Publications

Here are the recent publications. For the complete list, please visit my Google Scholar page.

  1. Chaterji, Somali, Nathan DeLay, John Evans, Nathan Mosier, Bernard Engel, Dennis Buckmaster, and Ranveer Chandra. "Artificial Intelligence for Digital Agriculture at Scale: Techniques, Policies, and Challenges." arXiv preprint arXiv:2001.09786 (2020). Paper

  2. Bagchi, Saurabh, Vaneet Aggarwal, Somali Chaterji, Fred Douglis, Aly El Gamal, Jiawei Han, Brian J. Henz et al. "Grand Challenges of Resilience: Autonomous System Resilience through Design and Runtime Measures." arXiv preprint arXiv:1912.11598 (2019). Paper

  3. Chaterji, Somali, Parinaz Naghizadeh, Muhammad Ashraful Alam, Saurabh Bagchi, Mung Chiang, David Corman, Brian Henz et al. "Resilient Cyberphysical Systems and their Application Drivers: A Technology Roadmap." arXiv preprint arXiv:2001.00090 (2019). Paper

  4. Abdallah, Mustafa, Ashraf Mahgoub, Hany Ahmed, and Somali Chaterji. "Athena: Automated tuning of k-mer based Genomic error correction Algorithms using Language Models." Nature scientific reports 9, no. 1 (2019): 1-13. Paper

  5. Fang, Chih-Hao, Nawanol Theera-Ampornpunt, Michael A. Roth, Ananth Grama, and Somali Chaterji. "AIKYATAN: mapping distal regulatory elements using convolutional learning on GPU." BMC bioinformatics 20, no. 1 (2019): 488. Paper

  6. Mahadik, Kanak, Christopher Wright, Milind Kulkarni, Saurabh Bagchi, and Somali Chaterji. "Scalable genome assembly through parallel de bruijn graph construction for multiple k-mers." Nature scientific reports 9, no. 1 (2019): 1-15. Paper

  7. Mahgoub, A., Wood, P., Medoff, M., Mitra, S., Meyer, F., Chaterji, S., Bagchi, S., ''Sophia: Online Reconfiguration of Clustered NoSQL Databases for Time-Varying Workloads,'' Accepted to appear at the USENIX Annual Technical Conference USENIX ATC 2019, pp. 1--13, July 10--12, 2019. Paper

  8. Kumar, R., Buckmaster, D., and Chaterji, S., "Interpretable Modeling for Yield Trends of Corn and Soybean in the Midwest," Accepted to appear at the 2019 Annual Meeting of the American Society of Agricultural and Biological Engineers, pp. 1--6, July 7--10, 2019. Paper

  9. Mahgoub, A. and Chaterji, S., "Iris: Tuning the Configuration Parameters of NoSQL Databases for High-Throughput Digital Agricultural Processing Pipelines," 2019 Annual Meeting of the American Society of Agricultural and Biological Engineers, pp. 1--6, July 7--10, 2019. Paper

  10. Chaterji, S., ''Panel 1 Position Paper: Man versus Machines---Humans Need Not Apply,'' Proceedings of the 11th International Conference on COMmunication Systems & NETworkS, IEEE-COMSNETS, pp. 1--3, 2019.

  11. Chaterji, S., ''Panel 2 Position Paper: AI could Solve the World's Healthcare Problems and that too at Scale!,'' Proceedings of the 11th International Conference on COMmunication Systems & NETworkS, IEEE-COMSNETS, pp. 1--4, 2019.

  12. Nagaraj, M. and Chaterji, S., ''Panel 3 Position Paper: Blockchain can be the Backbone of India's Economy,'' Proceedings of the 11th International Conference on COMmunication Systems & NETworkS, IEEE-COMSNETS, pp. 1--4, 2019.

