Chris Oehmen, Ph.D.
Senior Research Scientist
Richland, WA 99352
USA
Phone: (509)375-2038
Fax: (509)372-4720
URL: http://emslbios.pnl.gov/id/oehmen_cs
Organization
WR Wiley Environmental Molecular Sciences Laboratory, MSCF Visualization & User Services
Matrixed Organization
Fundamental and Computational Sciences, Computational Biology and Bioinformation
Current Activities and Projects
I am currently involved in several high-performance computing applications for bioinformatics and computational biology. I lead the ScalaBLAST project which is a highly scalable implementation of the NCBI BLAST algorithm for use on clusters and large-scale supercomputers. In conjunction with the Joint Genome Institute, ScalaBLAST is being used to perform the large-scale biosequence comparisons needed to maintain the Integrated Microbial Genome (IMG). ScalaBLAST is also being used by several other university and DoE Laboratory groups for a broad range of biological research.
I am also involved in machine learning in the context of Data Intensive Computing applications in biology and other areas. I view data intensive computing as a valuable path to solving some classes of problems which have undesirable scaling characteristics using conventional flop-based methods. For problems where having a small memory footprint requires large-scale data moving (repeatedly reading large files for instance) the push toward flop-intensive computing offers diminishing returns. We are exploring examples of this class of problems, such as training binary classifiers using Support Vector Machine implementations with an emphasis on improving time to solution by taking advantage of large-scale aggregate system memory on cluster or shared memory platforms.
Research Interests
My current research interests include
1)high-throughput bioinformatics and memory management optimization for this problem space
2)applications and implementations of support vector machines to binary classification in data-intensive problems
3)high-performance computing and optimization in general
Past Experience
Development of a parallel platform for integrating single cell electrophysiological models into tissue structures with microanatomical resolution.
Development of a parallel platform for modeling DNA strand motion and hybridization for molecular computing applications.
Education
Ph.D. Biomedical Engineering, Joint Graduate Program in Biomedical Engineering, The University of Memphis and The University of Tennessee, HSC (8/2003)
M.S. Biomedical Engineering, Joint Graduate Program in Biomedical Engineering, The University of Memphis and The University of Tennessee, Memphis (5/1999)
B.A. Physics and Mathematics, Saint Louis University (5/1995)
Awards, Honors, & Appointments
Selected as UM representative to attend 51st Annual Meeting of Nobel Prize Laureates in Lindau, Germany (ORISE, 2001)
Computational Science Graduate Fellow (Krell Institute, 8/99-5/03)
Presidential Scholarship recipient (Saint Louis University, 8/91-5/95)
Frances Regan Award for Excellence in Mathematics (Saint Louis University, 5/95)
Selected Publications
Webb-Robertson, B.M., E.S. Peterson, M. Singhal, K.R. Klicker, C.S. Oehmen, J.N. Adkins and S.L. Havre (2007) PQuad – a visual analysis platform for proteomics data exploration of microbial organisms. Bioinformatics; 23(13): 1705-1707.
Shah, A.R., C.S. Oehmen and B.M. Webb-Robertson (2007) Integrating subcellular location for improving machine learning models of remote homology detection in eukaryotic organisms. Computational Biology and Chemistry; 31(2): 138-142.
Oehmen, C.S. and J. Nieplocha (2006) ScalaBLAST: A scalable implementation of BLAST for high-performance data-intensive bioinformatics analysis, IEEE Transactions on Parallel and Distributed Systems, 17(8): 740-9.
Oehmen, C.S., T. Straatsma, G.A. Anderson, G. Orr, B.M. Webb-Robertson, R.C. Taylor, R.W. Mooney, D.J. Baxter, D.R. Jones and D.A. Dixon (2006) New challenges facing integration biological sciences in the post-genomic era. Journal of Biological Systems, 14(2): 275-293.
Webb-Robertson, B.M., C.S. Oehmen and M.M. Matzke (2005) SVM-BALSA: remote homology detection based on Bayesian sequence alignment. Computational Biology and Chemistry, 29(6): 440-443.
Cannon, W.R., K.H. Jarman, B.M. Webb-Robertson, D.J. Baxter, C.S. Oehmen, K.D, Jarman, A. Heredia-Langner, K.J. Auberry and G.A. Anderson (2005) A comparison of probability and likelihood models for peptide identification from tandem mass spectrometry data. Journal of Proteome Research, 4(5): 1687-1698.
Recent peer-reviewed conference proceedings
Shah, A. Markowitz, VM., Oehmen, C.S., (2007) High-throughput computation of pairwise sequence similarities for multiple genome comparisons using ScalaBLAST, Proceedings of IEEE-NIH Life Science Systems and Applications (LISSA 2007).
Webb-Robertson, BM, WR Cannon and CS Oehmen (2007) Support vector machine classification of probability models and peptide features for improved peptide identification from shotgun proteomics. The Sixth International Conference on Machine Learning and Applications (ICMLA '07), December 13-15, 2007, Cincinnati Ohio, 500-505.
