|I am working at the intersection of bioengineering and machine learning, on challenging and potentially ground-breaking problems in precision medicine.||
With the Seed of Success acorn award given to Purdue investigators winning > $1M grants (Oct '16; W Lafayette, IN)
Somali Chaterji (pronounced: SHOH-MAH-LEE CHA-ter-JEE) is a Visiting Assistant Professor at Purdue University, where she specializes in developing algorithms and statistical models for bioengineering and computational genomics.
Somali got her PhD in Biomedical Engineering from Purdue University, winning the Chorafas International Award (2010), College of Engineering Best Dissertation Award (2010), and the Future Faculty Fellowship Award (2009). She did her Post-doctoral Fellowship at the University of Texas at Austin in the Department of Biomedical Engineering, where her work was supported by an American Heart Association award. Dr. Chaterji is also a technology commercialization enthusiast and has been consulting for the IC2 Institute at the University of Texas at Austin, since Spring 2014.
My current areas of interest and expertise are:
Here is a succinct vision statement for my research. [ WWW ]
From my post-doctoral days, I have expertise in cellular mechanotransduction, nanolithographic fabrication, and vascular biomechanics, with translation of laboratory discoveries to clinical practice through collaboration with cardiologists at St. David's Healthcare in Austin. In my PhD work, my areas of study were cardiovascular engineering, vascular extracellular microenvironments, and cardiovascular devices. I have collaborations with both wet-lab experimentalists (UT Austin, U of Washington, UNC Medical School) and computer engineers (Purdue, U of Maryland, U of Chicago).
Here are the most recent publications (while at Purdue) and some older ones, which are harder to find online. For the complete list, please visit my Google Scholar page.
Ghoshal, A., Zhang, J., Roth, M., Xia, K. M., Grama, A., and Chaterji, S., "A Distributed Kernel SVM Algorithm for Predicting Non-Canonical MicroRNA Targets and Verified Using TCGA-derived Expression Data," Accepted to IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), pp. 1-23, 2017.
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 ]
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 ]
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 ]
Ashraf Mahgoub, Paul Wood, Sachandhan Ganesh, Subrata Mitra (Adobe Research), Wolfgang Gerlach (Argonne National Laboratory), Travis Harrison (Argonne National Laboratory), Folker Meyer (Argonne National Laboratory), Ananth Grama, Saurabh Bagchi, and Somali Chaterji, “Rafiki: A Middleware for Parameter Tuning of NoSQL Datastores for Dynamic Metagenomics Workloads,” Accepted to appear at the ACM/IFIP/USENIX Middleware Conference, pp. 1-13, Dec 11-15, 2017, Las Vegas, Nevada. (Acceptance rate: 20/85 = 23.5%) [ Paper ]
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 ]
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 ]
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 ]
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 ]
Chaterji S., Koo J., Li N., Meyer F., Grama A., and Bagchi S., “Federation in Genomics Pipelines: Techniques and Challenges,” Accepted to appear in Oxford Briefings in Bioinformatics, bbx102, pp. 1-10, acceptance date: August 2017. [ Paper ]
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 ]
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 ]
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 ]
Theera-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 ]
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%) (Winner of the best paper award) [ Paper ] [ Presentation ] [ Recording of the presentation (in wav) ]
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 ]
Ghoshal A, Shankar R, Bagchi S, Grama A, and Chaterji S. MicroRNA target prediction using thermodynamic and sequence curves. Accepted for publication in BMC Genomics, notification: September 2015. [ Paper ]
Purdue University, "Orion: A fine grained parallel implementation for genomic search," At: https://github.com/purdue-dcsl/Orion (January 2015).
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 ]
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 ]
Vedantham K (+), Chaterji S (+), Kim SW, Park K. Development of a probucol‐releasing antithrombogenic drug eluting stent." Journal of Biomedical Materials Research Part B: Applied Biomaterials 100, no. 4 (2012): 1068-1077. (+ = Equal contribution) [ Paper ]
Google Scholar Page http://scholar.google.com/citations?sortby=pubdate&hl=en&user=ujT7bLwAAAAJ&view_op=list_works
I am fortunate to work with the following brilliant graduate students:
The following are alums from our group:
And the following stellar undergraduate students work with us:
Examples of questions that we are looking to answer are:
If all of this excites you and you are looking to be a part of this exciting “omics” revolution, come join us!
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