Computational Systems Bioengineering

Achieving a coherent picture of how tissues function requires measurements of cells and biomolecules, as well as quantitative models of how they work together in time and space. Techniques for high-throughput biology are constantly advancing and have emphasized the need for computational approaches that can fully exploit complex datasets. The challenge of linking molecules to cell and tissue function is daunting but important. Many human diseases — including cardiovascular disorders, microbial infections, and cancer — are caused by disruptions in molecular and cellular networks that ultimately affect clinical outcomes. Approaching biomedical problems from a systems perspective allows one to identify the properties that emerge when individual molecular and cellular components are wired together as a network.

Researchers at UVa are helping to define this expanding field. In the Department of Biomedical Engineering, faculty members are working on the reconstruction, simulation, and large-scale measurement of cellular networks implicated in tissue mechanics and morphogenesis, tumorigenesis, and host-pathogen interactions. Models that make accurate high-level predictions from quantitative molecular measurements will provide an important foundation for rational therapies and the design of cell and tissue behavior.

Primary Faculty

Brett Blackman: endothelial cell mechanotransduction, epigenetic factors regulating vascular cell differentiation & phenotype

Edward Botchwey: polymeric biomaterials, musculoskeletal tissue engineering, and vascular remodeling

Brian Helmke: intracellular mechanics and signaling, extracellular matrix assembly, nanotechnology tools for engineering cell structure and function

Kevin Janes: design of high-throughput and multiplex assays for intracellular signaling; data-driven modeling of signal-transduction networks

Jason Papin: cell-cell signaling network reconstruction and analysis; pathogen-host interactions

Shayn Peirce: combinations of angiogenic growth factors in microvascular remodeling, computational modeling of vascular stem cell interactions and vessel remodeling

Richard J. Price: computational reactive oxygen species transport models linking endothelial activation and arteriogenesis

Jeff Saucerman: multi-scale modeling of signaling networks and their regulation of cardiac contractility, remodeling, and heart failure

Thomas Skalak: multisignal molecular circuits and cell lineages controlling blood vessel remodeling, multicellular computer simulation of vascular pattern formation

Affiliated Faculty

Silvia Salinas Blemker: multi-scale modeling of skeletal muscle mechanics, image-based modeling of muscle structure and geometry

Andrew Grimshaw, Computer Science: bioinformatics, GRID computing, development of Global BioGRID

Richard Kent: computational and experimental studies of traumatic injury biomechanics and mechanical modeling of biological structures

Jae Lee, Health Evaluation Sciences: large scale gene array analysis, cancer genomics

Ian Macara, Center for Cell Signaling: computer simulation of intracellular signaling pathways, experimental cell biology

William Pearson, Biochemistry and Computer Science: bioinformatics, gene sequence homology searching, protein evolution

Gabriel Robins, Computer Science: bioinformatics, network topology