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"Guest Editor's Introduction: Computationally Driven Experimental Biology",
Computer, vol. 45, Los Alamitos, CA, USA, IEEE Computer Society, pp. 22-23, 2012.
Abstract
"Sensitive detection of pathway perturbations in cancers",
BMC Bioinformatics, vol. 13, no. Suppl 3, pp. S9+, 2012.
"Discovering networks of perturbed biological processes in hepatocyte cultures.",
PLoS one, vol. 6, no. 1, 2011.
"Network-based functional enrichment",
BMC Bioinformatics, vol. 12, no. Suppl 13, pp. S9+, 2011.
"Network-Based Prediction and Analysis of HIV Dependency Factors",
PLoS Comput Biol, vol. 7, no. 9: Public Library of Science, pp. e1002164+, 2011.
"Supervised learning and prediction of physical interactions between human and {HIV} proteins.",
Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases, vol. 11, no. 5, pp. 917–923, 2011.
"Networks in Computational Systems Biology",
Problem Solving Handbook in Computational Biology and Bioinformatics, second edition: Springer-Verlag, 2010.
"Capturing Truthiness: Mining Truth Tables in Binary Datasets",
Proceedings of the 24th Annual ACM Symposium on Applied Computing (SAC'09; Data Mining Track): ACM, pp. 1467–1474, March, 2009.
"Computational Systems Biology",
Algorithms and Theory of Computation Handbook, second edition: Chapman & Hall/CRC Press, 2009.
"A Comparative Study of Transcriptional Profiles of Primary Hepatocytes in Collagen Sandwich and Monolayer Cultures",
American Institute of Chemical Engineers (AIChE) Annual Meeting, 11/2009.
"Cross-conditional Analysis of Host Response to Pathogen Infection",
17th Annual International Conference on Intelligent Systems for Molecular Biology, 06/2009.
"PIG–the pathogen interaction gateway.",
Nucleic Acids Res, vol. 37, no. Database issue, pp. D647-50, 2009.
Abstract
"Compositional Mining of Multi-relational Biological Datasets",
ACM Transactions on Knowledge Discovery from Data, vol. 2, no. 1, March, 2008.
"Compositional Mining of Multirelational Biological Datasets",
ACM Transactions on Knowledge Discovery from Data, vol. 2, no. 1, 03/2008.
"Atomic level computational identification of ligand migration pathways between solvent and binding site in myoglobin",
Proceedings of the National Academy of Sciences, vol. 105, no. 27, pp. 9204-9209, 2008.
Abstract
"The landscape of human proteins interacting with viruses and other pathogens.",
PLoS Pathog, vol. 4, no. 2, pp. e32, 2008.
Abstract
"Network Legos: Building Blocks of Cellular Wiring Diagrams",
Journal of Computational Biology, 2008.
"Computational prediction of host-pathogen protein-protein interactions.",
Bioinformatics, vol. 23, no. 13, Genetics, Bioinformatics and Computational Biology Program, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA. dyermd@vbi.vt.edu, pp. i159-66, 2007.
Abstract
"Expression Divergence of Tandemly Arrayed Genes in Human and Mouse",
Comparative and Functional Genomics, vol. 2007, pp. Article ID 60964, 8 pages, 2007.
"Expression divergence of tandemly arrayed genes in human and mouse.",
Comp Funct Genomics, pp. 60964, 2007.
Abstract
"Network Legos: Building Blocks of Cellular Wiring Diagrams",
Proceedings of the Eleventh Annual International Conference on Research in Computational Molecular Biology (RECOMB), pp. 47–61, 2007.
"The Art of Gene Function Prediction",
Nature Biotechnology, vol. 12, pp. 1474–1475, 2006.
"Automatic Layout and Visualisation of Biclusters",
Algorithms in Molecular Biology, pp. 15, 2006.
"Response diversity of Arabidopsis thaliana ecotypes in elevated CO/2 in the field.",
Plant Mol Biol, vol. 62, no. 4-5, pp. 593-609, 2006.
Abstract