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"ClaMS: A Classifier for Metagenomic Sequences",
Standards in Genomic Sciences, vol. 5, pp. 248-253, 2011.
"Generating Random Graphs with Tunable Clustering Coefficient",
Physica A, vol. 390, pp. 4577-4587, 2011.
"Generating Random Graphs with Tunable Clustering Coefficient",
Physica A, vol. 390, pp. 4577-4587, 2011.
"A Network of Hidden Markov Models and Its Analysis",
2011 International Conference on Bioinformatics and Computational Biology (BIOCOMP'11), Las Vegas, Nevada, 2011.
"A Network of SCOP Hidden Markov Models and Its Analysis",
BMC Bioinformatics, vol. 12, pp. 11 pages, 2011.
"Optimizing a Cost Matrix to Solve Rare-Class Biological Problems",
2011 International Conference on Bioinformatics and Computational Biology (BIOCOMP'11), Las Vegas, Nevada, 2011.
The Problem Solving Handbook for Computational Biology and Bioinformatics,
, Berlin, Springer, pp. 347, 2011.
"A Theoretical Model for Whole Genome Alignment",
Journal of Computational Biology, vol. 18, no. 5, pp. 705-728, 2011.
"Extracting Temporal Signatures for Comprehending Systems Biology Models",
16th ACM SIGKDD Conference on Knowledge Discovery and Data Mining (KDD-2010), Washington, DC, ACM, pp. 453-462, 2010.
"A Genome Compression Algorithm Supporting Manipulation",
9th Annual International Conference on Computational Systems Bioinformatics (CSB 2010), Stanford, California, pp. 38-49, 2010.
"Differential Expression of Heat Shock Protein Genes in Preconditioning for Photosynthetic Acclimation in Water-Stressed Loblolly Pine",
Plant Biochemistry and Physiology, vol. 48, pp. 256-264, 2010.
"Correlation Between Computed Equilibrium Secondary Structure Free Energy and siRNA Efficiency",
IEEE International Conference on Bioinformatics and Biomedicine Workshop, Washington, DC, pp. pp. 351–351, 2009.
"Multimodal Networks: Structure and Operations",
IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 6, pp. 321-332, 2009.
Abstract
"Semantics of Multimodal Network Models",
IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 6, pp. 271-280, 2009.
"CMGSDB: Integrating Heterogeneous Caenorhabditis elegans Data Sources Using Compositional Data Mining",
Nucleic Acids Research, vol. 36, pp. D69-76, 2008.
"Molecular and Physiological Adaptation to Prolonged Drought Stress in the Leaves of two Andean Potato Genotypes",
Functional Plant Biology, vol. 35, pp. 669-688, 2008.
"Tuber Development Phenotypes in Adapted and Acclimated, Drought-stressed Solanum tuberosum ssp. andigena Have Distinct Expression Profiles of Genes Associated with Carbon Metabolism",
Plant Physiology and Biochemistry, vol. 46, pp. pp. 34-45, 2008.
"Genomic signatures from DNA word graphs (poster)",
Grace Hopper Celebration of Women in Computing, , 10/2007.
"Early PLD$\alpha$-Mediated Events in Response to Progressive Drought Stress in Arabidopsis: A Transcriptome Analysis",
Journal of Experimental Botany, vol. 58, pp. pp. 241-252, 2007.
"Genomic Signatures from DNA Word Graphs",
Proceedings of the Third International Symposium on Bioinformatics Research and Applications, ISBRA , vol. 4463, pp. pp. 317-328., 2007.
"Genomic Signatures in de Bruijn Chains",
Proceedings of the Workshop on Algorithms in Bioinformatics (WABI), vol. 4645, pp. pp. 216-227. , 2007.
"Multimodal Networks: Structure and Operations",
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2007.
"Predicting Markov Chain Order in Genomic Sequences",
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine (BIBM): IEEE Computer Society Press, 2007.
"Semantics of Multimodal Network Models,",
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2007.
"Accessions of Solanum tuberosum ssp. andigena Show Differences in Photosynthetic Recovery After Drought Stress as Reflected in Gene Expression Profiles",
Plant Science , vol. 171, pp. pp. 745-758. , 2006.