PNNL

Chris Oehmen leads the computational biology group in the Biological Sciences Division at PNNL, and he has more than 18 years of experience developing, leading, and executing research programs for a variety of sponsors. He previously served as chief scientist for the cyber research group and led the Asymmetric Resilient Cybersecurity Initiative. His research is built on a foundation of high performance computing applications in biology, with emphasis on how biological approaches can be used as a new paradigm for other fields such as cybersecurity. 

Beginning with ScalaBLAST, an open source high performance biosequence analysis application developed by his team at PNNL, Oehmen has led efforts exploring a variety of connections between sequence analysis and national security applications, including analysis of software binaries and network traffic. He has developed applications in both of these areas, which are being transitioned into operational use. More recently, he has led multiple efforts focused on adaptive, resilient cyber systems inspired in part by complex biological systems. His resilience and active defense work rely on a foundational application of biological principles for survivability and regeneration.

• Computational Biology
• Cyber Security
• High Performance Computing (HPC)

• PhD in Biomedical Engineering, University of Memphis
• MS in Biomedical Engineering, University of Tennessee
• BA in Physics and Mathematics, Saint Louis University

• R&D 100 award for MLSTONES (2019)
• Federal Laboratory Consortium award for MLSTONES commercialization (2018)
• Ronald L. Brodzinski award for Early Career Exceptional Achievement (2009)
• Supercomputing 2008 HPC Analytics challenge winner (team lead) (2008)
• Supercomputing 2006 HPC Analytics challenge finalist (team lead) (2006)
• Computational Science Graduate Fellow (Krell Institute) (1999-2003)
• Francis Regan award for excellence in mathematics (1995)
• Presidential scholarship, Saint Louis University (1991-1995)
• National merit scholarship recipient (1991)

• U.S. Application No. 15/130,837. Biosequence-based approach to analyzing binaries. Filed:  April 15, 2016. IPID:  30751-E
  • Licensed to Cynash, a startup funded by the IP Group and led by Rich Robinson, formerly CTO of Telos Corporation, to develop machine learning and artificial intelligence systems for cyber and cyber physical systems. (2017)
  • Awarded patent- 2019-04-25 Publication of US20190121627A1
  • Awarded patent- 2020-01-28 Publication of US10545746B2
  • R&D 100 awardee (2020)

Software Releases

• Oehmen CS, and DJ Baxter. ScalaBLAST 2.0 (2012)
• Oehmen CS. PHaCT (Parallel Pearson and Hierarchical Clustering Toolsuite). (2010)
• Oehmen CS, and DJ Baxter. ScalaBLAST 1.0 (High performance biosequence analysis) (2009)
• Shah AR, CS Oehmen, and BJM Webb-Robertson. SVM-HUSTLE (Machine-learning-based protein family classifier) (2008)

2021

Oehmen C.S., S.L. Clements, and A.E. Chastain. 2021. "Infrastructure Resiliency from a Macro Cyber Perspective: A Note from the Guest Editors." Journal of Information Warfare 20, no. 2:i-ii. PNNL-SA-157925.

Peterson E.S., A.R. Phillips, R.L. Griswold, K.T. Star, and C.S. Oehmen. 2021. "Flexible and Adaptive Malware Identification Using Techniques from Biology." Journal of Information Warfare 20, no. 2:81-92. PNNL-SA-154741.

2020

Alexander F.J., A. Almgren, J. Bell, A. Bhattacharjee, J.H. Chen, P. Colella, and D. Daniel, et al. 2020. "Exascale applications: skin in the game." Philosophical Transactions of the Royal Society A. Mathematical, Physical & Engineering Sciences 378, no. 2166:Article No. 20190056. PNNL-SA-150649. doi:10.1098/rsta.2019.0056

2019

Caswell J., J. Gans, N. Generous, C.M. Hudson, E.D. Merkley, C. Johnson, and C.S. Oehmen, et al. 2019. "Defending our public biological databases as a global critical infrastructure." Frontiers in Bioengineering and Biotechnology 7. PNNL-SA-139972. doi:10.3389/fbioe.2019.00058

Oehmen C.S., and S.L. Clements. 2019. "Preparing for a Future of Critical Infrastructure Under Autonomic Control: A Note From the Guest Editors." Journal of Information Warfare 18, no. 4 (Special Edition):i-ii. PNNL-SA-149608.

