Kisan Thapa
PhD Candidate in Computer Science at UMass Boston, specializing in computational biology and deep
learning. I conduct research as part of the Network
Biology
Laboratory under the guidance of Prof.
Özgün Babur.
I am passionate about developing computational methods, leveraging deep learning and graph
neural networks(GNNs) techniques to
analyze and model biological networks. Additionally, I am dedicated to creating
user-friendly
software tools that empower biologists to extract meaningful insights from their data with
efficiency and precision.
Website:
https://www.cs.umb.edu/~kisan/
Education
2021 - Present
PhD in Computer Science
University of Massachusetts Boston
2013 - 2017
Bachelor of Computer Engineering
Pokhara University, Nepal
News
🗓️ Mar 14, 2025
🎉 Published my first-author paper
"A Review of Strategies for Incorporating Prior Knowledge into Omics Analysis Using Deep Neural Networks"
in CellPress Patterns 🏆📖.
🗓️ Feb 14, 2025
🎤 Presented our paper
"A Review of Strategies for Incorporating Prior Knowledge
into Omics Analysis Using Deep Neural Networks"
at the Graduate Symposium at the University of Massachusetts Boston 🏛️.
🗓️ Jan 12, 2025
📰 The paper
"A Review of Strategies for Incorporating Prior Knowledge
into Omics Analysis Using Deep Neural Networks"
has been accepted in Cell Press Patterns 🎉🏆.
🌐 Dec 14, 2024
🚀 This personal portfolio website went live! 🎨💻
🎓 Dec 20, 2023
✅ Successfully passed the PhD qualifying exam! 🎉📜
Selected Publications
Strategies to include prior knowledge in omics analysis with deep neural networks
Kisan Thapa, Meric Kinali, Shichao Pei, Augustin Luna, and Ozgun Babur
Protein Kinase Signaling Networks Driven by Oncogenic Gq/11 in Uveal
Melanoma Identified by Phosphoproteomic and Bioinformatic Analyses
Michael D Onken, Petra Erdmann-Gilmore, Qiang Zhang, Kisan Thapa, Emily King, Kevin M Kaltenbronn, Sarah E Noda, Carol M Makepeace, Dennis Goldfarb, Özgün Babur, R Reid Townsend, Kendall J Blumer
A framework for considering prior information in network‐based approaches
to omics data analysis
Julia Somers, Madeleine Fenner, Garth Kong, Dharani Thirumalaisamy, William M Yashar, Kisan Thapa, Meric Kinali, Olga Nikolova, Özgün Babur, Emek Demir
Performance of ChatGPT on USMLE: Unlocking the potential of large language
models for AI-assisted medical education
Prabin Sharma, Kisan Thapa, Dikshya Thapa, Prastab Dhakal, Mala Deep Upadhaya, Santosh Adhikari, Salik Ram Khanal