CCB Seminar - Prof Daniel Jacobson
- Centre for Computational Biology, Haworth building, Room 320
- Engineering and Physical Sciences, Lectures Talks and Workshops, Life and Environmental Sciences, Medical and Dental Sciences, Research
Jordan Lee - CCB Administrative Assistant
Prof Daniel Jacobson
Oak Ridge National Laboratory
University of Tennessee, United States
"Seeing the Forest for the Trees: Adventures in Systems Biology for Plants and Humans"
Biological organisms are complex systems that are composed of pleiotropic functional networks of interacting molecules and macro-molecules. Complex phenotypes are the result of orchestrated, hierarchal, heterogeneous collections of expressed genomic variants regulated by and related to biotic and abiotic signals. However, the effects of these variants are the result of historic selective pressure and current environmental as well as epigenetic interactions, and, as such, their co-occurrence can be seen as genome- wide associations in a number of different manners. In this context, a plant’s association with its microbiome is a complex set of interactions involving many genes and metabolites. We are using data derived from the re-sequenced genomes from over 1000 alternate Populus trichocarpa genotypes in combination with transcriptomics, metabolomics and phenomics data across this population in order to better understand the molecular interactions involved in plant-microbe interfaces. The resulting Genome-Wide Association Study networks, integrated with SNP correlations and co-expression networks, are proving to be a powerful approach to determine the pleiotropic and epistatic relationships underlying cellular functions and, as such, some of the molecular underpinnings for plant-microbiome associations. We have also found that, although separated by great evolutionary distances, plants and humans share many fundamental biological mechanisms. Surprisingly, we have found that the same allelic variants can lead to similar phenotypes in both organisms. As a result of these observations, we are starting to systematically explore these highly conserved functions and their phenotypic relationships in both plants and humans.
Dan’s career as a computational/systems biologist has included leadership roles in academic, NGO, corporate and national lab settings. His lab focuses on the development and subsequent application of mathematical, statistical and computational methods to biological datasets in order to yield new insights into complex biological systems. His lab’s approaches include the use of Network Theory and Topology Discovery/Clustering, Wavelet Theory, Machine Learning (amongst others: Random Forests, Iterative Random Forests, Tensor Iterative Random Forests, etc.) and Linear Algebra (primarily as applied to large-scale multivariate modeling), together with advanced supercomputing architectures. Areas of statistics of particular interest to his lab include the use of both frequentist (parametric and non-parametric) and Bayesian methods as well as the development of new methods for Genome-Wide Association Studies (GWAS) and Phenome-Wide Associations Studies (PheWAS). These mathematical and statistical methods are applied to various population and (meta)multiomics data sets (Genomics, Phylogenomics, Transcriptomics, Proteomics, Metabolomics, Microbiomics, Viriomics, Phytobiomics, Chemiomics, etc.) individually as well as in combination in an attempt to better understand the functional relationships as well as biosynthesis, signaling, transcriptional, translational, degradation and kinetic regulatory networks at play in biological organisms and communities. His group at ORNL takes a broad view of biological complexity and evolution that stretches from viruses to microbes to plants to humans (including cancer and neuroscience). His lab uses petascale computing to analyze and model complex biological systems and is actively involved in the development of exascale applications for biology.
The seminars are an opportunity for the CCB Community and external speakers to present their work or topics of interest to the bioinformatics community.
Wednesday 13 December 12.00 to 1.00 pm.
CCB Large Meeting & Teaching Room, Haworth Building.
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