Computational Biology Publications

Computational Biology Journal Articles and Book Chapters:

Chaitankar, V., Zhang, C., Ghosh, P., Perkins, E., Gong, P., & Deng, Y. (2011). Predictive minimum description length principle approach to infer gene regulatory networks Springer Computational Biology and Bioinformatics.

Chen, J. (2010). A hybrid direct visual editing method for architectural massing study in virtual environments Collaborative Design in Virtual Environments.

Gene Ontology Consortium. (2010). The Gene Ontology in 2010: extensions and refinements. Nucleic Acids Reseach, 38(Database issue), D331-335.

Ghosh, P., Basu, K., Das, S., & Zhang, C. (2010). Discrete diffusion models to study the effects of Mg2+ concentration on the PhoPQ signal transduction system. BMC Genomics, 11(Suppl 3).

Harhay, G., Smith, T., Alexander, L., Haudenschild, C., Keele, J., Matukumalli, L., Schroeder, S. G., Van Tassell, C. P., Gresham, C. R., Bridges, S. M., Burgess, S. C., Sonstegard, T. S. (2010). An atlas of bovine gene expression reveals novel distinctive tissue characteristics and evidence for improving genome annotation. Genome Biology, 11(10), R102.

Isokpehi, R., Cohly, H., Matthew, A., Rajendram, R., Tchounwou, P., Udensi, U., et al. (2010). Candidate single nucleotide polymorphism markers for arsenic responsiveness of protein targets. Bioinformatics and Biology Insights, 4, 99-111.

Isokpehi, R., Shaneka, S., Hari, C., Stephen, E., Gregorio, B., & Wellington, A. (2011). Identification of Drought Responsive Viridiplantae Universal Stress Proteins. Bioinformatics and Biology Insights, 5, 7-16.

Jankun-Kelly, T. J., Lindeman, A. D., & Bridges, S. M. (2009). Exploratory visual analysis of conserved domains on multiple sequence alignments. BMC Bioinformatics, 10 Suppl 11(10), S7.

Johnson, M., Isokpehi, R. D., Cohly, H. H. P., & Awofolu, O. (2010). The case for visual analytics of arsenic concentrations in foods. International Journal of Environmental Research Public Health, 7(5), 1970-1983.

Kelley, R., Gresham, C., Harper, J., Bridges, S., Warburton, M., Hawkins, L., et al. (2010). Integrated database for identifying candidate genes for Aspergillus flavus resistance in maize. BMC Bioinformatics, 11(Suppl 6), S25.

Kelley, R. Y., Williams, W. P., Mylroie, J. E., Boykin, D. L., Hawkins, L. K., Windham, G. L., et al. (2009). Genomic profile of maize response to Aspergillus flavus infection. Toxin Reviews, 28(203), 229-241.

Kostyuk, N., Isokpehi, R. D., Rajnarayanan, R., & Cohly, H. H. P. (2010). Autism from a biometric perspective. International Journal of Environmental Research and Public Health, 7(5), 1984-1995.

Kostyuk, N., Meghanathan, N., Isokpehi, R. D., Bell, T., Rajnarayanan, R., Mahecha, O., et al. (2010). Biometric evaluation of anxiety in learning English as a second language. International Journal of Computer Science and Network Security, 10(1), 220-229.

Li, Y., Wang, N., Perkins, E., Zhang, C., & Gong, P. (2010). Identification and Optimization of Classifier Genes from Multi-Class Earthworm Microarray Dataset. PLoS One, 5(10).

Manda, P., Freeman, M., Bridges, S., Jankun-Kelly, T., Nanduri, B., McCarthy, F., et al. (2010). GOModeler--a tool for hypothesis-testing of functional genomics datasets. BMC Bioinformatics, 11(Suppl 6), s29.

Malone, B., M., Perkins, A. D., & Bridges, S. M. (2009). Integrating phenotype and gene expression data for predicting gene function. BMC Bioinformatics, 10(Suppl 11), S20.

McCarthy, F., Gresham, C., Buza, T., Chouvarine, P., Pillai, L., Kumar, R., Ozkan, S., Wang, H., Manda, P., Arick, T., Bridges, S. M., Burgess, S. C. (2011). AgBase: supporting functional modeling in agricultural organisms. Nucleic Acids Reseach, 30, D497-506.

Meghanathan, N. (2010). A Proposal for Graph Theoretic Analysis of Protein- Protein Interaction (PPI) Networks. Journal of Computer Technology and Applications, 1(1), 4-7.

