ashwin dhakal

Assistant Professor

School of Computing and Analytics, Northern Kentucky University

Highland Heights, Kentucky, USA

20+ Publications
700+ Citations
2 Books
ashwin dhakal

About

I am an Assistant Professor at the School of Computing and Analytics, Northern Kentucky University. I completed my PhD in Computer Science from the University of Missouri.

During my PhD, I worked as a Graduate Research Assistant at the Bioinformatics and Machine Learning Lab with Dr. Jianlin Cheng (Mizzou, MO) and Dr. Liguo Wang (Brookhaven National Laboratory, NY). I did my ’25 summer internship as a Machine Learning Intern at Generate: Biomedicines in Boston. My research lies at the intersection of artificial intelligence, computer vision, and bioinformatics, with a particular focus on developing deep learning–driven methods for Cryo-Electron Microscopy (Cryo-EM) and Cryo-Electron Tomography (Cryo-ET). My work aims to advance the integration of modern AI into structural biology and biomedical informatics, including applications in biomolecular structure analysis and drug–target interactions.

I was selected as the Doctoral Student Marshal for the Graduate School Commencement Ceremony in recognition of my academic excellence and contributions to the university, and delivered the commencement address on behalf of the graduating doctoral students.

While at the University of Missouri, I served in several student bodies. I served as the President of the University of Missouri Nepalese Student Association (MUNSA) and as the Director of Programming for the Graduate Professional Council (GPC). My impact as an international student and leader was also recognized by the university when I was featured during International Education Week by Show Me Mizzou.

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

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

Professional Experience

Assistant Professor

School of Computing and Analytics, Northern Kentucky University

Aug 2026 – Present

Highland Heights, Kentucky

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