Publications

Refereed Conference and Workshop Papers
18 results

2017

  • 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. BIB
  • Karan, S. and Zola, J., "Scalable Exact Parent Sets Identification in Bayesian Networks Learning with Apache Spark", In Proc. IEEE Int. Conference on High Performance Computing, Data, and Analytics (HiPC), 2017. BIB

2016

  • 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. BIB DOI

2014

  • 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. BIB DOI

2013

  • 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. BIB
  • 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) BIB

2011

  • 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. BIB DOI

2009

  • 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) BIB DOI
  • 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. BIB DOI

2008

  • 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. BIB DOI

2007

  • 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. BIB PDF
  • 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) BIB DOI

2006

  • 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. BIB DOI

2005

  • 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. BIB DOI

2004

  • 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. BIB DOI
  • Zola, J., "CaLi, Efficient Library for Cache Implementation", In Proc. Mexican International Conference on Computer Science (ENC), pp. 415–420, 2004. BIB DOI
  • 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. BIB DOI

2002

  • 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. BIB DOI
Journal Articles
14 results

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. BIB DOI
  • Samudrala, S.K., Zola, J., Aluru, S. and Ganapathysubramanian, B., "Parallel Framework for Dimensionality Reduction of Large-Scale Datasets", In Scientific Programming, 2015. BIB DOI
  • 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. BIB DOI

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. BIB DOI

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) BIB DOI
  • 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. BIB DOI
  • 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) BIB DOI

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. BIB DOI
  • 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) BIB DOI

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. BIB DOI

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. BIB DOI

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. BIB DOI

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. BIB DOI
Book Chapters
4 results

2014

  • Zola, J., "Parallel Computing for Gene Networks Reverse Engineering", In Approaches in Integrative Bioinformatics, Springer, 2014. BIB DOI

2011

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

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. BIB

2007

  • Trystram, D. and Zola, J., "Multiple Sequence Alignment and Phylogenetic Inference", In Grids for Bioinformatics and Computational Biology, John Wiley and Sons, 2007. BIB DOI
Other Publications
1 result

2013

  • "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. BIB


Talks

  1. Invited talk: Sketching Biological Sequences for Storage and Computation. Presented at Workshop on Parallel Software Libraries for Sequence Analysis (pSALSA), Seattle, October 2016.
  2. Invited talk: Parallel Computing for Large-scale Computational Biology. Presented at Pharmacology and Toxicology Seminar Series at University at Buffalo, October 2015.
  3. Invited talk: Similarity Detection in Large Sequence Collections. Presented at Workshop on Parallel Software Libraries for Sequence Analysis (pSALSA), September 2015.
  4. 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.
  5. Invited talk: Constructing Similarity Graphs from Large-scale Biological Sequence Collections. Presented at Drexel University, March 2013.
  6. Panelist: Big Data Standards and the Potential Long Term Benefits for Research and Clinical Development. Webinar organized by NGSLeaders, December 2012.
  7. 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.
  8. Three-hours tutorial: Not Too Short Introduction to Metagenomics. Presented at Czestochowa University of Technology, Poland, December 2011.
  9. 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.
  10. Invited lectures: Introduction to Bioinformatics; and High Performance Computational Biology. Presented at Pannon University, Hungary, May 2006.
  11. 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.
  12. Seminar: Parallel Server for Large Scale Multiple Sequence Alignment. Presented at Poznan University of Technology, Institute of Computing Science, Poland, May 2005.
  13. 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.