Computational Biology & Bioinformatics
Pacific Northwest National Laboratory
PO Box 999
Richland, WA 99352
Chris Oehmen is currently involved in several high-performance computing applications for bioinformatics and computational biology. He leads 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.
Dr. Oehmen is also involved in machine learning in the context of Data Intensive Computing applications in biology and other areas. He views 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. He and his colleagues 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.
- High throughput bioinformatics and memory management optimization for this problem space
- Applications and implementations of support vector machines to binary classification in data-intensive problems
- High-performance computing and optimization
Education and Credentials
- B.A. Physics and Mathematics, Saint Louis University, (1995)
- M.S. Biomedical Engineering, The Joint Graduate Program in Biomedical Engineering, The University of Memphis and The University of Tennessee Health Science Center
- Ph.D. Biomedical Engineering, The Joint Graduate Program in Biomedical Engineering, The University of Memphis and The University of Tennessee Health Science Center
Affiliations and Professional Service
- IEEE, Engineering in Medicine and Biology Society
- IEEE, Computer Society
Awards and Recognitions
- Ronald L. Brodzinski Award for Early Career Exceptional Achievement (PNNL, 2009)
- 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)
- Oehmen CS, ES Peterson, and A Cox. 2015. "Behavior Models to Express and Share Threat Information." IT Professional 17(5):12-14. doi:10.1109/MITP.2015.93
- Oehmen CS, TE Carroll, PR Paulson, DM Best, CF Noonan, SR Thompson, JL Jensen, GA Fink, and ES Peterson. 2015. "Behavior-dependent Routing: Responding to Anomalies with Automated Low-cost Measures." In SafeConfig 2015: Proceedings of the 2015 Workshop on Automated Decision Making for Active Cyber Defense, October 12-16, 2015, Denver, Colorado, pp. 55-58. Association for Computing Machinery, New York, NY. doi:10.1145/2809826.2809835
- Oehmen CS, DS Curtis, AR Phillips, and ES Peterson. 2013. "Novel Visual and Analytical Methods in Repurposing Legacy Scientific Code - A Case Study." In Proceedings of the The 2013 International Conference on Software Engineering Research and Practice (SERP 2013), July 22-25, 2013, Las Vegas, Nevada, ed. HR Arabnia, et al, pp. 455-461. CSREA Press, Athens, GA.
- Oehmen CS, and DJ Baxter. 2013. "ScalaBLAST 2.0: Rapid and robust BLAST calculations on multiprocessor systems." Bioinformatics 29(6):797-8. doi:10.1093/bioinformatics/btt013
- Peterson ES, DS Curtis, AR Phillips, JR Teuton, and CS Oehmen. 2013. "A Generalized Bio-inspired Method for Discovering Sequence-based Signatures." In IEEE International Conference on Intelligence and Security Informatics (ISI 2013), June 4-7, 2013, Seattle, Washington, ed. K Glass, et al, pp. 330-332. IEEE, Piscataway, NJ. doi:10.1109/ISI.2013.6578853
- Teuton JR, ES Peterson, DJ Nordwall, BA Akyol, and CS Oehmen. 2013. "LINEBACkER: Bio-inspired Data Reduction Toward Real Time Network Traffic Analysis." In 6th International Symposium on Resilient Control Systems (ISRCS 2013), August 13-15, 2013, San Francisco, California, pp. 170-174. IEEE, Piscataway, NJ. doi:10.1109/ISRCS.2013.6623771
- Barber CA, and CS Oehmen. 2012. "An Efficient Machine Learning Approach To Low-Complexity Filtering In Biological Sequences." In IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), May9-12, 2012, San Diego, CA, pp. 237-243. IEEE, Piscataway, NJ. doi:10.1109/CIBCB.2012.6217236
- Fink GA, and CS Oehmen. 2012. Final Report for Bio-Inspired Approaches to Moving-Target Defense Strategies. PNNL-21854, Pacific Northwest National Laboratory, Richland, WA.
- Fink GA, KS Berenhaut, and CS Oehmen. 2012. "Directional Bias and Pheromone for Discovery and Coverage on Networks." In IEEE Sixth International Conference on Self-Adaptive and Self-Organizing Systems (SASO), September 10-14, 2012, Lyon, France. IEEE Computer Society, Los Alamitos, CA. doi:10.1109/SASO.2012.32
- Janik T, AM White, NH Pawley, KL Myers, and CS Oehmen. 2012. Annotated Bibliography for the MATADOR Project. PNNL-21448, Pacific Northwest National Laboratory, Richland, WA.
