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

Optum2023-current
Director of Clinical Informatics

  • Knowledge engineering to develop computable and executable clinical content for use within clinical decision support systems

Kaiser Permanente2022-2023
Principal Data Scientist

  • Content search, recommendation, personalization for patients using knowledge graphs and graph data science and machine learning methods

Elsevier Inc.2019-2022
Principal Data Scientist
Senior Data Scientist

  • Research and development of Elsevier’s healthcare knowledge graph (HG) created from heterogeneous data and knowledge sources and medical literature.
  • HG is used to power Elsevier’s top commercial priority for health: delivering clinical decision support and point-of-care content discovery for clinicians and patients.
  • Develop machine learning and graph traversal methods to extract clinical relations from unstructured text in Elsevier medical journals and scientific literature.
  • Build a cross-platform product through collaboration with Stanford University and industry partners to enable knowledge engineers to curate the HG and map content to clinical terminologies used in electronic medical record systems.
  • Develop a visualization interface to showcase the capabilities of the HG platform for powering Elsevier Health Markets products to key stakeholders.
  • Develop the core infrastructure for scalable automated deployment, testing, monitoring, and documentation of the HG platform and other products.

Stanford University2014-2019
Graduate Student Researcher

  • Developed a semantic web architecture PhLeGrA for integrating biomedical data and knowledge from multiple sources. PhLeGrA can generate a pharmacology network (~8,000 concepts, ~100,000 relations, 8 biomedical sources) and was used to mine pharmacological associations from FDA adverse event reporting system.
  • Collaborated with the Stanford BDS Opioid Working Group and Foundation for Precision Medicine to develop the Opioid Knowledge Graph and understand US consumption patterns and potential risk factors for addiction.
  • Developed a convolutional recurrent neural network architecture to predict MGMT methylation status from brain MRI scans of glioblastoma patients.
  • Developed a Samsung wearable application to collect physiological, environmental and interactions data, and built machine learning models to predict emotions.
  • Analyzed how users explore, query and reuse concept terms across more than 300 biomedical ontologies. This research has been used to improve ontology repositories and the quality of biomedical ontologies.
  • Developed the Ebola Virus knowledgebase by aggregating and linking data on genes, proteins, domains, binding ligands, pathways and publications

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

  • Developed and successfully launched the first scalable prototype of the Ireland’s Open Data Initiative Data.gov.ie platform in June 2014 for search and access of open Irish datasets. Data.gov.ie currently hosts ~8,800 datasets from 109 Irish data publishers and is accessed by ~15,000 unique users every month.
  • Involved in Linked Cancer Genome Atlas project to develop a scalable platform that integrates and visualizes genomics and pathway knowledge (~20,000 genes, 500 pathways, ~10,000 publications) with cancer patient data (9,000 patients across 27 cancer types).
  • Collaborated with 7 research groups through the European FP7 Granatum project on cancer chemoprevention. 
  • Developer and inventor of ReVeaLD, a visual interface that enabled cancer biologists to search and visualize integrated content from 80+ databases relevant to cancer chemoprevention research. ReVeaLD was accessed to formulate more than 20,000 queries by ~400 researchers over a period of 2 years.

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 web, 8(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. Database, 2015.
  11. Kamdar, M. R., Tudorache, T., & Musen, M. A. (2015). Investigating term reuse and overlap in biomedical ontologies. ICBO, 2015, 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 letters, 20(2), 173-179.