2018

Duan Q., E. Al-Shaer, S. Chatterjee, M. Halappanavar, and C.S. Oehmen. 2018. "Proactive Routing Mutation Against Stealthy Distributed Denial of Service Attacks - Metrics, Modeling and Analysis." Journal of Defense Modeling and Simulation 15, no. 2:219-230. PNNL-SA-128859. doi:10.1177/1548512917731002

2016

Oehmen C.S., E.S. Peterson, A.R. Phillips, and D.S. Curtis. 2016. "A Biosequence-based Approach to Software Characterization." In IEEE Security and Privacy Workshops (SPW 2016), May 22-26, 2016, San Jose, California, 118-125. Palo Alto, California:IEEE Computer Society. PNNL-SA-115860. doi:10.1109/SPW.2016.43

Oehmen C.S., P.J. Bruillard, B.D. Matzke, A.R. Phillips, K.T. Star, J.L. Jensen, and D.J. Nordwall, et al. 2016. "LINEBACKER: LINE-speed Bio-inspired Analysis and Characterization for Event Recognition." In IEEE Symposium on Security and Privacy Workshops, May 23-25, 2016, San Jose, California, 88-95. Palo Alto, California:IEEE Computer Society. PNNL-SA-115629. doi:10.1109/SPW.2016.44

Rauf U., F. Gillani, E. Al-Shaer, M. Halappanavar, S. Chatterjee, and C.S. Oehmen. 2016. "Formal Approach For Resilient Reachability based on End-System Route Agility." In Third ACM Workshop on Moving Target Defense (MTD 2016), October 24-28, 2016, Vienna, Austria, 117-127. New York, New York:ACM. PNNL-SA-121212. doi:10.1145/2995272.2995275

Tardiff M.F., G.T. Bonheyo, K.A. Cort, T.W. Edgar, N.J. Hess, W.J. Hutton, and E.A. Miller, et al. 2016. "Applying the Scientific Method of Cybersecurity Research." In IEEE Symposium on Technologies for Homeland Security (HST 2016), May 10-11, 2016, Waltham, MA. Piscataway, New Jersey:IEEE. PNNL-SA-117303. doi:10.1109/THS.2016.7568886

2015

Oehmen C.S., E.S. Peterson, and A. Cox. 2015. "Behavior Models to Express and Share Threat Information." IT Professional 17, no. 5:12-14. PNNL-SA-110938. doi:10.1109/MITP.2015.93

Oehmen C.S., T.E. Carroll, P.R. Paulson, D.M. Best, C.F. Noonan, S.R. Thompson, and J.L. Jensen, et al. 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, 55-58. New York, New York:Association for Computing Machinery. PNNL-SA-111823. doi:10.1145/2809826.2809835

2013

Oehmen C.S., and D.J. Baxter. 2013. "ScalaBLAST 2.0: Rapid and robust BLAST calculations on multiprocessor systems." Bioinformatics 29, no. 6:797-8. PNNL-SA-87629. doi:10.1093/bioinformatics/btt013

Oehmen C.S., D.S. Curtis, A.R. Phillips, and E.S. 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, edited by HR Arabnia, et al, 455-461. Athens, Georgia:CSREA Press. PNNL-SA-95422.

Peterson E.S., D.S. Curtis, A.R. Phillips, J.R. Teuton, and C.S. 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, edited by K Glass, et al, 330-332. Piscataway, New Jersey:IEEE. PNNL-SA-94757. doi:10.1109/ISI.2013.6578853

Teuton J.R., E.S. Peterson, D.J. Nordwall, B.A. Akyol, and C.S. 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, 170-174. Piscataway, New Jersey:IEEE. PNNL-SA-95878. doi:10.1109/ISRCS.2013.6623771

2012

Barber C.A., and C.S. 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, 237-243. Piscataway, New Jersey:IEEE. PNNL-SA-84473. doi:10.1109/CIBCB.2012.6217236

Fink G.A., and C.S. Oehmen. 2012. Final Report for Bio-Inspired Approaches to Moving-Target Defense Strategies. PNNL-21854. Richland, WA: Pacific Northwest National Laboratory. Final Report for Bio-Inspired Approaches to Moving-Target Defense Strategies

