Harnessing FABRIC for Scalable Human Genome Sequence Analysis

Publications

1. Shivika Prasanna, Ajay Kumar, Deepthi Rao, Eduardo J. Simoes, and Praveen Rao - A Scalable Tool for Analyzing Genomic Variants of Humans Using Knowledge Graphs and Machine Learning. In Frontiers in Big Data - Data Science, 19 pages, 2025. [Online]
2. Manas Das, Praveen Rao, and Lisong Xu - Impact of the Networking Infrastructure on the Performance of Variant Calling on Human Genomes in Commodity Clusters. In 15th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (BCB 2024), 11 pages, Shenzhen, China, 2024. [PDF] [Slides]
3. Khawar Shehzad, Ajay Kumar, Matthew Schutz, Chase Webb, Polycarp Nalela, Manas Das, and Praveen Rao - A Scalable Tool for Democratizing Variant Calling on Human Genomes Using Commodity Clusters. In 33rd ACM Conference on Information and Knowledge Management (CIKM 2024), 5 pages, Boise, 2024. (demo) [PDF]
4. Praveen Rao, Khawar Shehzad - A Technique for Secure Variant Calling on Human Genome Sequences Using SmartNICs. In 17th IEEE International Conference on Cloud Computing (CLOUD 2024), 8 pages, Shehzhen, China, 2024. [PDF] [Slides]
5. Vladimir Omelyusik, Khawar Shehzad, Tyler Banks, Praveen Rao, and Satish Nair - On Scaling Neuronal Network Simulations Using Distributed Computing. In 11th Annual International Workshop on Innovating the Network for Data-Intensive Science (INDIS 2024), 6 pages, Atlanta, 2024. [PDF]
6. Abdulmateen Adebiyi, Puja Adhikari, Praveen Rao, and Wai-Yim Ching - Bond Strength Between Receptor Binding Domain of Spike Protein and Human Angiotensin Converting Enzyme-2 Using Machine Learning. In BME Horizon, 2(1), 12 pages, 2024. [Online]
7. Manas Jyoti Das, Khawar Shehzad, Praveen Rao - Efficient Variant Calling on Human Genome Sequences Using a GPU-Enabled Commodity Cluster. In 32nd ACM International Conference on Information and Knowledge Management (CIKM 2023), 6 pages, Birmingham, UK, 2023. [PDF] [DOI] [Poster]
8. Andrew Rommitti, Jiya Shetty, Praveen Rao - Evaluating the Effectiveness of Synthetic Datasets for Dementia Diagnosis Using Deep Learning. In 52nd IEEE Applied Imagery and Pattern Recognition Workshop (AIPR), 5 pages, St. Louis, 2023. [PDF]

Tutorial

1. Praveen Rao - Advanced Cyberinfrastructure for Large-Scale Health Data Analysis. In 6th International Workshop on Health Data Management in the Era of AI (HeDAI 2024), co-located with EDBT/ICDT 2024, Paestum, Italy. [Tutorial slides]

Datasets Released

1. Manas Das, Khawar Shehzad, Praveen Rao - A Dataset of Network Traffic Collected During Large-Scale Human Genome Sequence Analysis. IEEE DataPort, May 2023. DOI

Resources

FABRIC: https://fabric-testbed.net/ CloudLab: https://cloudlab.us

For AVAH [CIKM '21], visit https://github.com/MU-Data-Science/EVA

Team

Principal Investigator: Dr. Praveen Rao

Other Faculty: Drs. Eduardo J. Simoes and Deepthi Rao

Ph.D. Students: Khawar Shehzad, Polycarp Nalela, Ajay Kumar

Project Alumni

Dr. Manas Jyoti Das (Postdoctoral Fellow, July 2022 - August 2023)

Dr. Shivika Prasanna (Ph.D, in Computer Science, July 2024)

B.S. Students: Matt Schutz (BS in Computer Science, 2024), Chase Webb (BS in Computer Science)

Acknowledgments

This work is supported by the National Science Foundation under Grant No. 2201583.