Nanduri, B., Wang, N., Lawrence, M. L., Bridges, S. M., & Burgess, S. C. (2010). Gene model detection using mass spectrometry Methods Mol Biol (Vol. 604, pp. 137-144).

Paul, D., Austin, F., Arick, T., Bridges, S., Burgess, S., Dandass, Y., et al. (2010). Geneome sequence of the solvent-producing bacterium Clostridium carboxidivorans strain P7T. Journal of Bacteriology, 192(20), 5554-5555.

Paul, D., Kumar, R., Nanduri, B., French, T., Pendarvis, K., Brown, A., et al. (2011). Proteome and membrane fatty acid analyses on Oligotropha carboxidovorans OM5 grown under chemolithoautotrophic and heterotrophic conditions. PLoS One. 6(2):e17111.

Pendarvis, K., Kumar, R., Burgess, S. C., & Nanduri, B. (2009). An automated proteomic data analysis workflow for mass spectrometry. BMC Bioinformatics, 10(Suppl 11), S17.

Rodriguez-Osorio, N., Wang, H., Rupinksi, J., Bridges, S. M., & Memili, E. (2007). Comparative functional genomics of mammalian DNA methyltransferases. Reprod. Biomed Online, 20(2), 243-255.

Sanders WS, W. N., Bridges SM, Malone BM, Dandass YS, McCarthy FM, Nanduri B, Lawrence ML, Burgess SC. (2011). The Proteogenomic Mapping Tool. BMC Bioinformatics, 12(1), 115.

Shah, P., Nanduri, B., Swiatlo, E., Ma, Y., & Pendarvis, K. (2011). Polyamine biosynthesis and transport mechanisms are crucial for fitness and pathogenesis of Streptococcus pneumoniae. Microbiology 157(Pt 2), 504-15.

Sivakumar, S., & Meghanathan, N. (2010). Medical Image Indexing using Attributed Relational Graphs and Rectangular Trees. Journal of Advanced Research in Computer Science, 1(4), 431-439.

Udensi, U., Cohly, H., Barbara, G.-E., Ndebele, K., Garcia-Reyero, N., Nanduri, B., et al. (2011). Aberrantly expressed genes in HaCaT keratinocytes chronically exposed to arsenic trioxide. Biomarker Insights, 5, 41-58.

Yuan, C., Lim, H. L., & Littman, M. L. (2011). Most relevant explanation: Computational complexity and approximation methods. Annals of Mathematics and Artificial Intelligence.

Wren, J. D., Gusev, Y., Isokpehi, R. D., Berleant, D., Braga-Neto, U., Wilkins, D., et al. (2009). Proceedings of the 2009 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) conference. Introduction. BMC Bioinformatics, 10 Suppl 11(10), S1.

Computational Biology Conference Papers and Presentations:

Ahmed, R., Ali, A., Wang, N., & Zhang, C. (2011). Parallel Implementation of Combined Binary and Multi-Class Support Vector Machines for Classification of Biological Data. Paper presented at the MCBIOS 2011, College Station, Texas.

Ammari, M., McCarthy, F. M., Nanduri, B., & Pinchuk, L. M. (2010). Analysis of Bovine Viral Diarrhea Viruses-infected monocytes: identification of cytopathic and non-cytopathic biotype differences. Paper presented at the BMC Bioinformtaics.

Anderson, R., & Dandass, Y. (2011). A Protocol for Realtime Switched Communication in FPGA Clusters. Paper presented at the Proceedings of the International Conference on Parallel and Distributed Processing Techniques and Applications (PDPTA'11),.

Bacim, F., Polys, N., Chen, J., Setareh, M., Li, J., & Ma, L. (2010). Cognitive scaffolding in Web3D learning Systems: A Case Study for Form and Structure. Paper presented at the ACM Web3D.

Chaitankar, V., Ghosh, P., Elasri, M., & Perkins, E. (2011). Gene Regulatory Network Inference Using Time Lagged Context Likelyhood of Relatedness. Paper presented at the IEEE ICCABS.

Chaitankar, V., Ghosh, P., Elasri, Mohamed, & Perkins, E. (2011). A scalable gene regulatory network reconstruction algorithm combining gene knock-out data. Paper presented at the 3rd International Conference on Bioinformatics and Computational Biology (BICoB).

Chaitankar, V., Ghosh, P., Zhang, C., & Perkins, E. (2010). Effects of CDNA microarray data size on gene regulatory network inference accuracy. Paper presented at the ACM BCB.