- Oehmen CS, ES Peterson, and JR Teuton. 2012. "Evolutionary Drift Models for Moving Target Defense." In CSIIRW '12: Proceedings of the 8th Annual Cyber Security and Information Intelligence Research Workshop, October 30-November 2, 2012, Oak RIdge, Tennessee. ACM, New York, NY.
- McDermott JE, AL Corrigan, ES Peterson, CS Oehmen, G Niemann, E Cambronne, D Sharp, JN Adkins, R Samudrala, and F Heffron. 2011. "Computational prediction of type III and IV secreted effectors in Gram-negative bacteria ." Infection and Immunity 79(1):23-32. doi:10.1128/IAI.00537-10
- McDermott JE, CS Oehmen, LA McCue, EA Hill, DM Choi, J Stockel, ML Liberton, HB Pakrasi, and LA Sherman. 2011. "A Model of Cyclic Transcriptomic Behavior in Cyanobacterium Cyanothece sp. ATCC 51142." Molecular Biosystems 7(8):2407-2418. doi:10.1039/C1MB05006K
- Gosney A, JH Miller, I Gorton, and CS Oehmen. 2011. "An Adaptive Middleware Framework for Optimal Scheduling on Large Scale Compute Clusters." In Eighth International Conference on Information Technology: New Generations (ITNG 2011), April 11-13, 2011, Las Vegas, Nevada, ed. S Latifi, pp. 713-718. IEEE Computer Society, Piscataway, NJ. doi:10.1109/ITNG.2011.126
- Stein DA, ST Perry, MD Buck, CS Oehmen, MA Fischer, E Poore, JL Smith, AM Lancaster, AJ Hirsch, MK Slifka, J Nelson, S Shresta, and K Fruh. 2011. "Inhibition of Dengue Virus Infections in Cell Cultures and in AG129 Mice by an siRNA Targeting a Highly Conserved Sequence." Journal of Virology 85(19):10154-10166. doi:10.1128/JVI.05298-11
- Oehmen CS, ES Peterson, and ST Dowson. 2010. "An Organic Model for Detecting Cyber Events." In Proceedings of the Sixth Annual Workshop on Cyber Security and Information Intelligence Research, p. Article No. 66. Association for Computing Machinery, New York, NY. doi:10.1145/1852666.1852740
- Webb-Robertson BJM, K Ratuiste, and CS Oehmen. 2010. "Physicochemical property distributions for accurate and rapid pairwise protein homology detection." BMC Bioinformatics 11:Article No. 145. doi:10.1186/1471-2105-11-145
- Gosney A, CS Oehmen, AS Wynne, and JP Almquist. 2010. "An Adaptive Middleware Framework for Scientific Computing at Extreme Scales." In The 2010 IEEE International Conference on Information Reuse and Integration (IRI 2010) , pp. 232-238. IEEE , Piscataway, NJ. doi:10.1109/IRI.2010.5558934
- Oehmen CS, and BJM Webb-Robertson. 2010. "Evaluating the Computational Requirements of using SVM software to train Data-Intensive Problems." In Machine Learning Research Progress, Nova Science Publishers. Nova Science, Hauppauge, NY.
- Shah AR, JN Adkins, DJ Baxter, WR Cannon, D Chavarría-Miranda, S Choudhury, I Gorton, DK Gracio, TD Halter, N Jaitly, JR Johnson, RT Kouzes, MC Macduff, A Marquez, ME Monroe, CS Oehmen, WA Pike, C Scherrer, O Villa, BJM Webb-Robertson, PD Whitney, and N Zuljevic. 2010. "Applications in Data-Intensive Computing." In Advances in Computers, vol. 79, ed. M Zelkowitz, pp. 1-70. Academic Press Inc., San Diego, CA.
- Cannon WR, BJM Webb-Robertson, AR Willse, M Singhal, LA McCue, JE McDermott, RC Taylor, KM Waters, and CS Oehmen. 2009. "An Integrative Computational Framework for Hypotheses-Driven Systems Biology Research in Proteomics and Genomics." Chapter 4 in Computational and Systems Biology: Methods and Applications, pp. 63-85. Research Signpost, Trivandrum, India.
- Oehmen CS. 2009. Annotated Bibliography for the DEWPOINT project. PNNL-18370, Pacific Northwest National Laboratory, Richland, WA.
