Resume


Education


Stanford University2014-current
Doctor of Philosophy (Ph.D.)
Biomedical Informatics


Indian Institute of Technology, Kharagpur2007-2012
Bachelor of Technology (B.Tech. Honors) and Master of Technology (M.Tech)
Biotechnology and Biochemical Engineering


Experience

Stanford University2014-current
Graduate Student Researcher

  • Research Website: http://onto-apps.stanford.edu/
  • Research on Semantic Web-based methods retrieve and analyze data and knowledge from multiple, heterogeneous sources. These methods are used for detecting novel pharmacological associations and predicting adverse reactions that manifest due to multiple drug intake.
  • Developed a convolutional recurrent neural network architecture to predict MGMT methylation status from brain MRI scans of glioblastoma patients.
  • Developed web and Samsung wearable applications to collect physiological, environmental and interactions data, and built machine learning models to predict user emotions.
  • Analyzed how users explore, query and reuse concept terms in biomedical ontologies, and developed visualization tools to summarize interaction patterns.
  • Developed the Ebola Virus knowledgebase and visualization dashboard by aggregating and linking data on genes, proteins, domains, binding ligands, pathways and publications

Digital Enterprise Research Institute, NUI Galway2012-2014
Linked Data Researcher

  • Contributed to the Ireland Open Data Initiative through the development of the 1st version of the Data.gov.ie platform for search and access of Irish public datasets.
  • Involved in Linked Cancer Genome Atlas project to develop a platform that integrates and visualizes GWAS, pathways and publications knowledge with the TCGA cancer patients data.
  • Involved in the European FP7 Granatum Project to develop a a federated query interface for search and visualization of 80+ linked data sources relevant to cancer chemoprevention.

Honors and Awards

Distinguished Paper Award – American Medical Informatics Association Symposium 2017
Student Best Paper Award (Resources Track) – 16th International Semantic Web Conference 2017
Best Poster Award (Graphics) – awarded for 3 consecutive years at the Stanford Biomedical Informatics Annual Poster Session 2015-2017
Best Paper Award – 7th Conference for Semantics in Healthcare and Life Sciences 2014
Semantic Web Challenge Award (Big Data Prize) – 12th International Semantic Web Conference 2013
Best Project Award – 10th Summer School on Ontology Engineering and Semantic Web 2013
Best Poster Award – 10th Summer School on Ontology Engineering and
Semantic Web
2013
Google Summer of Code fellowship – awarded for 3 consecutive years to work under Genome Informatics (Reactome) and Drupal 2010-2012
Honourable Mention in Technology – Indian Institute of Technology, Kharagpur 2012
Best Outgoing Student (Technology) – Meghnad Saha Hall of Residence,
IIT Kharagpur
2012
All India Rank 2737 (Top 1% of all applicants) – IIT Joint Entrance Examination 2007
Xavierite Super Award – St. Xaviers High School, Ahmedabad 2007

