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Quantitative Biology Ph.D Specialization
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Discover Quantitative Biology (qBio) at UC San Diego

qBio is the power of math-based reasoning and advanced instrumentation from physics and engineering harnessed to discover fundamental principles of living systems.

To make biology quantitative and predictive, it is necessary to draw upon a multitude of approaches from the physical sciences and engineering. These include theoretical concepts developed from studies in statistical mechanics and nonlinear dynamics, and experimental methods such as microfluidics and advanced imaging. Therefore the goal of the qBio graduate program is to provide the students with a mastery of both the theoretical knowledge and experimental skills, and guide them to employ both approaches to address fundamental biological problems during their thesis research.

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qBio researchers receive $8.6 million to investigate the 4D nucleome
Tue, Oct 13, 2015 11:54 am     A+ | a-
qBio researchers receive $8.6 million to investigate the 4D nucleome
Image by Yaojun Zhang and Olga Dudko

 By Susan Brown | 5 October 2015

UC San Diego faculty from physics, biology and health sciences will lead a new center to unravel the geometry of the genome, precisely track its motion and generate predictive models of how the structure and dynamics govern mammalian genetics.

Bing Ren in health sciences, Cornelis Murre in biological sciences, and Olga Dudko in physical sciences have been awarded $8.6 million for five years to establish the new center, one of six Nuclear Organization and Function Investigation Centers within the NIH 4D Nucleome project.

Human DNA if stretched out would measure two meters long. Inside a cell nucleus just six micrometers wide it coils around proteins to form chromatin, which itself forms loops and bundles that aren’t random. Instead the architecture can bring together distant regulatory elements on the string of genetic code to activate or silence specific genes. The pattern of which genes are active varies with the type and state of cells; disruptions of the pattern can lead to disease.

Mapping the three dimensional structure of the genetic material within the nucleus and tracking changes to the arrangement over time—the fourth dimension—are the goals of the 4D Nucleome project.

Bing Ren, professor of cellular and molecular medicine and member of Ludwig Cancer Research, maps contacts between distant elements to build a 3D picture of genomic structure using a technique called Hi-C. By cross-linking nearby chromatin, chopping it into a kind of genetic confetti, sequencing the bits and mapping them back to the sequence of the whole genome, Hi-C reveals which elements were adjacent within the nucleus.

Cornelis Murre, professor of biological sciences, studies the exquisite timing of the system that allows hundreds of genes to be regulated in synchrony. Murre has invented a way to tag specific individual elements of DNA and precisely track their motion in living cells, opening up the possibility to study how DNA elements that regulate genes are finding each other in space. The issue of timing has been little explored, Murre said. 

Olga Dudko associate professor of physics, uses the language of physics to make sense of the avalanche of data from these new techniques that map and track the genome. Dudko develops unifying theories that make concrete predictions. Her goal is to establish the principles that govern structure and dynamics of the mammalian genome. The new center will provide graduate students in theoretical physics with the unique opportunity to directly work with cutting-edge biological data.

Their grant is one of three to UC San Diego from this NIH Common Fund program.Together the campus has garnered more than a quarter of the $120 million allocated to the 4D Nucleome project nationwide.

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