Chaitankar, V., Ghosh, P., & Zhang, C. (2010, February 20-21, 2010). Transcriptional time lagged information approach to improving the accuracy of gene regulatory network reconstruction. Paper presented at the MCBIOS 2010, Jonesboro, Arkansas.

Chen, J., Riskin, D., Hubel, T. Y., Willis, D., Song, A., Liu, H., et al. (2010). Exploration of Bat Wing Morphology Through A Strip Method and Visualization. Paper presented at the SIGGRAPH (talk).

Fly, P., Meghanathan, N., & Isokpehi, R. (2011a). Implementation of the Binary Coding Scheme to Test for Ancestor-Descendant Relationships in K-ary Trees. Paper presented at the The 8th Annual Conference of the Mid-South Computational Biology and Bioinformatics Society (MCBIOS 2011), College Station, TX, USA.

Fly, P., Meghanathan, N., & Isokpehi, R. (2011b). Use of Binary Codes to Determine Ancestor-Descendant Relationships in K-ary Trees. Paper presented at the Journal of the Mississippi Academy of Sciences, Hattiesburg, MS, USA.

Fu, G., Liu, S., Nan, X., Zhao, Z., Chen, Y., Wilkins, D., et al. (2011). Implementation of Machine-Learning Algorithms for Identification and Development of Novel GSK-3? Inhibitors. Paper presented at the 242nd American Chemical Society (ACS) National Meeting & Exposition, Denver, CO, USA.

Gautam, D., Gaines, T., Ankala, A., Sonstegard, T., Schroeder, S., Wilkinson, J., Perksins, A. (2011). A Probabilistic Approach for Improved Sequence Mapping in Metatranscriptomic Studies. Paper presented at the MCBIOS 2011, College Station, TX.

Gautam, D., Johnston, I., Bhowmik, T., Ankala, A., Sonstegard, T., Schroeder, S., et al. (2010). High Throughput Sequence Analysis for Disease Resistance in Maize. Paper presented at the MCBIOS 2010.

Ghosh, P., Kumar, A., & Rangachari, V. (2010, February 20-21, 2010). Molecular level simulation of competing pathways in AB42 peptide aggregation towards a realistic understanding of Alzheimer's disease. Paper presented at the MCBIOS 2010, Jonesboro, Arkansas.

Ghosh, P., Kumar, A., Datta, B., & Rangachari, V. (2010). Estimating the dynamics of protofibril elongation involved in AB42 peptide aggregation in Alzheimer's disease. Paper presented at the ACM BCB.

Ghosh, P., Mayo, M., Chaitankar, V., Habib, T., Perkins, E., & Das, S. (2011). Principles of genomic robustness inspire fault-tolerant WSN topologies: A network science based case study. Paper presented at the Percom Workshops.

Gong, P., Wu, X., Li, Y., Li, P., Yang, Y., Zhang, C., et al. (2011). Network Analysis Sheds Light on Molecular Mechanisms for Chemical-Induced Reversible Neurotoxicity. Paper presented at the MCBIOS 2011, College Station, Texas.

Jay, J., Eblen, J., Zhang, Y., Benson, M., Perkins, A., Saxton, A., et al. (2011). A Systematic Comparison of Genome Scale Clustering Algorithms. Paper presented at the International Symposium on Bioinformatics Research and Applications.

Johnson, M., Gautam, D., Ankala, A., Sonstegard, T., Schroeder, S., Wilkinson, J., Ramkumar, M., Perkins, A. (2011). A Statistical Approach for Ambiguous Sequence Mappings. Paper presented at the MCBIOS 2011, College Station, TX.

Kostyuk, N., Rajnarayanan, R., Isokpehi, R. D., & Meghanathan, N. (2010, February 20-21, 2010). Non-invasive, real-time, mobile biometrics device: Pilot evaluation studies. Paper presented at the MCBIOS 2010, Jonesboro, Arkansas.

Kumar, R., & Nanduri, B. (2010). HPIDB--a unified resource for host-pathogen interactions. Paper presented at the BMC Bioinformatics.

Li, H., Gong, P., Perkins, E., Wang, Nan, & Zhang, C. (2011). Learn the Structure of Transition Gene Regulatory Networks from Time Series Microarray Data. Paper presented at the MCBIOS 2011, College Station, Texas.

Li, Y., Gong, P., Perkins, E. J., Zhang, C., & Wang, N. (2011). Microarray Data Mining and Gene Regulatory Network Analysis. Paper presented at the MCBIOS 2011, College Station, Texas.

