Refereed Conference and Workshop Papers

17 results
- Schoeneman, F., Mahapatra, S., Chandola, V., Napp, N. and Zola, J., "Error Metrics for Learning Reliable Manifolds from Streaming Data", In Proc. SIAM Int. Conference on Data Mining (SDM), pp. 750-758, 2017.

- Karan, S. and Zola, J., "Exact Structure Learning of Bayesian Networks by Optimal Path Extension", In Proc. IEEE Int. Conference on Big Data (IEEE BigData), pp. 48-55, 2016.

- Zola, J., "Constructing Similarity Graphs from Large-Scale Biological Sequence Collections", In Proc. IEEE Int. Workshop on High Performance Computational Biology (HiCOMB), pp. 500–507, 2014.

- Nihalani, R., Zola, J. and Aluru, S., "Resolving Read Assignment Ambiguities in Metagenomic Clustering", In Proc. ISCA Int. Conference on Bioinformatics and Computational Biology (BICoB), 2013.
- Diaz-Montes, J., Xie, Y., Rodero, I., Zola, J., Ganapathysubramanian, B. and Parashar, M., "Exploring the Use of Elastic Resource Federations for Enabling Large-Scale Scientific Workflows", In Proc. Workshop on Many-Task Computing on Clouds, Grids, and Supercomputers (MTAGS), 2013.
**(best paper award finalist)**

- Yang, X., Zola, J. and Aluru, S., "Parallel Metagenomic Sequence Clustering Via Sketching and Maximal Quasi-clique Enumeration on Map-Reduce Clouds", In Proc. IEEE Int. Parallel and Distributed Processing Symposium (IPDPS), pp. 1223–1233, 2011.

- Zola, J., Sarje, A. and Aluru, S., "Constructing Gene Regulatory Networks on Clusters of Cell Processors", In Proc. Int. Conference on Parallel Processing (ICPP), pp. 108–115, 2009.
**(joint first author)** - Nikolova, O., Zola, J. and Aluru, S., "A Parallel Algorithm for Exact Bayesian Network Inference", In Proc. Int. Conference on High Performance Computing (HiPC), pp. 342-349, 2009.

- Zola, J., Aluru, M. and Aluru, S., "Parallel Information Theory Based Construction of Gene Regulatory Networks", In Proc. Int. Conference on High Performance Computing (HiPC), vol. 5375, pp. 336–349, 2008.

- Zola, J., Yang, X., Rospondek, A. and Aluru, S., "Parallel T-Coffee: A Parallel Multiple Sequence Aligner", In Proc. ISCA Int. Conference on Parallel and Distributed Computing and Systems (PDCS), pp. 248-253, 2007.
- Ott, M., Zola, J., Aluru, S. and Stamatakis, A., "Large-Scale Maximum Likelihood-Based Phylogenetic Analysis on the IBM BlueGene/L", In Proc. ACM/IEEE Conference on Supercomputing, 2007.
**(best paper award finalist)**

- Zola, J., Trystram, D., Tchernykh, A. and Brizuela, C., "Parallel Multiple Sequence Alignment With Local Phylogeny Search by Simulated Annealing", In Proc. IEEE Int. Workshop on High Performance Computational Biology (HiCOMB), 2006.

- Trystram, D. and Zola, J., "Parallel Multiple Sequence Alignment with Decentralized Cache Support", In Proc. Int. European Conference on Parallel and Distributed Computing (Euro-Par), vol. 3648, pp. 1217–1226, 2005.

- Zola, J., Lacinski, L. and Wyrzykowski, R., "An Object Oriented Library for Evolution Programs", In Proc. IUTAM Symposium on Evolutionary Methods in Mechanics, vol. 117, pp. 351–360, 2004.
- Zola, J., "CaLi, Efficient Library for Cache Implementation", In Proc. Mexican International Conference on Computer Science (ENC), pp. 415–420, 2004.
- Parmentier, G., Trystram, D. and Zola, J., "Cache-Based Parallelization of Multiple Sequence Alignment Problem", In Proc. Int. European Conference on Parallel and Distributed Computing (Euro-Par), vol. 3149, pp. 1005-1012, 2004.