- Webb-Robertson BJM, MM Matzke, and CS Oehmen. 2009. "Dimension Reduction via Unsupervised Learning Yields Significant Computational Improvements for Support Vector Machine Based Protein Family Classification." In The Seventh International Conference on Machine Learning and Applications , pp. 457-462. IEEE Computer Society, Los Alamitos, CA.
- Webb-Robertson BJM, CS Oehmen, and AR Shah. 2008. "A Feature Vector Integration Approach for a Generalized Support Vector Machine Pairwise Homology Algorithm." Computational Biology and Chemistry 32(6):458-461. doi:10.1016/j.compbiolchem.2008.07.017
- Curtis DS, ES Peterson, and CS Oehmen. 2008. "A Secure Web Application Providing Public Access to High-Performance Data Intensive Scientific Resources - ScalaBLAST Web Application." In 4th Annual International Conference on Web Information Systems and Technologies, ed. J. Cordeiro, J. Filipe and S. Hammoudi, pp. 244-251. Springer, Berlin, Germany.
- Gorton I, CS Oehmen, and JE McDermott. 2008. "It Takes Glue to Tango: MeDICi integration framework creates data-intensive computing pipeline." Scientific Computing 25(7):16-24.
- Oehmen CS, and WR Cannon. 2008. "Bringing high performance computing to the biologist's workbench: approaches, applications and challenges." In SciDAC 2008: Journal of Physics: Conference Series, vol. 125, p. 012052. IOP Publishing Ltd., Bristol, United Kingdom. doi:10.1088/1742-6596/125/1/012052
- Shah AR, CS Oehmen, and BJM Webb-Robertson. 2008. "SVM-Hustle - An iterative semi-supervised machine learning approach for pairwise protein remote homology detection." Bioinformatics 24(6):783-790.
- Shah AR, VM Markowitz, and CS Oehmen. 2008. "High-throughput computation of pairwise sequence similarities for multiple genome comparison using ScalaBLAST." In Life Science Systems and Applications Workshop 2007, pp. 89-91. Institute of Electrical and Electronics Engineers, Pisctataway, NJ. doi:10.1109/LSSA.2007.4400891
- Webb-Robertson BJM, WR Cannon, CS Oehmen, AR Shah, V Gurumoorthi, MS Lipton, and KM Waters. 2008. "A Support Vector Machine model for the prediction of proteotypic peptides for accurate mass and time proteomics." Bioinformatics 24(13):1503-1509. doi:10.1093/bioinformatics/btn218
- Webb-Robertson BJM, ES Peterson, M Singhal, KR Klicker, CS Oehmen, JN Adkins, and SL Havre. 2007. "PQuad - A visual analysis platform for proteomic data exploration of microbial organism." Bioinformatics 23(13):1705-1707. doi:10.1093/bioinformatics/btm132
- De Jong WA, CS Oehmen, and DJ Baxter. 2007. "Greenbook Algorithms and Hardware Needs Analysis". PNNL-15739, Pacific Northwest National Laboratory, Richland, WA.
- Samatova NF, A Gorin, E Uberbacher, TV Karpinets, BH Park, C Pan, TP Straatsma, WR Cannon, H Resat, RD Lins, and CS Oehmen. 2007. "Data driven computing for Biological Systems." SciDAC Review 5(Fall 2007):10-25.
- Shah AR, CS Oehmen, JK Harper, and BJM 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. doi:10.1016/j.compbiolchem.2007.02.012
- Webb-Robertson BJM, CS Oehmen, and WR Cannon. 2007. "Support Vector Machine Classification of Probability Models and Peptide Features for Improved Peptide Identification from Shotgun Proteomics." In The Sixth International Conference on Machine Learning and Applications (ICMLA '07), pp. 500-505. IEEE Computer Society, Washington DC. doi:10.1109/ICMLA.2007.17
- Oehmen CS, 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):740-749.
- Oehmen CS, TP Straatsma, GA Anderson, G Orr, BJM Webb-Robertson, RC Taylor, RW Mooney, DJ Baxter, DR Jones, and DA Dixon. 2006. "New Challenges Facing Integrative Biological Science in the Post-Genomic Era." Journal of Biological Systems 14(2):275-293.
- Cannon WR, KH Jarman, BJM Webb-Robertson, DJ Baxter, CS Oehmen, KD Jarman, A Heredia-Langner, KJ Auberry, and GA 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.
- Webb-Robertson BJM, CS Oehmen, and MM Matzke. 2005. "SVM-BALSA: Remote Homology Detection based on Bayesian Sequence Alignment." Computational Biology and Chemistry 29(6):440-3.