Somali Chaterji

Assistant Professor
Department of Agricultural and Biological Engineering
Purdue University

[How to say my name: SHOH-MAH-LEE CHA-ter-JEE]


Publications

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

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

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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 ]

  8. 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

  9. 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 ]

  10. 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 ]

  11. 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 ]

  12. 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 ]

  13. 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 ]

  14. 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 ]

  15. 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 ]

  16. 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 ]

  17. 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 ]

  18. Kim SG, Harwani M, Grama A, and Chaterji S, “EP-DNN: A Deep Neural Network-Based Global Enhancer Prediction Algorithm,” In Nature Scientific Reports, pp. 1-21, vol. 6, 2016. [ Paper ]

  19. Kim SG, Ampornpunt N, Fang C-H, Harwani M, Grama A, and Chaterji S. Opening up the blackbox: An interpretable deep neural network-based classifier for cell-type specific enhancer predictions. In the BMC Systems Biology journal, pp. 1-26, 10(2), article 54, 2016. [ Paper ]
  20. Mahadik K, Wright C, Zhang J, Kulkarni M, Bagchi S, and Chaterji S. SARVAVID: A Domain Specific Language for Developing Scalable Computational Genomics Applications. At the International Conference on Supercomputing (ICS), pp. 1-13, June 1-3, 2016, Istanbul, Turkey. (Acceptance rate: 32/183 = 17.5%) [ Paper ]

  21. Ampornpunt N, Kim SG, Ghoshal A, Bagchi S, Grama A, and Chaterji S. Computational and network cost of training distributed Support Vector Machines for large genomics data. At the 8th International IEEE Conference on Communication Systems and Networks (COMSNETS), pp. 1-8, January 5-9, Bangalore, India. (Acceptance rate: 39/143 = 27.3%)[ Paper ]

  22. Ghoshal A, Grama A, Bagchi S, and Chaterji S. An Ensemble SVM Model for the Accurate Prediction of Non-Canonical MicroRNA Targets. In Proceedings of the 6th ACM Conference on Bioinformatics, Computational Biology and Health Informatics (BCB), pp. 403-412, September 9-12, 2015, Atlanta, GA. (Acceptance rate: 48/141 = 34%) (Best Paper) [ Paper ] [ Presentation ] [ Recording of the presentation (in wav) ]

  23. Kim S, Ampornpunt N, Grama A, and Chaterji S. Interpretable Deep Neural Networks for Enhancer Prediction. At the 9th IEEE International Conference on Bioinformatics and Biomedicin (BIBM), pp. 242-249, Nov 9-12, 2015. (Acceptance rate: 68/346 = 19.7%) [ Paper ]

  24. Ghoshal A, Shankar R, Bagchi S, Grama A, and Chaterji S. MicroRNA target prediction using thermodynamic and sequence curves. BMC Genomics, vol. 16, no. 1, November 2015. [ Paper ]

  25. Purdue University, Orion: A fine grained parallel implementation for genomic search, At: https://github.com/purdue-dcsl/Orion (January 2015).

  26. Mahadik K, Chaterji S, Zhou, B, Kulkarni, M, and Bagchi, S. Orion: Scaling Genomic Sequence Matching with Fine-Grained Parallelization. In Proceedings of the International Conference for High Performance Computing, Networking, Storage, and Analysis (Supercomputing), pp. 449-460, Nov 16-21, 2014. (Acceptance rate: 82/394 = 20.8%) [ Paper ]

  27. Chaterji S, Kim P, Choe SH, Ho DS, Tsui JH, Baker AB, Kim DH. Synergistic Effects of Matrix Nanotopography and Stiffness on Vascular Smooth Muscle Cell Function. Tissue Engineering Part A, 2014, 20(15-16): 2115-2126. [ Paper ]

  28. Vedantham K§, Chaterji S§, Kim SW, Park K. Development of a probucolā€releasing antithrombogenic drug eluting stent. Journal of Biomedical Materials Research Part B: Applied Biomaterials 100, no. 4 (2012): 1068-1077. (§ = Equal contribution) [ Paper ]