Ashwin Dhakal

Computer Science PhD Candidate

University of Missouri

Columbia, Missouri, USA

15+ Publications
500+ Citations
2 Books
Ashwin Dhakal

About

I am a Computer Science PhD Candidate at the University of Missouri. I currently work as a Graduate Research Assistant at Bioinformatics and Machine Learning Lab with Dr. Jianlin Cheng (Mizzou, MO) and Dr. Liguo Wang (Brookhaven National Laboratory, NY). My research lies at the intersection of artificial intelligence, computer vision, and structural biology, with a particular focus on developing deep learning–driven pipelines for Cryo-Electron Microscopy (Cryo-EM) and Cryo-Electron Tomography (Cryo-ET). Through my research, I aim to bridge modern AI with biomedical informatics that involves Drug-Target interactions and structural biology.

Having earned a Master's Degree in Computer Science from Mizzou, I also authored two books, namely "Software Engineering" and "Diversity and Immigrants' Dream in America." I hail from the land of the majestic Himalayas, Nepal, and dream about reaching Mt. Everest's summit. I am married to Aliza and am grateful for her unwavering support.

Education

PhD in Computer Science

University of Missouri

Excellence in Research Award 2025

Outstanding Computer Science PhD Award 2024

May 2026 (Expected)

Columbia, MO, USA

MS in Computer Science

University of Missouri

May 2023

Columbia, MO, USA

B.Eng. in Computer Engineering

Tribhuvan University

Oct 2018

Pokhara, Nepal

Professional Experience

Research Experience

Graduate Research Assistant

University of Missouri - Bioinformatics and Machine Learning Lab

Jan 2021 – Present

Columbia, Missouri

Machine Learning Intern

Generate: Biomedicines

Jun 2025 – Aug 2025

Boston, Massachusetts

Teaching Experience

Teaching Assistant [Graduate Teaching Experience]

University of Missouri-Columbia

Fall 2024

Faculty Lecturer [Undergraduate Teaching Experience]

Tribhuvan University - Sagarmatha Engineering College

Nov 2019 – Dec 2020

Kathmandu, Nepal

Industry Experience

Business Intelligence Engineer

LIS Nepal

Oct 2018 - Apr 2019

Kathmandu, Nepal

Research Interests

Artificial Intelligence
Machine Learning
Cryo-Electron Microscopy
Advanced Computer Vision
Natural Language Processing
Big Data in Bioinformatics
Applied Deep Learning
Data Science & Analytics
Computational Biology
Health Informatics
Protein-Drug Interaction
Databases & Data Engineering

Selected Research Publications

CryoTransformer Publication

CryoTransformer: A Transformer Model for Picking Protein Particles from Cryo-EM Micrographs

A. Dhakal, R. Gyawali, L. Wang, and J. Cheng

Bioinformatics, 2024

Cryo-EM Dataset Publication

A Large Expert-Curated Cryo-EM Image Dataset for Machine Learning Protein Particle Picking

A. Dhakal, R. Gyawali, L. Wang, and J. Cheng

Nature Scientific Data, 2023

AI in Cryo-EM Publication

Artificial intelligence in cryo-EM protein particle picking: recent advances and remaining challenges

A. Dhakal, R. Gyawali, L. Wang, and J. Cheng

Briefings in Bioinformatics, 2025

Protein-Ligand Interactions Publication

Artificial Intelligence in the Prediction of Protein-Ligand Interactions: Recent Advances and Future Directions

A. Dhakal, C. Mckay, J. Tanner, J. Cheng

Briefings in Bioinformatics, 2021

Multimodal Deep Learning Publication

Multimodal deep learning integration of cryo-EM and AlphaFold3 for high-accuracy protein structure determination

R. Gyawali, A. Dhakal, J. Cheng

Nature Communications Chemistry, 2025

CryoSegNet Publication

CryoSegNet: accurate cryo-EM protein particle picking by integrating the foundational AI image segmentation model and attention-gated U-Net

R. Gyawali, A. Dhakal, L. Wang, and J. Cheng

Briefings in Bioinformatics, 2024