- Zola, J. and Wyrzykowski, R., "EPL-Julia the High-Performance Library for Evolutionary Computations", In Proc. Int. Conference on Parallel Processing and Applied Mathematics (PPAM), vol. 2328, pp. 652–659, 2002.

Journal Articles

14 results
- Wodo, O., Zola, J., Pokuri, B.S.S., Du, P. and Ganapathysubramanian, B., "Automated, High Throughput Exploration of Process-structure-property Relationships Using the MapReduce Paradigm", In Materials Discovery, vol. 1, pp. 21–28, 2015.
- Samudrala, S.K., Zola, J., Aluru, S. and Ganapathysubramanian, B., "Parallel Framework for Dimensionality Reduction of Large-Scale Datasets", In Scientific Programming, 2015.
- Clauvelin, N., Lo, P., Kulaeva, O.I., Nizovtseva, E.V., Diaz-Montes, J., Zola, J., Parashar, M., Studitsky, V.M. and Olson, W.K., "Nucleosome Positioning and Composition Modulate In Silico Chromatin Flexibility", In Journal of Physics: Condensed Matter, vol. 27, no. 6, pp. 064112, 2015.

- Diaz-Montes, J., Xie, Y., Rodero, I., Zola, J., Ganapathysubramanian, B. and Parashar, M., "Federated Computing for the Masses – Aggregating Resources to Tackle Large-Scale Engineering Problems", In Computing in Science and Engineering, vol. 16, no. 4, pp. 62–72, 2014.

- Yang, X., Zola, J. and Aluru, S., "Large-Scale Metagenomic Clustering on Map-Reduce Clusters", In Journal of Bioinformatics and Computational Biology, vol. 11, no. 1, pp. 1340001, 2013.
**(joint first author)** - Nikolova, O., Zola, J. and Aluru, S., "Parallel Globally Optimal Structure Learning of Bayesian Networks", In Journal of Parallel and Distributed Computing, vol. 73, no. 8, pp. 1039–1048, 2013.
- Aluru, M., Zola, J., Nettleton, D. and Aluru, S., "Reverse Engineering and Analysis of Large Genome-Scale Gene Networks", In Nucleic Acids Research, vol. 41, no. 1, pp. e24, 2013.
**(joint first author)**

- Yu, X., Li, L., Zola, J., Aluru, M., Ye, H., Foudree, A., Guo, H., Anderson, S., Aluru, S., Liu, P., Rodermel, S. and Yin, Y., "A Brassinosteroid Transcriptional Network Revealed by Genome-Wide Identification of BESI Target Genes in Arabidopsis thaliana", In Plant Journal, vol. 65, no. 4, pp. 634–646, 2011.
- Sarje, A., Zola, J. and Aluru, S., "Accelerating Pairwise Computations on Cell Processors", In IEEE Transactions on Parallel and Distributed Systems, vol. 22, no. 1, pp. 69–77, 2011.
**(joint first author)**

- Zola, J., Aluru, M., Sarje, A. and Aluru, S., "Parallel Information-Theory-Based Construction of Genome-Wide Gene Regulatory Networks", In IEEE Transactions on Parallel and Distributed Systems, vol. 21, no. 12, pp. 1721–1733, 2010.

- Aluru, M.R., Zola, J., Foudree, A. and Rodermel, S.R., "Chloroplast Photooxidation-Induced Transcriptome Reprogramming in Arabidopsis Immutans White Leaf Sectors", In Plant Physiology, vol. 150, no. 2, pp. 904–923, 2009.

- Ott, M., Zola, J., Aluru, S. and others, "Large-Scale Phylogenetic Analysis on Current HPC Architectures", In Scientific Programming, vol. 16, no. 1-2, pp. 255-270, 2008.