Fink G.A., K.S. Berenhaut, and C.S. 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. Los Alamitos, California:IEEE Computer Society. PNNL-SA-87555. doi:10.1109/SASO.2012.32

Janik T., A.M. White, N.H. Pawley, K.L. Myers, and C.S. Oehmen. 2012. Annotated Bibliography for the MATADOR Project. PNNL-21448. Richland, WA: Pacific Northwest National Laboratory. Annotated Bibliography for the MATADOR Project

Oehmen C.S., E.S. Peterson, and J.R. 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. New York, New York:ACM. PNNL-SA-90818.

2011

Gosney A., J.H. Miller, I. Gorton, and C.S. 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, edited by S Latifi, 713-718. Piscataway, New Jersey:IEEE Computer Society. PNWD-SA-9182. doi:10.1109/ITNG.2011.126

McDermott J.E., A.L. Corrigan, E.S. Peterson, C.S. Oehmen, G. Niemann, E. Cambronne, and D. Sharp, et al. 2011. "Computational prediction of type III and IV secreted effectors in Gram-negative bacteria." Infection and Immunity 79, no. 1:23-32. PNNL-SA-72872. doi:10.1128/IAI.00537-10

McDermott J.E., C.S. Oehmen, L.A. McCue, E.A. Hill, D.M. Choi, J. Stockel, and M.L. Liberton, et al. 2011. "A Model of Cyclic Transcriptomic Behavior in Cyanobacterium Cyanothece sp. ATCC 51142." Molecular Biosystems 7, no. 8:2407-2418. PNNL-SA-74409. doi:10.1039/C1MB05006K

Stein D.A., S.T. Perry, M.D. Buck, C.S. Oehmen, M.A. Fischer, E. Poore, and J.L. Smith, et al. 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, no. 19:10154-10166. PNWD-SA-9500. doi:10.1128/JVI.05298-11

2010

Gosney A., C.S. Oehmen, A.S. Wynne, and J.P. 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), 232-238. Piscataway, New Jersey:IEEE. PNNL-SA-71671. doi:10.1109/IRI.2010.5558934

Oehmen C.S., and B.M. Webb-Robertson. 2010. "Evaluating the Computational Requirements of using SVM software to train Data-Intensive Problems." In Machine Learning Research Progress, Nova Science Publishers. Hauppauge, New York:Nova Science. PNNL-SA-59493.

Oehmen C.S., E.S. Peterson, and S.T. Dowson. 2010. "An Organic Model for Detecting Cyber Events." In Proceedings of the Sixth Annual Workshop on Cyber Security and Information Intelligence Research, Article No. 66. New York, New York:Association for Computing Machinery. PNNL-SA-71113. doi:10.1145/1852666.1852740

Shah A.R., J.N. Adkins, D.J. Baxter, W.R. Cannon, D. Chavarr�a-Miranda, S. Choudhury, and I. Gorton, et al. 2010. "Applications in Data-Intensive Computing." In Advances in Computers, edited by M Zelkowitz. 1-70. San Diego, California:Academic Press Inc. PNNL-SA-67358.

Webb-Robertson B.M., K. Ratuiste, and C.S. Oehmen. 2010. "Physicochemical property distributions for accurate and rapid pairwise protein homology detection." BMC Bioinformatics 11. PNWD-SA-8719. doi:10.1186/1471-2105-11-145

2009

Cannon W.R., B.M. Webb-Robertson, A.R. Willse, M. Singhal, L.A. McCue, J.E. McDermott, and R.C. Taylor, et al. 2009. "An Integrative Computational Framework for Hypotheses-Driven Systems Biology Research in Proteomics and Genomics." In Computational and Systems Biology: Methods and Applications. 63-85. Trivandrum:Research Signpost. PNNL-SA-57999.

Oehmen C.S. 2009. Annotated Bibliography for the DEWPOINT project. PNNL-18370. Richland, WA: Pacific Northwest National Laboratory. Annotated Bibliography for the DEWPOINT project

Webb-Robertson B.M., M.M. Matzke, and C.S. 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, 457-462. Los Alamitos, California:IEEE Computer Society. PNNL-SA-60288.

