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Madhavi K. Ganapathiraju, PhD
- Associate Professor of Biomedical Informatics
Department of Biomedical Informatics (DBMI) | University of Pittsburgh School of Medicine
Biography
Prof. Madhavi K. Ganapathiraju is an Associate Professor in the Department of Biomedical Informatics at the University of Pittsburgh, with joint appointments in the Intelligent Systems Program and the Clinical and Translational Science Institute. Her research focuses on developing computational and machine learning methods to discover molecular mechanisms of diseases and to translate those discoveries into actionable hypotheses for experimental biology and clinical trials. She leads work in protein-protein interaction prediction, systems biology, and translational bioinformatics, and is also developing generative AI tools for biologists. Her recent efforts additionally include computational phenotyping and related clinical informatics applications.
Computational & Clinical Expertise
Dr. Ganapathiraju’s clinical informatics expertise centers on computational phenotyping and the application of machine learning methods to clinically relevant biomedical problems. Her current work includes phenotyping efforts in rehabilitation medicine and the translation of computational discoveries into hypotheses and tools that can support healthcare and biomedical research.
Research Interests
Dr. Ganapathiraju’s research focuses on discovering molecular mechanisms by which genes contribute to human disease and on translating these findings to bench and bedside through collaboration with experimental biologists and clinicians. She develops computational and AI methods and agents for large-scale prediction and prioritization of protein-protein interactions, genomic patterns, and disease-associated mechanisms. Her work also includes web-based knowledge dissemination tools and open science infrastructure to accelerate biomedical discovery. Current projects span rare diseases, developmental and neuropsychiatric disorders, and cancer.
Specialties
- Translational Bioinformatics
- Artificial Intelligence
- Machine Learning in Biomedicine
- Protein-Protein Interaction Prediction
- Drug Repurposing
- Systems Biology
- Clinical Informatics and Computational Phenotyping
Websites & Links
Education & Training
- B.Sc., Electronics, Mathematics and PhysicsDelhi University, New Delhi, India1990–1993
- M.Engg., Electronics and Communications EngineeringIndian Institute of Science, Bangalore, India1993–1998
- Ph.D., Language and Information Technologies (Computer Science)Carnegie Mellon University, Pittsburgh, PA2001–2007
Awards & Distinctions
- Biobehavioral Research Awards for Innovative New Scientists (BRAINS) AwardNational Institute of Mental Health2011
- Graduate Student ScholarshipIndian Institute of Science1994–1996
- Bhavishya Jyothi (Light of the Future) Graduate Training ScholarshipNational Institute of Information Technology, India1990–1993
Representative Publications
Ganapathiraju MK, Thahir M, Handen A, et al. Schizophrenia interactome with 504 novel protein-protein interactions. NPJ Schizophr. 2016;2:16012.
Ganapathiraju MK, Triptish B, Deshpande S, et al. Schizophrenia interactome derived repurposable drugs and randomized control trials of two candidates. Biol Psychiatry. 2024;96(8):651–658.
Ganapathiraju MK, Subramanian S, Chaparala S, Karunakaran KB. A reference catalog of DNA palindromes in the human genome and their variations in 1000 Genomes. Hum Genome Var. 2020;7(1):40.
Li Y, Klena NT, Gabriel GC, et al.; Ganapathiraju MK. Global genetic analysis in mice unveils central role for cilia in congenital heart disease. Nature. 2015;521(7553):520–524.
Orii N, Ganapathiraju MK. Wiki-pi: a web-server of annotated human protein-protein interactions to aid in discovery of protein function. PLoS One. 2012;7(11):e49029.
Research Grants
| Grant / Funding Agency | Role | Grant Number | Years |
|---|---|---|---|
| National Mesothelioma Virtual Bank, Continued Innovation National Institute for Occupational Safety and Health (NIOSH), CDC | Co-I | 5U24OH009077-11 | 2021-present |
Trainees
| Trainee | Degree Program / Role & Years |
|---|---|
| Manikya Rathna | Research Advisor │ 2025–2026 |
| Anirudh Rajesh | Independent-Study Guide, Pitt SCI Undergraduate Student │ 2025 |
| Asher Peng | High School Student Mentee │ 2025 |
| Zeenia Pirani | High School Student Mentee │ 2025 |
| Kavinaya Murali | High School Student Mentee │ 2025 |
| Carlie Mendoza Hoffman | Biomedical Informatics Certificate Student │ 2026–Present |