Li, Y., Gong, P., Zhang, C., & Wang, N. (2011). RefNet : A Cyber-based Tool for Building Homologous Gene Regulatory Networks from Expressed Sequence Tags (ESTs). Paper presented at the MCBIOS 2011, College Station, Texas.

Li, Y., Gong, P., Zhang, C., Perkins, E. J., & Wang, N. (2010). ETK: A knowledgebase for earthworm toxicogenomics. Paper presented at the MCBIOS 2010.

Li, Y., Wang, N., Perkins, E. J., Zhang, C., & Gong, P. (2010). Statistics measurements for increased confidence in target-decoy search strategy. Paper presented at the MCBIOS 2010.

Lim, H., & Yuan, C. (2010, January 6-8). Computational complexity and approximation methods of most relevant explanation. Paper presented at the Eleventh International Symposium on Artificial Intelligence and Mathematics (ISAIM-10), Ft. Lauderdale, FL.

Liu, S., Chen, Y., & Wilkins, D. (2010). Diffusion kernel large margin random forests classification for integrated biological prediction. Paper presented at the MCBIOS 2010.

Liu, H., Bragdon, A., Bergou, A., & Chen, J. (2011). Programming by sketch for scientific computing. Paper presented at the ACM SIGGRAPH Symposium on Interactive 3D Graphics and Games, San Fransisco, CA.

Liu, S., Chen, Y., & Wilkins, D. (2010). Large Margin Classifiers and Random Forests for Integrated Biological Prediction on Mixed Type Data. Paper presented at the The 7th Annual Biotechnology and Bioinformatics Symposium (BIOT), Lafayette, LA.

Liu, S., Chen, Y., Wilkins, D., & Doerksen, R. J. (2011). Joint Rule Extraction and Feature Selection from Multi-Class Biological Data. Paper presented at the The Eighth Annual Conference of the MidSouth Computational Biology and Bioinformatics Society, College Station, TX.

Liu, S., Huang, J., Wang, N., Doerksen, R. J., Chen, Y., & Wilkins, D. (2011). Improving Glycan Classification with TF/IDF Weighting Scheme. Paper presented at the The Eighth Annual Conference of the MidSouth Computational Biology and Bioinformatics Society, College Station, TX.

Malone, B., Yuan, C., & Hansen, E. (2011). Improving the scalability of optimal bayesian network learning with frontier breadth-first branch and bound search. Paper presented at the Proceedings of the 27th Conference on Uncertainty in Artificial Intelligence (UAI-11), San Francisco, CA.

Malone, B., Yuan, C., & Hansen, E. (2011). Memory-efficient dynamic programming for learning optimal bayesian networks. Paper presented at the Proceedings of the 25th AAAI Conference on Artificial Intel- ligence (AAAI-11), Barcelona, Spain.

Malone, B. M., Bridges, S. M., & Tan, F. (2010). Examining the relationship between H3K27me3 and gene expression in rice endosperm using Chip-Seq. Paper presented at the Plant and Animal Genomes XVIII.

Meghanathan, N., Kostyuk, N., Cohly, H. H. P., & Isokpehi, R. D. (2010a). A clustering model for English language anxiety in non-native speakers. Paper presented at the MCBIOS 2010.

Meghanathan, N., Kostyuk, N., Cohly, H. H. P., & Isokpehi, R. D. (2010b, February 20-21, 2010). Quadrant-based modeling for assessing functional state of human organ systems. Paper presented at the MCBIOS 2010, Jonesboro, Arkansas.

Meghanathan, N., & Isokpehi, R. (2011a). A Cross-Reference Data Mining Study of the Universal Stress Protein Datasets of Viridiplantae. Paper presented at the The 8th Annual Conference of the Mid-South Computational Biology and Bioinformatics Society (MCBIOS 2011), College Station, TX, USA.

Meghanathan, N., & Isokpehi, R. (2011b). On the Variations in the Cytotoxicity of Gold Nanoparticles of Different Shapes. Paper presented at the The 8th Annual Conference of the Mid-South Computational Biology and Bioinformatics Society (MCBIOS 2011), College Station, TX, USA.

Nan, X., Chen, Y., Wilkins, D., Wang, N., Gong, P., & Zhang, C. (2010). An Embedded Feature Selection Approach to Multiclass Gene Selection. Paper presented at the The 7th Annual Biotechnology and Bioinformatics Symposium (BIOT), Lafayette, LA.

