Juneja, N., Desai, P., Wodo, O., Zola, J. and Chandola, V., "Resource Efficient Bayesian Optimization", In IEEE International Conference on Cloud Computing (IEEE Cloud), 2024.
2023
Sayed, Z. and Zola, J., "SCoOL – Programming Model and Parallel Runtime for Optimization Problems", In IEEE International Conference on High Performance Computing, Data, and Analytics (HiPC), 2023.
2022
Niu, J., Zola, J. and Sariyuce, A.E., "Counting Induced 6-Cycles in Bipartite Graphs", In International Conference on Parallel Processing (ICPP), 2022.
Turkkan, B.O., Dai, T., Raman, A., Kosar, T., Chen, C., Bulut, M.F., Zola, J. and Sow, D., "GreenABR: Energy‐Aware Adaptive Bitrate Streaming with Deep Reinforcement Learning", In ACM Multimedia Systems Conference (MMSys), 2022. (DASH-IF excellence in DASH award (3rd place))
2021
Juneja, N., Zola, J., Chandola, V. and Wodo, O., "Graph-based Strategy for Establishing Morphology Similarity", In International Conference on Scientific and Statistical Database Management (SSDBM), pp. 169–180, 2021.
2020
Javanmard, M.M., Ahmad, Z., Zola, J., Pouchet, L.-N., Chowdhury, R. and Harrison, R., "Efficient Execution of Dynamic Programming Algorithms on Apache Spark", In IEEE Cluster, 2020.
Zheng, V., Sariyuce, A.E. and Zola, J., "Identifying Taxonomic Units in Metagenomic DNA Streams", In International Workshop on Data Mining in Bioinformatics (BioKDD), 2020.
2019
Schoeneman, F. and Zola, J., "Solving All-Pairs Shortest-Paths Problem in Large Graphs Using Apache Spark", In International Conference on Parallel Processing (ICPP), 2019.
2018
Karan, S., Eichhorn, M., Hurlburt, B., Iraci, G. and Zola, J., "Fast Counting in Machine Learning Applications", In Uncertainty in Artificial Intelligence (UAI), 2018.
Ko, S., Sassoubre, L. and Zola, J., "Applications and Challenges of Real-time Mobile DNA Analysis", In International Workshop on Mobile Computing Systems and Applications (HotMobile), pp. 1-6, 2018.
Schoeneman, F., Chandola, V., Napp, N., Wodo, O. and Zola, J., "Entropy-Isomap: Manifold Learning for High-dimensional Dynamic Processes", In IEEE International Conference on Big Data (IEEE BigData), pp. 1655–1660, 2018.
Schoeneman, F. and Zola, J., "Scalable Manifold Learning for Big Data with Apache Spark", In IEEE International Conference on Big Data (IEEE BigData), pp. 272-281, 2018.
2017
Karan, S. and Zola, J., "Scalable Exact Parent Sets Identification in Bayesian Networks Learning with Apache Spark", In IEEE International Conference on High Performance Computing, Data, and Analytics (HiPC), pp. 33-41, 2017.
Schoeneman, F., Mahapatra, S., Chandola, V., Napp, N. and Zola, J., "Error Metrics for Learning Reliable Manifolds from Streaming Data", In SIAM International Conference on Data Mining (SDM), pp. 750-758, 2017.
2016
Karan, S. and Zola, J., "Exact Structure Learning of Bayesian Networks by Optimal Path Extension", In IEEE International Conference on Big Data (IEEE BigData), pp. 48-55, 2016.
2014
Zola, J., "Constructing Similarity Graphs from Large-Scale Biological Sequence Collections", In IEEE International Workshop on High Performance Computational Biology (HiCOMB), pp. 500–507, 2014.
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 Workshop on Many-Task Computing on Clouds, Grids, and Supercomputers (MTAGS), 2013. (best paper award finalist)
Nihalani, R., Zola, J. and Aluru, S., "Resolving Read Assignment Ambiguities in Metagenomic Clustering", In ISCA International Conference on Bioinformatics and Computational Biology (BICoB), 2013.
2011
Yang, X., Zola, J. and Aluru, S., "Parallel Metagenomic Sequence Clustering Via Sketching and Maximal Quasi-clique Enumeration on Map-Reduce Clouds", In IEEE International Parallel and Distributed Processing Symposium (IPDPS), pp. 1223–1233, 2011.
2009
Nikolova, O., Zola, J. and Aluru, S., "A Parallel Algorithm for Exact Bayesian Network Inference", In International Conference on High Performance Computing (HiPC), pp. 342-349, 2009.
