EPL-Julia the High-Performance Library for Evolutionary Computations. - Jaroslaw Zola; Roman Wyrzykowski (PPAM, 2001)

CaLi, Efficient Library for Cache Implementation. - Jaroslaw Zola (ENC, 2004)

Cache-Based Parallelization of Multiple Sequence Alignment Problem. - Gilles Parmentier; Denis Trystram; Jaroslaw Zola (Euro-Par, 2004)

Parallel Multiple Sequence Alignment with Decentralized Cache Support. - Denis Trystram; Jaroslaw Zola (Euro-Par, 2005)

Parallel multiple sequence alignment with local phylogeny search by simulated annealing. - Jaroslaw Zola; Denis Trystram; Andrei Tchernykh; Carlos A. Brizuela (IPDPS, 2006)

Large scale multiple sequence alignment with simultaneous phylogeny inference. - Gilles Parmentier; Denis Trystram; Jaroslaw Zola (J. Parallel Distributed Comput., 2006)

Multiple Sequence Alignment and Phylogenetic Inference. - Denis Trystram; Jaroslaw Zola (Grid Computing for Bioinformatics and Computational Biology, 2007)

PARALLEL-TCOFFEE: A parallel multiple sequence aligner. - Jaroslaw Zola; Xiao Yang 019; Adrian Rospondek; Srinivas Aluru (PDCS, 2007)

Large-scale maximum likelihood-based phylogenetic analysis on the IBM BlueGene/L. - Michael Ott 001; Jaroslaw Zola; Alexandros Stamatakis; Srinivas Aluru (SC, 2007)

Parallel Information Theory Based Construction of Gene Regulatory Networks. - Jaroslaw Zola; Maneesha Aluru; Srinivas Aluru (HiPC, 2008)

Large-scale phylogenetic analysis on current HPC architectures. - Michael Ott 001; Jaroslaw Zola; Srinivas Aluru; Andrew D. Johnson; Daniel Janies; Alexandros Stamatakis (Sci. Program., 2008)

A parallel algorithm for exact Bayesian network inference. - Olga Nikolova; Jaroslaw Zola; Srinivas Aluru (HiPC, 2009)

Constructing Gene Regulatory Networks on Clusters of Cell Processors. - Jaroslaw Zola; Abhinav Sarje; Srinivas Aluru (ICPP, 2009)

Pairwise Computations on the Cell Processor. - Abhinav Sarje; Jaroslaw Zola; Srinivas Aluru (Scientific Computing with Multicore and Accelerators, 2010)

Parallel Information-Theory-Based Construction of Genome-Wide Gene Regulatory Networks. - Jaroslaw Zola; Maneesha Aluru; Abhinav Sarje; Srinivas Aluru (IEEE Trans. Parallel Distributed Syst., 2010)

Parallel Metagenomic Sequence Clustering Via Sketching and Maximal Quasi-clique Enumeration on Map-Reduce Clouds. - Xiao Yang 019; Jaroslaw Zola; Srinivas Aluru (IPDPS, 2011)

Accelerating Pairwise Computations on Cell Processors. - Abhinav Sarje; Jaroslaw Zola; Srinivas Aluru (IEEE Trans. Parallel Distributed Syst., 2011)

Systems Biology, Network Inference in. - Jaroslaw Zola; Srinivas Aluru (Encyclopedia of Parallel Computing, 2011)

BigLS - The 1st International Workshop on Big Data in Life Sciences. - Ananth Kalyanaraman; Jaroslaw Zola (ICCABS, 2013)

HiCOMB Introduction. - Jaroslaw Zola; David A. Bader; Srinivas Aluru (IPDPS Workshops, 2013)

Large-Scale metagenomic sequence Clustering on Map-Reduce Clusters. - Xiao Yang 019; Jaroslaw Zola; Srinivas Aluru (J. Bioinform. Comput. Biol., 2013)

Parallel globally optimal structure learning of Bayesian networks. - Olga Nikolova; Jaroslaw Zola; Srinivas Aluru (J. Parallel Distributed Comput., 2013)

Parallel Computing for Gene Networks Reverse Engineering. - Jaroslaw Zola (Approaches in Integrative Bioinformatics, 2014)

Constructing Similarity Graphs from Large-Scale Biological Sequence Collections. - Jaroslaw Zola (IPDPS Workshops, 2014)

Federated Computing for the Masses-Aggregating Resources to Tackle Large-Scale Engineering Problems. - Javier Diaz Montes; Yu Xie; Ivan Rodero; Jaroslaw Zola; Baskar Ganapathysubramanian; Manish Parashar (Comput. Sci. Eng., 2014)

Parallel Framework for Dimensionality Reduction of Large-Scale Datasets. - Sai Kiranmayee Samudrala; Jaroslaw Zola; Srinivas Aluru; Baskar Ganapathysubramanian (Sci. Program., 2015)

Exact structure learning of Bayesian networks by optimal path extension. - Subhadeep Karan; Jaroslaw Zola (IEEE BigData, 2016)

HiCOMB Introduction and Committees. - Srinivas Aluru; David A. Bader; Ananth Kalyanaraman; Jaroslaw Zola (IPDPS Workshops, 2016)

Scalable Exact Parent Sets Identification in Bayesian Networks Learning with Apache Spark. - Subhadeep Karan; Jaroslaw Zola (HiPC, 2017)

