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

• Turkkan, B.O., Dai, T., 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.
• Niu, J., Zola, J. and Sariyuce, A.E., "Counting Induced 6-Cycles in Bipartite Graphs", In International Conference on Parallel Processing (ICPP), 2022.

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

• 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.
• 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.

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

• 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.
• 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.
• 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.
• Karan, S., Eichhorn, M., Hurlburt, B., Iraci, G. and Zola, J., "Fast Counting in Machine Learning Applications", In Uncertainty in Artificial Intelligence (UAI), 2018.

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.
• 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.

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

• 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.
• 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)

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

• 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)
• 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.

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

• Zola, J., Yang, X., Rospondek, A. and Aluru, S., "Parallel T-Coffee: A Parallel Multiple Sequence Aligner", In ISCA International 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 ACM/IEEE Conference on Supercomputing, 2007. (best paper award finalist)

2006

• 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

• 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.
• Zola, J., "CaLi, Efficient Library for Cache Implementation", In 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 International European Conference on Parallel and Distributed Computing (Euro-Par), vol. 3149, pp. 1005-1012, 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.

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.

2021

• Mullin, S., Zola, J., Lee, R., Hu, J., MacKenzie, B., Brickman, A., Anaya, G., Sinha, S., Li, A. and Elkin, P.L., "Longitudinal K-Means Approaches to Clustering and Analyzing EHR Opioid Use Trajectories for Clinical Subtypes", In Journal of Biomedical Informatics, 2021.

2020

• 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

• 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.

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

• 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)

2011

• 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)

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.

2007

• 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.

2006

• 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.

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.

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.
• Blanton, M., Kang, A.R., Karan, S. and Zola, J., "Privacy Preserving Analytics on Distributed Medical Data", 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.