  13. Ghoshal, A., Zhang, J., Roth, M., Xia, K. M., Grama, A., and Chaterji, S., "A Distributed Classifier for MicroRNA Target Prediction with Validation through TCGA Expression Data," IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), pp. 1-16, April 2018 (DOI: 10.1109/TCBB.2018.2828305). [ Paper ]

  14. Koo J., Zhang J., and Chaterji, S., "Tiresias: Deep Learning Approach to Decipher MicroRNA Regulatory Networks," Theranostics, vol. 8, issue 1, pp. 277-291, 2018. [ Paper

  15. Le, V., Lee, J., Chaterji, S., Spencer, A., Liu, Y-L., Kim, P., Yeh, H-C., Kim, D-H., Baker, A. B., "Syndecan-1 in mechanosensing of nanotopological cues in engineered materials," Biomaterials, volume 155, pp. 13-24, February 2018. [ Paper ]

  16. Thomas, T. E., Koo J., Chaterji, S., and Bagchi, S., "Minerva: A reinforcement learning-based technique for optimal scheduling and bottleneck detection in distributed factory operations," At the 10th IEEE Conference on Communication Systems & Networks (COMSNETS), pp. 1-8, Jan 3-7, 2018, Bangalore, India. (Acceptance rate: 38/125 (30.4%)) [ Paper ]

  17. Mahgoub, A., Wood, P., Ganesh, S., Mitra, S. (Adobe Research), Gerlach, W. (Argonne National Laboratory), Harrison T. (Argonne National Laboratory), Meyer, F., (Argonne National Laboratory), Grama, A., Bagchi, S., and Chaterji, S., “Rafiki: A Middleware for Parameter Tuning of NoSQL Datastores for Dynamic Metagenomics Workloads,” At the ACM/IFIP/USENIX Middleware Conference, pp. 1-13, Dec 11-15, 2017, Las Vegas, Nevada. (Acceptance rate: 20/85 = 23.5%) [ Paper ]

  18. Chaterji, S., Ahn E. H., and Kim D-H., “CRISPR Genome Engineering for Human Pluripotent Stem Cell Research,” Theranostics, vol. 7, pp. 1–25, 2017. [ Paper ]

  19. Theera-Ampornpunt, N. and Chaterji, S., Prediction of Enhancer RNA Activity Levels from ChIP-seq-derived Histone Modification Combinatorial Codes, IEEE Workshop on Deep Learning in Bioinformatics, Biomedicine, and Healthcare Informatics (DLB2H 2017), pp. 1–9, Nov 13-16, 2017. [ Paper ]

  20. Kannan, S., Wood, P., Chaterji S., and Bagchi, S., “TopHat: Topology-based Host-Level Attribution for Multi-Stage Attacks in Enterprise Systems using Software Defined Networks,” At the 13th EAI International Conference on Security and Privacy in Communication Networks (SecureComm), pp. 1–22, Oct 23-25, 2017. (Acceptance rate: 31/105 = 29.5% (full papers)) [ Paper ]

  21. Meyer F., Bagchi S., Chaterji S., Gerlach W., Grama A., Harrison T., Paczian T., Trimble W., Wilke A., “MG-RAST Version 4 — Lessons learned from a decade of low-budget ultra-high throughput metagenome analysis,” Oxford Briefings in Bioinformatics, bbx105, pp. 1-9, September 2017. [ Paper ]

  22. Chaterji S., Koo J., Li N., Meyer F., Grama A., and Bagchi S., “Federation in Genomics Pipelines: Techniques and Challenges,” Oxford Briefings in Bioinformatics, bbx102, pp. 1-10, August 2017. [ Paper ]

  23. Mahadik K., Wright C., Kulkarni M., Bagchi S., and Chaterji S., “Scalable Genomic Assembly through Parallel de Bruijn Graph Construction for Multiple K-mers,” At the 8th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM BCB), pp. 1-7, Aug 20-23, 2017, Boston, MA. [ Paper ]

All the above publications are accompanied by open-source software packages freely available to the research community, with visualization modules where applicable.