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.

GitHub | LinkedIn | Resume

Email: Kisan [DOT] Thapa001 [AT] umb.edu

Website: https://www.cs.umb.edu/~kisan/

2021 - Present

PhD in Computer Science

University of Massachusetts Boston

2013 - 2017

Bachelor of Computer Engineering

Pokhara University, Nepal

🗓️ 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! 🎉📜

Strategies to include prior knowledge in omics analysis with deep neural networks

Kisan Thapa, Meric Kinali, Shichao Pei, Augustin Luna, and Ozgun Babur

CellPress Patterns 2025

Journal Bib URL

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

Molecular & Cellular Proteomics 22 (11)

Journal Bib URL

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

Proteomics 23 (21-22)

Journal Bib URL

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

arXiv preprint arXiv:2307.00112

Journal Bib URL