Indika Kahanda

Assistant Professor, School of Computing, Montana State University

Office: 362 Barnard Hall
Address: 357 Barnard Hall, Montana State University, Bozeman, MT 59717
Phone: (406) 994-4067
Email: indika.kahanda (at)

Research Interests

My research interests lie in the areas of Bioinformatics, Computational Biology, and Biomedical Natural Language Processing. I focus on the application of machine learning and natural language processing techniques to solve problems involving large-scale biological, molecular, and biomedical data. In particular, I investigate approaches to (1) develop computational methods for functional genomics and (2) develop natural language processing tools for biomedical literature. Current projects include developing an automated biocuration pipeline for mental health and developing computational methods for predicting phenotypic abonormalities for proteins.


09/20/18:MSU featured Indika Kahanda's work with the Montana branch of the National Alliance on Mental Illness in this news item.

08/24/18: Indika Kahanda is a collaborator on a one-year, $50K grant from the Institute of Museum and Library Services (IMLS). The project is titled "Data-Driven Improvement to Institutional Repository Access and Visibility". Dr. Kahanda will oversee investigating whether machine learning can improve the quality of institutional repository content metadata.

08/17/18: Indika Kahanda, recently received $36K in funding from MSU's Center for Mental Health Research and Recovery (CMHRR) to support a graduate research assistant for two years. The GRA will explore machine learning techniques that assist MSU researchers conduct better brain analysis using Electroencephalograms and Functional Near-Infrared Spectroscopy.

08/05/18: Our paper titled "Exploring Frequented Regions in Pan-Genomic Graphs." was accepted for Special Issue of the IEEE/ACM Transactions on Computational Biology and Bioinformatics.

07/15/18: Brendan Mumey (PI) and Indika Kahanda (co-PI) recently recieved a new, 3-year $379K NSF grant titled "Pioneering New Approaches to Explore Pangenomic Space at Scale". The project will develop new software tools for pangenomic analysis that help scientists understand how organisms adapt their genomes to their environments. Their approach makes use of a graph-based representation of a pangenome and exploits this representation to efficiently find both shared and unique regions of interest.

07/08/18: Morteza presented our work titled "A Look Back at the Quality of Protein Function Prediction Tools in CAFA" as a talk and a poster at the Function COSI in ISMB.

07/08/18: Buwani presented our work titled "Ab initio Identification of Novel microRNAs in Plants: A Systematic Review" as a poster at the Intergrative RNA Biology COSI in ISMB.

06/01/18: Morteza has been awarded the travel fellowship award for the Function COSI 2018 at ISMB this year. Congratulations!

04/23/18: Mohammed Annai was awarded Outstanding M.S. Researcher at the 2018 Gianforte School of Computing Awards. Morteza Pourreza-Shahri was a honourable mention for the Outstanding Ph.D. Researcher award. Congratulations!