Zola, J., Sarje, A. and Aluru, S., "Constructing Gene Regulatory Networks on Clusters of Cell Processors", In International Conference on Parallel Processing (ICPP), pp. 108–115, 2009. (joint first author)
2008
Zola, J., Aluru, M. and Aluru, S., "Parallel Information Theory Based Construction of Gene Regulatory Networks", In International Conference on High Performance Computing (HiPC), vol. 5375, pp. 336–349, 2008.
2007
Ott, M., Zola, J., Aluru, S. and Stamatakis, A., "Large-Scale Maximum Likelihood-Based Phylogenetic Analysis on the IBM BlueGene/L", In 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 IEEE International Workshop on High Performance Computational Biology (HiCOMB), 2006.
2005
Trystram, D. and Zola, J., "Parallel Multiple Sequence Alignment with Decentralized Cache Support", In International European Conference on Parallel and Distributed Computing (Euro-Par), vol. 3648, pp. 1217–1226, 2005.
2004
Parmentier, G., Trystram, D. and Zola, J., "Cache-Based Parallelization of Multiple Sequence Alignment Problem", In International European Conference on Parallel and Distributed Computing (Euro-Par), vol. 3149, pp. 1005-1012, 2004.
Zola, J., "CaLi, Efficient Library for Cache Implementation", In Mexican International Conference on Computer Science (ENC), pp. 415–420, 2004.
Zola, J., Lacinski, L. and Wyrzykowski, R., "An Object Oriented Library for Evolution Programs", In IUTAM Symposium on Evolutionary Methods in Mechanics, vol. 117, pp. 351–360, 2004.
2002
Zola, J. and Wyrzykowski, R., "EPL-Julia the High-Performance Library for Evolutionary Computations", In International Conference on Parallel Processing and Applied Mathematics (PPAM), vol. 2328, pp. 652–659, 2002.
Journal Articles
2024
Desai, P., Juneja, N., Chandola, V., Zola, J. and Wodo, O., "COMODO: Configurable Morphology Distance Operator", In Computational Materials Science, 2024.
Karan, S., Sayed, Z. and Zola, J., "End-to-End Bayesian Networks Exact Learning in Shared Memory", In IEEE Transactions on Parallel and Distributed Systems, vol. 35, no. 4, pp. 634-645, 2024.
Turkkan, B.O., Dai, T., Raman, A., Kosar, T., Chen, C., Bulut, M.F., Zola, J. and Sow, D., "GreenABR+: Generalized Energy-Aware Adaptive Bitrate Streaming", In ACM Transactions on Multimedia Computing, Communications and Applications, 2024.
2023
Mikalsen, A. and Zola, J., "Coriolis: Enabling Metagenomic Classification on Lightweight Mobile Devices", In Bioinformatics, vol. 39, 2023.
2022
Zheng, V., Sariyuce, A.E. and Zola, J., "Identifying Taxonomic Units in Metagenomic DNA Streams on Mobile Devices", In IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2022.
Schoeneman, F., Chandola, V., Napp, N., Wodo, O. and Zola, J., "Learning Manifolds from Dynamic Process Data", In MDPI Algorithms, vol. 13, no. 30, 2020.
2018
Du, P., Zebrowski, A., Zola, J., Ganapathysubramanian, B. and Wodo, O., "Microstructure Design Using Graphs", In Nature Computational Materials, vol. 4, no. 50, 2018.
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.
Samudrala, S.K., Zola, J., Aluru, S. and Ganapathysubramanian, B., "Parallel Framework for Dimensionality Reduction of Large-Scale Datasets", In Scientific Programming, 2015.
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.
2014
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.
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)
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.
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)
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)
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.
2010
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.
2009
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.
2008
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.
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
2014
Zola, J., "Parallel Computing for Gene Networks Reverse Engineering", In Approaches in Integrative Bioinformatics, Springer, 2014.
2011
Zola, J. and Aluru, S., "Network Inference in Systems Biology", In Encyclopedia of Parallel Computing, Springer, 2011.
2010
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.
2007
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
2018
Blanton, M., Kang, A.R., Karan, S. and Zola, J., "Privacy Preserving Analytics on Distributed Medical Data", 2018.
Zola, J., Fillmore, N., Samudrala, R., Mushi, N., Brophy, M. and Do, N., "Bayesian Network Model of Multiple Myeloma Patients Based on Pharmaceutical Records", Extended Abstract, 30th Anniversary AACR Conference on Convergence: Artificial Intelligence, Big Data, and Prediction in Cancer, 2018.
2013
Diaz-Montes, J., Ganapathysubramanian, B., Parashar, M., Rodero, I., Xie, Y. and Zola, J., "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.