2008

Curtis D.S., E.S. Peterson, and C.S. 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, edited by J. Cordeiro, J. Filipe and S. Hammoudi, 244-251. Berlin:Springer. PNNL-SA-57895.

Gorton I., C.S. Oehmen, and J.E. McDermott. 2008. "It Takes Glue to Tango: MeDICi integration framework creates data-intensive computing pipeline." Scientific Computing 25, no. 7:16-24. PNNL-SA-62541.

Oehmen C.S., and W.R. Cannon. 2008. "Bringing high performance computing to the biologist’s workbench: approaches, applications and challenges." In SciDAC 2008: Journal of Physics: Conference Series, 125, 012052. Bristol:IOP Publishing Ltd. PNNL-SA-61076. doi:10.1088/1742-6596/125/1/012052

Shah A.R., C.S. Oehmen, and B.M. Webb-Robertson. 2008. "SVM-Hustle - An iterative semi-supervised machine learning approach for pairwise protein remote homology detection." Bioinformatics 24, no. 6:783-790. PNNL-SA-56589.

Shah A.R., V.M. Markowitz, and C.S. Oehmen. 2008. "High-throughput computation of pairwise sequence similarities for multiple genome comparison using ScalaBLAST." In Life Science Systems and Applications Workshop 2007, 89-91. Pisctataway, New Jersey:Institute of Electrical and Electronics Engineers. PNNL-SA-56203. doi:10.1109/LSSA.2007.4400891

Webb-Robertson B.M., C.S. Oehmen, and A.R. Shah. 2008. "A Feature Vector Integration Approach for a Generalized Support Vector Machine Pairwise Homology Algorithm." Computational Biology and Chemistry 32, no. 6:458-461. PNWD-SA-8160. doi:10.1016/j.compbiolchem.2008.07.017

Webb-Robertson B.M., W.R. Cannon, C.S. Oehmen, A.R. Shah, V. Gurumoorthi, M.S. Lipton, and K.M. Waters. 2008. "A Support Vector Machine model for the prediction of proteotypic peptides for accurate mass and time proteomics." Bioinformatics 24, no. 13:1503-1509. PNNL-SA-60074. doi:10.1093/bioinformatics/btn218

2007

De Jong W.A., C.S. Oehmen, and D.J. Baxter. 2007. "Greenbook Algorithms and Hardware Needs Analysis". PNNL-15739. Richland, WA: Pacific Northwest National Laboratory. "Greenbook Algorithms and Hardware Needs Analysis"

Samatova N.F., A. Gorin, E. Uberbacher, T.V. Karpinets, B. Park, C. Pan, and T. Straatsma, et al. 2007. "Data driven computing for Biological Systems." SciDAC Review 5, no. Fall 2007:10-25. PNNL-SA-55247.

Shah A.R., C.S. Oehmen, J.K. Harper, 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, no. 2:138-142. PNNL-SA-48402. doi:10.1016/j.compbiolchem.2007.02.012

Webb-Robertson B.M., C.S. Oehmen, and W.R. 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), 500-505. Washington Dc:IEEE Computer Society. PNNL-SA-58675. doi:10.1109/ICMLA.2007.17

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 proteomic data exploration of microbial organism." Bioinformatics 23, no. 13:1705-1707. PNNL-SA-52772. doi:10.1093/bioinformatics/btm132

2006

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, no. 8:740-749. PNNL-SA-46431.

Oehmen C.S., T. Straatsma, G.A. Anderson, G. Orr, B.M. Webb-Robertson, R.C. Taylor, and R.W. Mooney, et al. 2006. "New Challenges Facing Integrative Biological Science in the Post-Genomic Era." Journal of Biological Systems 14, no. 2:275-293. PNNL-SA-45428.

2005

Cannon W.R., K.H. Jarman, B.M. Webb-Robertson, D.J. Baxter, C.S. Oehmen, K.D. Jarman, and A. Heredia-Langner, et al. 2005. "A Comparison of Probability and Likelihood Models for Peptide Identification from Tandem Mass Spectrometry Data." Journal of Proteome Research 4, no. 5:1687-1698. PNNL-SA-45622.

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, no. 6:440-3. PNNL-SA-45823.