Department News

NSF Graduate Research Fellowships awarded to Gabriel Pratt and Kunal Bhutani

May 8, 2013

The National Science Foundation has awarded Graduate Research Fellowships to Ph.D. students Gabriel Pratt and Kunal Bhutani in the Bioinformatics Graduate Program.

Paul G. Allen Family Foundation Awards $1.6 Million to Young Investigator Suckjoon Jun

March 7, 2013

One of the newest faculty members at UC San Diego—Suckjoon Jun, an assistant professor of physics and molecular biology—has won a $1.6 million award from the Paul G. Allen Family Foundation. This is the first award given to a UC San Diego recipient from the foundation, which was established by the co-founder of Microsoft to support high-risk, high-reward ideas in science. Jun’s effort is one of five awards announced by the foundation last week to projects “that aim to unlock key questions in the areas of cellular decision making and modeling dynamic biological systems.”

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Olga Botvinnik: Finalist for Hertz Foundation Fellowship

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.

Paper accepted to be presented at RECOMB 2013 (Beijing)

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.

In Memoriam: Virgil L. Woods, Jr., MD

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.


Binding Sites for LIN28 Protein Found in Thousands of Human Genes

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.


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

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.

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Tumor Cells' Inner Workings Predict Cancer Progression

July 27, 2012

Using a new assay method to study tumor cells, researchers at the University of California, San Diego School of Medicine and UC San Diego Moores Cancer Center have found evidence of clonal evolution in chronic lymphocytic leukemia (CLL). The assay method distinguishes features of leukemia cells that indicate whether the disease will be aggressive or slow-moving, a key factor in when and how patients are treated.

The findings are published in the July 26, 2012 First Edition online issue of Blood.

Coauthors include two members of the Bioinformatics program: alumnus Han-Yu Chuang, Ph.D. (lead author) and Prof. Trey Ideker.

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Discovery of Chemical That Affects Biological Clock Offers New Way to Treat Diabetes

July 12, 2012

Biologists at UC San Diego have discovered a chemical that offers a completely new and promising direction for the development of drugs to treat metabolic disorders such as type 2 diabetes—a major public health concern in the United States due to the current obesity epidemic.

Their discovery, detailed in a paper published July 13 in an advance online issue of the journal Science, initially came as a surprise because the chemical they isolated does not directly control glucose production in the liver, but instead affects the activity of a key protein that regulates the internal mechanisms of our daily night and day activities, which scientists call our circadian rhythm or biological clock.

The team was headed by Prof. Steve Kay, dean of the Division of Biological Sciences and a faculty member of the Bioinformatics and Systems Biology program.

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