- Dziubecki, P. and Zola, J., "Grid Portal for Multiple Sequence Alignment", In Computing, Multimedia and Intelligent Techniques, vol. 3, no. 1, pp. 33-42, 2007.

- Parmentier, G., Trystram, D. and Zola, J., "Large Scale Multiple Sequence Alignment with Simultaneous Phylogeny Inference", In Journal of Parallel and Distributed Computing, vol. 66, no. 12, pp. 1534–1545, 2006.

Book Chapters

4 results
- Zola, J., "Parallel Computing for Gene Networks Reverse Engineering", In Approaches in Integrative Bioinformatics, Springer, 2014.

- Zola, J. and Aluru, S., "Network Inference in Systems Biology", In Encyclopedia of Parallel Computing, Springer, 2011.

- Sarje, A., Zola, J. and Aluru, S., "Pairwise Computations on the Cell Processor with Applications in Computational Biology", In Scientific Computing with Multicore and Accelerators, Chapman and Hall/CRC, 2010.

- Trystram, D. and Zola, J., "Multiple Sequence Alignment and Phylogenetic Inference", In Grids for Bioinformatics and Computational Biology, John Wiley and Sons, 2007.

Other Publications

2 results
- Karan, S. and Zola, J., "Scalable Exact Parent Sets Identification in Bayesian Networks Learning with Apache Spark", 2017.

- "Federated Computing for the Masses – Aggregating Resources to Tackle Large-Scale Engineering Problems", Technical report, Rutgers Discovery Informatics Institute, no. TR-RDI2-20130515-0, 2013.

- Invited talk: Sketching Biological Sequences for Storage and Computation. Presented at Workshop on Parallel Software Libraries for Sequence Analysis (pSALSA), Seattle, October 2016.
- Invited talk: Parallel Computing for Large-scale Computational Biology. Presented at Pharmacology and Toxicology Seminar Series at University at Buffalo, October 2015.
- Invited talk: Similarity Detection in Large Sequence Collections. Presented at Workshop on Parallel Software Libraries for Sequence Analysis (pSALSA), September 2015.
- Three-hours tutorial: How to Find Who Lives in Your Belly Button: Not Too Short Introduction to Metagenomics. Presented at DIMACS Center for Discrete Mathematics and Theoretical Computer Science, June 2014.
- Invited talk: Constructing Similarity Graphs from Large-scale Biological Sequence Collections. Presented at Drexel University, March 2013.
- Panelist: Big Data Standards and the Potential Long Term Benefits for Research and Clinical Development. Webinar organized by NGSLeaders, December 2012.
- Keynote talk: Large Scale Metagenomic Clustering. Presented at International Conference on the Bioinformatics of Genome Regulation and Structure/Systems Biology in Novosibirsk, Russia, June 2012.
- Three-hours tutorial: Not Too Short Introduction to Metagenomics. Presented at Czestochowa University of Technology, Poland, December 2011.
- Keynote talk: Computational Biology: Can We Do Without Parallel Computing? Presented at Corporacion Universitaria para el Desarrollo de Internet meeting in Puebla, Mexico, April 2009.
- Invited lectures: Introduction to Bioinformatics; and High Performance Computational Biology. Presented at Pannon University, Hungary, May 2006.
- Two-hours talk with Denis Trystram: Bio-Computing Today: What to Expect from Parallel and Distributed Systems? Presented at 4th Franco-Mexican School on Distributed Systems in Grenoble, France, July 2005.
- Seminar: Parallel Server for Large Scale Multiple Sequence Alignment. Presented at Poznan University of Technology, Institute of Computing Science, Poland, May 2005.
- Invited talk with Roman Wyrzykowski and Tomasz Olas: Parallel FEM Computations on PC-Based Cluster Using Myrinet. Presented at Myrinet User's Group Conference in Vienna, Austria, May 2002.

© 2014-2017 Jaroslaw Zola