U.S. Department of Energy

Pacific Northwest National Laboratory

Computational Biology & Bioinformatics

Use theory, model-based experimental design, and data analytics to elucidate and predict the fundamental organizational principles of biological systems

Biological systems can be large. A pond-size microbial mat, for instance, or a human organ.

They can be small—the size of cells, or as tiny as molecules performing an outsize metabolic task on which life or health depends.

Whatever size, biological systems are so complex that it is a grand challenge to understand them, let alone predict, design, or control them. Adding to these challenges is the complexity of the data derived from high-throughput metabolomics, proteomics, and genomics assays.

These grand challenges are our mission. We address them by combining data analytics, model-based experimental design, and theory to interpret, predict, and design biological systems.

We statistically analyze, mine, and visualize high-throughput biological data. We model system dynamics and energetics using mathematics and physics. And we perform integrated analyses of regulatory networks and metabolic pathways.

At PNNL, computational biology is the organizing framework that reveals fundamental processes and principles. These include biomolecular signatures of dysbiosis; regulatory network structure; dynamics of pathways, processes, and microbial interactions; the thermodynamic characterization of molecules, pathways, and cells; and the emergence of higher-order cellular and multicellular capabilities. 

We address issues of national importance ranging from scalable bioprocesses to health to evolving terrestrial and aquatic ecosystems. 

Our goal is to advance a fundamental understanding of biological processes by integrating data, modeling, and theory into the scientific process. 

Our projects: Github.com/PNNL-CompBio

Previous software page: http://cbb.pnnl.gov/portal/software/index.html

Our organism databases: cyc.pnnl.gov

Team

Dr. Jason McDermott, senior research scientist, has extensive research experience in molecular and structural virology and data resource design, data integration and prediction of biological networks, bridging experimental and computational biology...
Dr. Andrew Kuprat’s interests include modeling respiratory physiology, aerosol deposition, and gas dispersion in the lung using computational fluid dynamics and multi-scale modeling.
Dr. Cannon is author of more than 50 technical publications in modeling and simulation, data analysis and proteomics. His graduate work was in statistical thermodynamics in the laboratory of J. Andrew McCammon studying molecular recognition proteins...
Colin works in microbial ecology, focusing on informatics and visualization.
Dr. Dennis Thomas is a computational scientist with over 15 years of experience in applying mathematical modeling and computational methods to predict and understand the behavior of dynamic systems, in the area of fluid mechanics, complex fluid...
Dr Mitchell's research involves using computational analysis of 'omics data to identify key components of biological systems. Analyses focus on network inference and topology, and involves data from a diverse array of prokaryotic and eukaryotic...
Hyun Song’s research is directed toward developing modeling and computational tools for the simulation of cellular metabolism and microbial community dynamics. His research interest in metabolic modeling includes 1) omics data-guided estimation of...
Jason is interested in the molecular pathogenesis that underlies poor clinical outcomes in viral and protozoan infectious diseases.  His current research uses cutting-edge methods in machine learning and graph analytics to translate multi-omic data...
Over 15 years of experience integrating high-throughput systems biology data with computational methods to advance knowledge in the study of symbiosis, circadian rhythms, evolution, biofuels, human health and infectious disease.
Dr. Katrina Waters is the division director for Biological Sciences at the Pacific Northwest National Laboratory.  Waters has a Ph.D. in biochemistry and more than 15 years of experience in microarray and proteomics data analysis. Her research...
Lindsey Anderson’s research has been dedicated to the characterization and identification of novel metabolic functional interactions using a high-throughput systems biology and chemical biology approach. Her expertise in metabolism and...
Dr. Neeraj Kumar, research scientist, has extensive research experience in computational chemistry, biophysics, structural and molecular biology, bio/cheminformatics, multi-omics data analysis, metabolic network, molecular modeling and simulation of...
Sean Colby is an expert in the application of computational resources to solve multidisciplinary problems, often involving massive datasets (big data).  His focus has thus far included cheminformatics, bioinformatics, plant and soil sciences, and...
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