Somali Chaterji's Corner in Cyberspace

I am working at the intersection of bioengineering and machine learning, on challenging and potentially ground-breaking problems in precision medicine.
Best paper award at ACM BCB '15 (Sep '15; Atlanta, GA)
At Indiana U. for my talk in CS (Oct '17; Bloomington, IN)
NIH R01 project kickoff at Argonne National Lab (Jul '16; Argonne, IL)
With the Seed of Success acorn award given to Purdue investigators winning > $1M grants (Oct '16; W Lafayette, IN)
My first half marathon (Oct '15; W Lafayette, IN)
Finishing the Purdue half marathon (Oct '16; W Lafayette, IN)


Somali Chaterji (pronounced: SHOH-MAH-LEE CHA-ter-JEEis 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.

Research Interests:

My current areas of interest and expertise are:

  1. Systems and Synthetic Bioengineering
  2. Computational Genomics
  3. Nanofabrication and Nanosensing of Bioinspired Devices
  4. Data-Driven Molecular and Cell Engineering
  5. High-Performance Computing for Bioengineering

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).

News: breaking news

  1. February 2018: Our paper on force measurements in cell-based nanosensors comes out in the "Biomaterials" journal. This is work done jointly with collaborators at the University of Texas at Austin and University of Washington at Seattle. [ Paper ]

  2. January 2018: I gave the talk at the IEEE Comsnets conference in Bangalore, India on smart manufacturing of sensors using reinforcement learning to determine bottlenecks. [ Paper ]

  3. November 2017: We have a new paper in Theranostics (IF = 8.766) on microRNA-based precision therapeutics and one in Biomaterials (IF = 8.402) on biophysical aspects of cardivascular cell-based nanosensing to facilitate cell engineering paradigms. 

  4. August 2017: We have two papers accepted to Briefings in Bioinformatics, one to the Middleware conference, and one to Theranostics. See below under "Publications".

  5. June 2017: I gave a talk at the IFIP Working Group 10.4 workshop in Longmont, Colorado on the topic of "The Fault Tolerant Epigenome & its Data Profile". The working group comprises leading researchers and practitioners in the area of dependable computing and meets for two workshops each year. [ pdf ] [ WG web site ]

  6. March-June 2017: We have 3 papers accepted or under minor revision. They are on federation in bioinformatics cyber infrastructures (Briefings in Bioinformatics), genome editing (Theranostics journal), and parallelization of de novo genome assembly (ACM BCB). [ html ]

  7. January 2017: I am serving on the Organizing Committee and Program Committee of the 10th IEEE International Conference on Communication Systems and Networks (Comsnets) to be held Jan 3-7 in Bangalore, India.  [ html ]

News Archive


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.

  1. 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.

  2. 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

  3. 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 ]

  4. 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 ]

  5. 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 ]

  6. 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 ]

  7. 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 ]

  8. 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 ]

  9. 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 ]

  10. 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 ]

  11. 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 ]

  12. 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 ]

  13. Kim SG, Theera-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 ]
  14. 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 ]

  15. 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 ]

  16. 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) ]

  17. 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 ]

  18. 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 ]

  19. Purdue University, "Orion: A fine grained parallel implementation for genomic search," At: (January 2015).

  20. 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 ]

  21. 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 ]

  22. 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


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:



  1. How to predict new canonical and non-canonical microRNA targets?
  2. How do long non-coding RNAs act as enhancers of gene expression?
  3. How to build parallel algorithms for genomics applications?
  4. Check out others that are ongoing here:

Examples of questions that we are looking to answer are:

  1. How do you predict the function and targets of these non-coding regions using cutting-edge machine learning techniques?
  2. How to use graph-based methods to extend gene regulatory networks (
  3. How do you become a part of the $1000 genome? Is it for real ( Can you be a part of this Analysis Revolution, analyzing omics data?
  4. Can you decide to tweak your genes using epigenetics?

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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