Bioinformatics and Health Sciences

In the 21st century, biology has become a data-intensive field of research, relying extensively on high-end computational resources and cyberenvironments.

The Bioinformatics and Health Sciences thematic area provides a home to ongoing and novel explorations of topics in evolutionary and functional genomics and metagenomics, simulations of large-scale macromolecular complexes, properties of biomolecular networks, and multiscale modeling of biological systems, with potential applications to human health, bioenergy, and sustainability. Our approaches are strongly computational, and emphasize advances in algorithmic efficiency, parallelization, scaling, and deployment in HPC or cloud environments.

Current Projects

The activities of the Theme span multiple domains of biology. The Plants in Silico project, led by Steve Long and Amy Marshall-Colón from the Departments of Plant Biology and Crop Sciences, aims to build a framework for the multiscale modeling of plant growth, starting from the molecular level, through organelles, cells, organs, whole plants, and ecosystems. The ultimate goal of the project is to support the building of predictive models, where the parameters for the optimal growth of food or energy-producing plants can be optimized at all levels.

NCSA is an active participant in the CompGen (Computational Genomics) initiative, an interdisciplinary group of computational and life scientists that seeks to combine campus strengths in genomic research with our well-known expertise in building large-scale parallel systems and managing Big Data. Activities at NCSA include analyses of the behavior of petascale computer systems under stress from very large genome analysis workflows, and the design of systems optimized for high-throughput, data-intensive workloads.

NCSA is working with the NIH-funded Center of Excellence in Big Data Computing, KnowEnG, in building a robust cyberenvironment that integrates multiple analytical methods derived from the most advanced data mining and machine learning research for the analysis of genomic datasets.

The Theme will also be building upon the long-established and close relationship of NCSA with the Theoretical and Computational Biophysics Group at the Beckman Institute, which uses very large computational resources to study the structure and function of supramolecular systems in living cells.

Theme Lead: C. Victor Jongeneel

C. Victor Jongeneel is a Senior Research Scientist at the National Center for Supercomputing Applications (NCSA), Director of Bioinformatics at the Institute for Genomic Biology (IGB), and the Director of the High-Performance Biological Computing (HPCBio) group at the IGB, NCSA, and the Roy J. Carver Biotechnology Center. He is also a Research Professor in the Department of Bioengineering. He received his PhD from the University of North Carolina at Chapel Hill, and was a post-doctoral fellow at the University of California, San Francisco and at the Swiss Institute for Experimental Cancer Research.

Dr. Jongeneel’s career spans multiple domains of science. He was trained as a biochemist at the University of Lausanne (Switzerland), worked as a microbiologist during his graduate and post-doctoral years, and then became a group leader in molecular immunology at the Ludwig Institute for Cancer Research in Lausanne (Switzerland). In parallel to his experimental work, Dr. Jongeneel has had a life-long interest in the application of computational techniques to biological research. He was one of the founders and the first director of the Swiss Institute of Bioinformatics, where he is a lifetime member of the Board of Trustees. From 2007 to 2009 Dr. Jongeneel was the Vice-President for Research of the Cyprus Institute in Nicosia, Cyprus.

Theme Faculty and Affiliates