves a reliable footprint in high-throughput data. Using novel algorithms and simulation, we identify the surprisingly limited circumstances when the presence breakage-fusion-bridge can be inferred. Finally, we examine evidence for the phenomenon known as chromothripsis, the shattering and reannealing of chromosomes. We show that there are alternative hypotheses that can account for the structural variation patterns that form the currently proposed signature of chromothripsis.
Student Publications
Transcriptional architecture of the primate neocortex. Neuron. 2012;73(6):1083-99.
Library-free methylation sequencing with bisulfite padlock probes. Nat Methods. 2012;9(3):270-2.
SEQuel: improving the accuracy of genome assemblies. Bioinformatics. 2012;28(12):i188-96.
PMC
A sensing array of radically coupled genetic 'biopixels'. Nature. 2012;481(7379):39-44.
PMC
The metabolome of induced pluripotent stem cells reveals metabolic changes occurring in somatic cell reprogramming. Cell Res. 2012;22(1):168-77.
PMC
Deciphering the transcriptional regulatory logic of amino acid metabolism. Nat Chem Biol. 2012;8(1):65-71.
Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins. Cell Rep. 2012;1(2):167-178.
PMC
Control of RelB during dendritic cell activation integrates canonical and noncanonical NF-κB pathways. Nat Immunol. 2012;13(12):1162-70.
