U.S. Department of Energy

Pacific Northwest National Laboratory

SDI Publications

2012

An Analysis of Multi-type Relational Interactions in Foundational Model of Anatomy Using Graph Motifs

Zhang GQ, L Luo, C Ogbuji, CA Joslyn, J Mejino, S Sahoo. 2012. "An Analysis of Multi-type Relational Interactions in Foundational Model of Anatomy Using Graph Motifs", in American Medical Information Association 2012 Symposium.

Evolutionary Drift Models for Moving Target Defense

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. 

Directional Bias and Pheromone for Discovery and Coverage on Networks

Fink GA, KS Berenhaut, and CS Oehmen. 2012. "Directional Bias and Pheromone for Discovery and Coverage on Networks". In Proceedings of the 6th IEEE International Conference on Self Adaptive and Self-Organizing Systems, Paris, France. doi: 10.1109/SASO.2012.32

A comparative analysis of computational approaches to protein quantification in label-free LC-MS proteomics experiments

Matzke MM, JN Brown, MA Gritsenko, TO Metz, JG Pounds, KD Rodland, AK Shukla, RD Smith, KM Waters, JE McDermott, and BJ Webb-Robertson. 2013. "A comparative analysis of computational approaches to protein quantification in label-free LC-MS proteomics experiments." Proteomics Reviews. 13(3-4):493-503. doi: 10.1002/pmic.201200269

Suppressed Expression of T-Box Transcription Factors is Involved in Senescence in Chronic Obstructive Pulmonary Disease

Acquaah-Mensah G, D Malhotra, M Vulimiri, JE McDermott, and S Biswal. 2012. "Suppressed Expression of T-Box Transcription Factors is Involved in Senescence in Chronic Obstructive Pulmonary Disease." PLoS Computational Biology 8(7):e1002597. doi:10.1371/journal.pcbi.1002597.

Probabilistic Approximate Matrix Decomposition for Non-Negative Matrix Factorization

"Probabilistic Approximate Matrix Decomposition for Non-Negative Matrix Factorization." PNNL-SA-88302. Prepared for Neural Information Processing Conference.

Bayesian integration of isotope ratio for geographic sourcing of castor beans

Webb-Robertson BJ, HW Kreuzer, G Hart, J Ehleringer, J West, G Gill, and D Duckworth. 2012. Bayesian integration of isotope ratio for geographic sourcing of castor beans. Biomedical Research International. doi:10.1155/2012/450967.

An Efficient Machine Learning Approach To Low-Complexity Filtering In Biological Sequences

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), May 9-12, 2012, San Diego, CA, pp. 237-243. IEEE, Piscataway, NJ. doi:10.1109/CIBCB.2012.6217236.

An Efficient Machine Learning Approach To Low-Complexity Filtering In Biological Sequences

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

Orders on Intervals Over Partially Ordered Sets: Extending Allen's Algebra and Interval Graph Results

Joslyn CA, and EA Hogan. 2012. "Orders on Intervals Over Partially Ordered Sets: Extending Allen's Algebra and Interval Graph Results." Soft Computing. doi: 10.1007/s00500-013-1010-1

Visualizing semantic data through the use of partially ordered sets

Hogan E, and CA Joslyn. 2012. "Visualizing semantic data through the use of partially ordered sets," at the 2012 Joint Mathematics Meeting, January 2012, Boston, MA.

Challenges in Biomarker Discovery: Combining Expert Insights with Statistical Analysis of Complex Omics Data

McDermott JE, J Wang, HD Mitchell, BJM Webb-Robertson, RP Hafen, JA Ramey, II, and KD Rodland. 2012. "Challenges in Biomarker Discovery: Combining Expert Insights with Statistical Analysis of Complex Omics Data." Expert Opinion on Medical Diagnostics. doi:10.1517/17530059.2012.718329.

2011

Scientific Workflows Composition and Deployment on SOA Frameworks

Liu Y, I Gorton, AS Wynne, and AV Kulkarni. 2011. "Scientific Workflows Composition and Deployment on SOA Frameworks." In IEEE 6th International Symposium on Service Oriented System Engineering, (SOSE 2011), December 12-14, 2011, Irvine, California, pp. 134-139. IEEE Computer Society, Los Alamitos, CA. doi:10.1109/SOSE.2011.6139101.

Using Physicochemical Properties of Amino Acids to Induce Graphical Models of Residue Couplings

Hossain KSMT, C Bailey-Kellogg, AM Friedman, MJ Bradley, NA Baker, and N Ramakrishnan. 2011. "Using Physicochemical Properties of Amino Acids to Induce Graphical Models of Residue Couplings." Proceedings of the Tenth International Workshop on Data Mining in Bioinformatics (BioKDD 2011). doi:10.1145/2003351.2003354.

Informatics and Standards for Nanomedicine Technology

Thomas DG, F Klaessig, S Harper, M Fritts, MD Hoover, S Gaheen, R Reznik-Zellen, E Freund, J Klemm, D Paik, and NA Baker. September/October 2011. "Informatics and Standards for Nanomedicine Technology" Wiley Interdisciplinary Reviews (WIREs): Nanomedicine and Nanobiotechnology. 3(5): 511-522. doi:10.1002/wnan.152.

Complex Biological Event Extraction from Full Text using Signatures of Linguistic and Semantic Features

McGrath LR, KO Domico, CD Corley, and BJM Webb-Robertson. 2011. "Complex Biological Event Extraction from Full Text using Signatures of Linguistic and Semantic Features." In The 49th Annual Meeting of the Association for Computational Linguistics: Human Language Technologies: Proceedings of BioNLP Shared Task 2011 Workshop, June 24th, Portland, Oregon, pp. 130-137. Association for Computational Linguistics, Stroudsburg, PA.

Complex biological event extraction from full text using signatures of linguistic and semantic features

McGrath LR, K Domico, CD Corley, and BJ Webb-Robertson. 2011. "Complex biological event extraction from full text using signatures of linguistic and semantic features." Proceedings of the BioNLP Shared Task, 130-137.

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