Dhananjay Bhaskar

I am a Postdoctoral Associate in Department of Genetics at the Yale School of Medicine. My research, advised by Prof. Smita Krishnaswamy focuses on the development of novel methods, based on Machine Learning and Computational Topology, to address a variety of problems in biomedical research and representation learning. I received a Ph.D. in Biomedical Engineering and Sc.M. in Data Science from Brown University, where I worked in Prof. Ian Wong's lab on data-driven modeling and analysis of collective cell behavior in the course of tumorigenesis. Prior to Brown, I received training in Computer Science and Applied Mathematics (advised by Prof. Leah Edelstein-Keshet) at the University of British Columbia.


  1. A Methodology for Morphological Feature Extraction and Unsupervised Cell Classification. Bhaskar, D., Lee, D., Knútsdóttir, H., Tan, C., Zhang, M., Dean, P., Roskelley, C., Keshet, L. [bioRxiv preprint]
  2. Topological Data Analysis of Collective and Individual Epithelial Cells using Persistent Homology of Loops. Bhaskar, D., Zhang, W., Wong, I. Soft Matter 17, 4653-4664, 2021.
  3. Analyzing Collective Motion with Machine Learning and Topology. Bhaskar, D., Manhart, A., Milzman, J., Nardini, J., Storey, K., Topaz, C., Ziegelmeier, L. Chaos 29 (12), 123125, 2019.
  4. Breast Cancer Cells Transition from Mesenchymal to Amoeboid Migration in Tunable Three-Dimensional Silk-Collagen Hydrogels. Khoo, A., Valentin, T., Leggett, S., Bhaskar, D., Bye, E., Benmelech, S., Ip, B., Wong, I. ACS Biomaterials Science & Engineering 5 (9), 4341-4354, 2019.
  5. Motility-limited Aggregation of Mammary Epithelial Cells into Fractal-like Clusters. Leggett, S., Neronha, Z., Bhaskar, D., Sim, J., Perdikari, M., Wong, I. PNAS 116 (35), 17298-17306, 2019.
  6. 3D Printed Self-adhesive PEGDA-PAA Hydrogels as Modular Components for Soft Actuators and Microfluidics. Valentin, T., DuBois, E., Machnicki, C., Bhaskar, D., Cui, F., Wong, I. Polymer Chemistry 10 (16), 2015-2028, 2019.
  7. Coupling Mechanical Tension and GTPase Signaling to Generate Cell and Tissue Dynamics. Zmurchock, C., Bhaskar, D., Keshet, L. Physical Biology, 5 (4), 046004, 2018.
  8. Polarization and Migration in the Zebrafish Posterior Lateral Line System. Knútsdóttir, H., Zmurchock, C., Bhaskar, D., Palsson, E., Nogare, D., Chitnis, A., Keshet, L. PLoS Computational Biology, 13 (4), e1005451, 2017.


Online Presentation Creator (2013)
A HTML 5 Web Application

Designed to facilitate creation of health and wellness e-Learning modules for Clinemetrica Inc.

Features :
  • Customized CLEditor for rich text editing in English and French
  • Version control for module creation (save and reload)
  • Finished modules can be viewed in IE 7+
  • User tracking capability to monitor viewing time for each slide
Clinemetrica Inc. Web Interface (2013)
Database Front-end and Data Analysis Tool

Perform queries and view aggregate customer information from the web.

Features :
  • Requests are sent using AJAX and JSON
  • Secure, uses PHP Data Objects (PDO) to process requests
  • Organises information in neat graphs using HighCharts JS
Educational Simulations (2011)
Java Applets and HTML5 Applications

Created educational simulations demonstrating concepts in physics, computer science and mathematics.

The example on the right illustrates Monte Carlo methodology.

Features :
  • Intuitive and interactive
  • Facilitates learning visually
  • Advanced mechanics and electrodynamics simulations created using EJS framework

Estimation of Pi

Number of points : 0

Points inside circle : 0