Computational Systems Bioengineering

The publication of the initial human genome sequence in 2001 marked a tremendous accomplishment in the burgeoning era of high-throughput biology. Now, the protein and metabolic composition of an entire cell can be cataloged, the dynamic expression programs of complete genomes can be measured, and the set of interactions between cellular components can be characterized. With such an onslaught of biological data, the impending need for computational approaches to integrate and analyze this data is now clearly apparent. With these computational systems-level analyses, the connection between genotype and phenotype will be explicitly described, and the predictive power of such models will allow for rational design of cell and tissue behavior.

Researchers at UVa are on the cutting edge of this expanding field. Faculty members are working on the reconstruction of cellular signaling networks, cellular automata models of vascular morphogenesis and embryogenesis, coupling multi-scale biological processes, bioinformatics of protein-protein interaction networks, and cellular signaling components of pathogen-host interactions. These research efforts are applied to critical human disease processes such as cancer and cardiovascular disease. This integration of computational approaches with high-throughput biological research will produce tremendous strides in the development of therapies for human disease.

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

Jeffrey Saucerman: signaling mechanisms of cardiovascular disease

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