Peer-reviewed Conference Publications

O. Nikolova and S. Aluru. Parallel Algorithm for Large-scale Bayesian Network Structure Learning. To appear in Proc. ACM/IEEE Supercomputing 2012 (acceptance rate: ~21%, 100/472).

O. Nikolova and S. Aluru. Parallel Discovery of Direct Causal Relations and Markov Boundaries with Applications to Gene Networks. Proc. IEEE International Conference on Parallel Processing (ICPP), pp. 512-521, 2011 (acceptance rate: ~22%, 81/363).

O. Nikolova and S. Aluru. Parallel Algorithms for Bayesian Networks Structure Learning with Applications to Systems Biology. Proc. IEEE International Symposium on Parallel and Distributed Processing (IPDPS), Ph.D. Forum, pp. 2045-2048, 2011.

O. Nikolova, J. Zola, S. Aluru. A Parallel Algorithm for Exact Structure Learning of Bayesian Networks. Neural Information Processing Systems (NIPS) Workshop on Learning on Cores, Clusters and Clouds, 2010.

O. Nikolova, J. Zola, S. Aluru. Parallel Algorithm for Exact Bayesian Network Inference. Proc. IEEE International Conference on High Performance Computing (HiPC), pp. 342-349, 2009 (acceptance rate ~18%, 49/261).

J. Beck, B. Buckner, O. Nikolova, D. J. Buckner. Using interdisciplinary bioinformatics undergraduate research to recruit and retain computer science students. In ACM Proc. of the 38th SIGCSE Technical Symposium on Computer Science Education, pp. 358-361, 2007.

Journal Publications

¤ O. Nikolova, M. Aluru, J. Zola, S. Aluru. Bayesian Network Analysis of Regulatory Mechanisms in Arabidopsis Thaliana Using Whole-genome Expression Profiles. In preparation.

¤ O. Nikolova and S. Aluru. Parallel Framework for Large-scale Bayesian Networks Structure Learning. In preparation.

O. Nikolova, J. Zola, S. Aluru. Parallel Globally Optimal Structure Learning of Bayesian Networks. In Press. Journal of Parallel and Distributed Computing. 2013.

L. Guo, H. D. Chen, A. P. Hsia, O. Nikolova, C. T. Yeh, K. Viswanathan, T.J. Wen, N. Zazubovits, K. Ying, S. J. Emrich, R. Swanson-Wagner, D. A. Ashlock, D. Nettleton, P. S. Schnable. Analysis of a new High-density Genetic Map Reveals Chromosome-Level Organization of Gene Expression in Maize. (View preprint)

B. Buckner, J. Beck, K. F. Browning, A. E. Fritz, E. Hoxha, L. D. Grantham, Z. N. Kamvar, A. N. Lough, O. Nikolova, P. S. Schnable, M. J. Scanlon and D. Janick-Buckner. Involving Undergraduates in the Annotation and Analysis of Global Gene Expression Studies: Creation of a Maize Shoot Apical Meristem Expression Database. Genetics, April 2007.

Selected Talks and Presentations

O. Nikolova and S. Aluru. Parallel Discovery of Direct Causal Relations and Markov Boundaries with Applications to Gene Networks. IEEE International Conference on Parallel Processing (ICPP), 2011. (Talk)

O. Nikolova and S. Aluru. Parallel Algorithms for Bayesian Networks Structure Learning with Applications to Systems Biology. IEEE International Symposium on Parallel and Distributed Processing (IPDPS), Ph.D. Forum, 2011. (Poster)

O. Nikolova, J. Zola, S. Aluru. A Parallel Algorithm for Exact Structure Learning of Bayesian Networks. Neural Information Processing Systems (NIPS) Workshop on Learning on Cores, Clusters and Clouds, 2010. (Poster)

O. Nikolova, S. Aluru. Parallel Algorithms for Structure Learning of Bayesian Networks with Applications to Microarray Expression Data. WiML. Vancouver, Canada, 2010. (Poster)

O. Nikolova, R. Swanson-Wagner, C. Yeh, D. Nettleton, P. S. Schnable. Chromosome-level Organization of Gene Expression in Maize. New Mexico Bioinformatics Symposium, 2008. (Poster)

M. Lawrence, H. Hofmann, S. Choi, D. Cook, O. Nikolova, E. Wurtele. Detecting Peaks in Gas and Liquid Chromatography Mass Spectrometric Metabolomics Data. Proc. of 39th Symposium on the Interface: Computing Science and Statistics. Philadelphia, Pennsylvania, 2007. (Talk)

O. Nikolova. Gene Expression and Visualization Application (GENEVA): Development and Use in Shoot Apical Meristem Gene Expression Analysis. 48th Maize Genetics Conference. Pacific Grove, California, 2006. (Poster)

O. Nikolova. Gene Expression and Visualization Application (GENEVA): Development and Use in Shoot Apical Meristem Gene Expression Analysis. Presented at International Maize and Wheat Improvement Center (CIMMYT). El Batan, Mexico, and Argonne Symposium for Undergraduates in Science, Engineering, and Mathematics, Chicago, Illinois (2005). (Talk)