Kalpana Raja, PhD, MRSB, CSci

Professional Summary

Dr. Kalpana Raja is an interdisciplinary computer scientist, molecular informatics expert, and a Research Scientist in the Department of Biomedical Informatics & Data Science (BIDS) at the Yale School of Medicine. Since joining the department in February 2023, her research has focused on the cutting-edge intersection of natural language processing (NLP), large language models (LLM), artificial intelligence (AI), and data harmonization & standardization, with a core emphasis on biomedical text extraction, automated knowledge curation, and the advancement of open science.

Current Research & Initiatives

At Yale, Dr. Raja focuses on the development of Python-based NLP pipelines, deep learning paradigms, and large language model (LLM) workflows to accelerate biomedical discoveries. A strong advocate for the FAIR (Findable, Accessible, Interoperable, and Reusable) data principles, she is currently leading an NIH SBIR grant to evaluate the reliability of immunology datasets using information extraction and sentiment analysis.

She also serves as a key co-investigator and point person within the Data Coordination Center (DCC) for the $7.88 million NIH-funded IMPACT-MH program, managing informatics infrastructure to build standard data representation models. Additionally, in collaboration with Dr. Hua Xu and Dr. Lucila Ohno-Machado, Dr. Raja won Phase 1 of an NIH-organized challenge for proposing the S-index—a refined data-sharing metric designed to reward the explicit reuse of biomedical datasets—and she is currently leading the technical development of its web platform.

Academic Background & Past Experience

Before moving to New Haven, Dr. Raja served as an Assistant Professor at the School of Biomedical Informatics at UTHealth Houston and as a scientist at Sema4, a patient-centered healthcare data company in Stamford, CT.

Dr. Raja’s unique interdisciplinary foundation begins with a bachelor’s degree in pharmacy from Tamil Nadu Dr. M.G.R. Medical University in Chennai, India, where she is also a registered pharmacist. Driven by a vision to develop software for biological applications, she earned a master’s degree in Computing (Software Technology) from The Robert Gordon University in Aberdeen, UK. During this time, she developed ProfileSKiM, an intelligent document retrieval tool that won a university reward in 2005 and the prestigious Technology Award from the British Computer Society in 2006. She subsequently completed a second master’s degree in Bioinformatics and an interdisciplinary PhD in Computing (Software Technology – Bioinformatics) from Bharathiar University in Coimbatore, India. She presented her doctoral findings at the 2012 Asia Pacific Bioinformatics Conference (APBC) in Melbourne and BioCreative Conference V in Washington, DC.

Publications & Recognition

Dr. Raja’s methodologies for information retrieval, literature-based discovery, and automated hypothesis generation have been applied across diverse biological domains, including protein-protein interactions, drug repurposing, and disease comorbidities. She has published over 100 articles in peer-reviewed journals, books, and conference proceedings, and frequently provides NLP support for complex genomics and transcriptomics projects.

Recognized globally for her scientific contributions, she was elected as a Member of the Royal Society of Biology (MRSB) in 2019 and honored as a Chartered Scientist (CSci) in 2022 by the Royal Society of Biology, London. She is also the recipient of the 2019 Women Scientist Award from the Society for Bioinformatics and Biological Sciences, a non-profit organization in India.

Areas of Expertise

• Natural Language Processing (NLP)
• Artificial Intelligence (AI) & Large Language Models (LLMs)
• Machine Learning & Deep Learning
• Biomedical Informatics & Literature Mining
• Data Harmonization & Standardization
  
• FAIR Data Principles & Data Quality

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