Publications


  1. Maitra, A., Zulman D.M., Kamdar, M. R., Haverfield, M. C., Thadaney, S., Verghese A., Musen, M. A. (2018) Using Anthropological Methods to Classify the Human Experience in Medicine: A Case Study of the Presence Ontology. AMIA Annual Symposium 2018 (under review).
  2. Kamdar, M. R. (2018). Mining the Web of Life Sciences Linked Open Data for Mechanism-Based Pharmacovigilance. In Proceedings of The Web Conference 2018 (Doctoral Symposium).
  3. Han, L.*, & Kamdar, M. R.* (2018). MRI to MGMT: predicting methylation status in glioblastoma patients using convolutional recurrent neural networks. In Pacific Symposium on Biocomputing(Vol. 23, p. 331).
  4. Kamdar, M. R., Walk, S., Tudorache, T., & Musen, M. A. (2017). Analyzing user interactions with biomedical ontologies: A visual perspective. Journal of Web Semantics (in press).
  5. Kamdar, M. R., & Musen, M. A. (2017). Mechanism-based Pharmacovigilance over the Life Sciences Linked Open Data Cloud. Proceedings of the AMIA Annual Symposium 2017. DISTINGUISHED PAPER AWARD.
  6. Kamdar, M. R., Walk, S., Tudorache, T., & Musen, M. A. (2017). BiOnIC: A catalog of user interactions with biomedical ontologies. In International Semantic Web Conference (pp. 130-138). STUDENT BEST PAPER AWARD.
  7. Kamdar, M. R., & Musen, M. A. (2017). PhLeGrA: Graph analytics in pharmacology over the web of life sciences linked open data. In Proceedings of the 26th International Conference on World Wide Web (pp. 321-329).
  8. Kamdar, M. R., Tudorache, T., & Musen, M. A. (2017). A systematic analysis of term reuse and term overlap across biomedical ontologies. Semantic web8(6), 853-871. IMIA YEARBOOK HONOURABLE MENTION.
  9. Kamdar, M. R.*, & Wu, M. J.* (2016). PRISM: a data-driven platform for monitoring mental health. In Biocomputing 2016: Proceedings of the Pacific Symposium (pp. 333-344).
  10. Kamdar, M. R., & Dumontier, M. (2015). An Ebola virus-centered knowledge base. Database2015.
  11. Kamdar, M. R., Tudorache, T., & Musen, M. A. (2015). Investigating term reuse and overlap in biomedical ontologies. ICBO2015, 42-46.
  12. Saleem, M., Kamdar, M. R., Iqbal, A., Sampath, S., Deus, H. F., & Ngonga, A. C. (2014). Big linked cancer data: Integrating Linked TCGA and pubmed. Journal of Web Semantics, 27, 34-41.
  13. Hasnain, A., e Zainab, S. S., Kamdar, M. R., Mehmood, Q., Warren, C. N., et al. (2014, November). A roadmap for navigating the life sciences linked open data cloud. In Joint International Semantic Technology Conference (pp. 97-112). Springer, Cham.
  14. Hasnain, A., Kamdar, M. R., Hasapis, P., Zeginis, D., Warren, C.N., Deus, H.F., Ntalaperas, D., Tarabanis, K., Mehdi, M. and Decker, S. (2014). Linked biomedical dataspace: lessons learned integrating data for drug discovery. In International Semantic Web Conference (pp. 114-130).
  15. Kazemzadeh, L., Kamdar, M. R., Beyan, O. D., Decker, S., & Barry, F. (2014, October). LinkedPPI: Enabling Intuitive, Integrative Protein-Protein Interaction Discovery. In LISC@ ISWC (pp. 48-59).
  16. Kamdar, M. R., Iqbal, A., Saleem, M., Deus, H. F., & Decker, S. (2014). GenomeSnip: Fragmenting the Genomic Wheel to augment discovery in cancer research. In Conference on Semantics in Healthcare and Life Sciences 2014 (CSHALS). ISCB. BEST PAPER AWARD.
  17. Kamdar, M. R., Zeginis, D., Hasnain, A., Decker, S., & Deus, H. F. (2014). ReVeaLD: A user-driven domain-specific interactive search platform for biomedical research. Journal of biomedical informatics, 47, 112-130.
  18. Saleem, M., Kamdar, M. R., Iqbal, A., Sampath, S., Deus, H. F., & Ngonga, A. C. (2013). Fostering serendipity through big linked data. Semantic Web Challenge at ISWC 2013. SEMANTIC WEB CHALLENGE AWARD.
  19. Croft, D., Mundo, A.F., Haw, R., Milacic, M., Weiser, J., Wu, G., Caudy, M., Garapati, P., Gillespie, M., Kamdar, M.R., Jassal, B., et al. (2013). The Reactome pathway knowledgebase. Nucleic acids research, 42(D1), pp.D472-D477.
  20. Dey, P., Kamdar, M. R., M Mandal, S., & K Maiti, M. (2013). Identification of an extracellular antifungal protein from the endophytic fungus Colletotrichum sp. DM06. Protein and peptide letters20(2), 173-179.