Error Metrics for Learning Reliable Manifolds from Streaming Data. - Frank Schoeneman; Suchismit Mahapatra; Varun Chandola; Nils Napp; Jaroslaw Zola (SDM, 2017)

Entropy-Isomap: Manifold Learning for High-dimensional Dynamic Processes. - Frank Schoeneman; Varun Chandola; Nils Napp; Olga Wodo; Jaroslaw Zola (IEEE BigData, 2018)

Scalable Manifold Learning for Big Data with Apache Spark. - Frank Schoeneman; Jaroslaw Zola (IEEE BigData, 2018)

Fast Counting in Machine Learning Applications. - Subhadeep Karan; Matthew Eichhorn; Blake Hurlburt; Grant Iraci; Jaroslaw Zola (UAI, 2018)

Applications and Challenges of Real-time Mobile DNA Analysis. - Steven Y. Ko; Lauren Sassoubre; Jaroslaw Zola (HotMobile, 2018)

Privacy Preserving Analytics on Distributed Medical Data. - Marina Blanton; Ah Reum Kang; Subhadeep Karan; Jaroslaw Zola (CoRR, 2018)

Solving All-Pairs Shortest-Paths Problem in Large Graphs Using Apache Spark. - Frank Schoeneman; Jaroslaw Zola (ICPP, 2019)

Performance of All-Pairs Shortest-Paths Solvers with Apache Spark. - Frank Schoeneman; Jaroslaw Zola (CoRR, 2019)

Efficient Execution of Dynamic Programming Algorithms on Apache Spark. - Mohammad Mahdi Javanmard; Zafar Ahmad; Jaroslaw Zola; Louis-Noël Pouchet; Rezaul Chowdhury; Robert J. Harrison (CLUSTER, 2020)

Learning Manifolds from Dynamic Process Data. - Frank Schoeneman; Varun Chandola; Nils Napp; Olga Wodo; Jaroslaw Zola (Algorithms, 2020)

Parallelization and Auto-scheduling of Data Access Queries in ML Workloads. - Pawel Bratek; Lukasz Szustak; Jaroslaw Zola (Euro-Par Workshops, 2021)

Graph-based Strategy for Establishing Morphology Similarity. - Namit Juneja; Jaroslaw Zola; Varun Chandola; Olga Wodo (SSDBM, 2021)

Longitudinal K-means approaches to clustering and analyzing EHR opioid use trajectories for clinical subtypes. - Sarah Mullin; Jaroslaw Zola; Robert Lee; Jinwei Hu; Brianne Mackenzie; Arlen Brickman; Gabriel Anaya; Shyamashree Sinha; Angie Li; Peter L. Elkin (J. Biomed. Informatics, 2021)

Counting Induced 6-Cycles in Bipartite Graphs. - Jason Niu; Jaroslaw Zola; Ahmet Erdem Sariyüce (ICPP, 2022)

GreenABR: energy-aware adaptive bitrate streaming with deep reinforcement learning. - Bekir Oguzhan Turkkan; Ting Dai; Adithya Raman; Tevfik Kosar; Changyou Chen; Muhammed Fatih Bulut; Jaroslaw Zola; Daby Sow (MMSys, 2022)

GraSPI: Extensible software for the graph-based quantification of morphology in organic electronics. - Devyani Jivani; Jaroslaw Zola; Baskar Ganapathysubramanian; Olga Wodo (SoftwareX, 2022)

Parallel Auto-Scheduling of Counting Queries in Machine Learning Applications on HPC Systems. - Pawel Bratek; Lukasz Szustak; Jaroslaw Zola (Euro-Par Workshops, 2023)

SCoOL - Scalable Common Optimization Library. - Zainul Abideen Sayed; Jaroslaw Zola (HiPC, 2023)

Coriolis: enabling metagenomic classification on lightweight mobile devices. - Andrew J. Mikalsen; Jaroslaw Zola (Bioinform., 2023)

Predicting the Impact of Batch Refactoring Code Smells on Application Resource Consumption. - Asif Imran; Tevfik Kosar; Jaroslaw Zola; Muhammed Fatih Bulut (CoRR, 2023)

Identifying Taxonomic Units in Metagenomic DNA Streams on Mobile Devices. - Vicky Zheng; Ahmet Erdem Sariyüce; Jaroslaw Zola (IEEE ACM Trans. Comput. Biol. Bioinform., 2023)

Towards Sustainable Cloud Software Systems through Energy-Aware Code Smell Refactoring. - Asif Imran; Tevfik Kosar; Jaroslaw Zola; Muhammed Fatih Bulut (CLOUD, 2024)

Resource Efficient Bayesian Optimization. - Namit Juneja; Varun Chandola; Jaroslaw Zola; Olga Wodo; Parth Desai (CLOUD, 2024)

End-to-End Bayesian Networks Exact Learning in Shared Memory. - Subhadeep Karan; Zainul Abideen Sayed; Jaroslaw Zola (IEEE Trans. Parallel Distributed Syst., 2024)

SKiM: accurately classifying metagenomic ONT reads in limited memory. - Trevor Schneggenburger; Jaroslaw Zola (Bioinform., 2025)

Disambiguating a Soft Metagenomic Clustering. - Rahul Nihalani; Jaroslaw Zola; Srinivas Aluru (J. Comput. Biol., 2025)

Fast Counting and Utilizing Induced 6-Cycles in Bipartite Networks. - Jason Niu; Jaroslaw Zola; Ahmet Erdem Sariyüce (IEEE Trans. Knowl. Data Eng., 2025)