Nan, X., Fu, G., Zhao, Z., Liu, S., Patel, R. Y., Liu, H., Daga, P. R., Doerksen, R. J., Chen, Y., Wilkins, D. (2011). Leveraging Domain Information to Restructure Biological Prediction. Paper presented at the The Eighth Annual Conference of the MidSouth Computational Biology and Bioinformatics Society, College Station, TX.

Nan, X., Wang, N., Gong, P., Zhang, C., Chen, Y., & Wilkins, D. (2010). Gene Selection Using 1-Norm Regularization for Multi-Class Microarray Data. Paper presented at the IEEE International Conference on Bioinformatics and Biomedicine, Hongkong, China.

Nan, X., Chen, Y., Dang, X., & Wilkins, D. (2010). Learning to Rank Using 1-norm Regularization and Convex Hull Reduction. Paper presented at the ACM-SE 48: Proceedings of the 48th Annual Southeast Regional Conference, Oxford, Mississippi.

Pechan, T., & Gwaltney, S. (2011). Fragment ions in CID, HCD and PQD MSMS spectra of doubly charged penta-peptides, versus theoretical calculations of their relative intensities. Paper presented at the 59th Conference on Mass Spectrometry and Allied Topics, Denver, CO.

Perkins, A. D., & Langston, M. A. (2010). Comparing the effect of microarray preprocessing methods on differential gene correlation. Paper presented at the MCBIOS 2010.

Sanders, W. S., Wang, N., Bridges, S. M., McCarthy, F., & Burgess, S. C. (2010). A staged search strategy for proteomics based structural genome annotation in chicken. Paper presented at the Plant and Animals Genomes XVIII.

Sonstegard, T., Harhay, G., Alexander, L. J., Schroeder, S., Keele, J. W., Matukumalli, L., et al. (2010). Information theoretical analysis of a Bovine Gene Atlas reveals chromosomal regions with tissue specific gene expression. Paper presented at the Plant and Animal Genomes XVIII

Tang, J. D., Perkins, A. D., Sonstegard, T., Burgess, S. C., & Diehl, S. (2010). Assembling a novel fungal genome from short read sequencing data. Paper presented at the MCBIOS 2010.

Tang, J., Perkins, A., & Diehl, S. (2011). Gene expression analysis of a copper-tolerant brown rot fungus on MCQ-treated wood. Paper presented at the Proceedings of the 42nd annual meeting of the International Research Group on Wood Protection, Queenstown, New Zealand.

Vicknair, C. (2010). Research issues in data provenance. Paper presented at the ACM-SE 48: Proceedings of the 48th Annual Southeast Regional Conference, Oxford, Mississippi.

Vicknair, C., Macias, M., Zhendong, Z., Nan, X., Chen, Y., & Wilkins, D. (2010a). A comparison of a graph database and a relational database: A data provenance perspective. Paper presented at the ACM-SE 48: Proceedings of the 48th Annual Southeast Regional Conference, Oxford, MS.

Vicknair, C., Macias, M., Zhendong, Z., Nan, X., Chen, Y., & Wilkins, D. (2010b). An empirical comparison of data management methods for scientific workflow metadata. Paper presented at the MCBIOS 2010.

Wang, N., Xing, J., Gong, P., Meyers, J., & Zhang, C. (2011). miRDisc: An Approach for Prediction and Identification of Novel microRNAs. Paper presented at the MCBIOS 2011, College Station, Texas.

Wang, N., Zhou, Y., & McLean, T. (2011). Karenia Brevis Knowledge Base (KbKB): A Functional Genomics Resource for Karenia brevis. Paper presented at the MCBIOS 2011, College Station, Texas.

Yuan, C. Y., Malone, B., & Wu, X. (2011). Learning optimal Bayesian networks using A* search. Paper presented at the Proceedings of the 27th Conference on Uncertainty in Artificial Intelligence (UAI-11), Barcelona, Spain.

Yuan, C., & Wu, X. (2010, January 608). Solving influence diagrams using heuristic search. Paper presented at the Eleventh International Symposium on Artificial Intelligence and Mathematics (ISAIM-10), Ft. Lauderdale, FL.

Zhou, Y., Yang, Y., Wu, X., Wang, N., Gong, P., Perkins, E., et al. (2011). Web-BLOM: A Web-based Application for Network Reconstruction and Analysis. Paper presented at the MCBIOS 2011, College Station, Texas.