Khanh Dao Duc, University of British Columbia

Research

Biophysical modeling and analysis Endoplasmic Reticulum Mathematical modeling mRNA transport Optimization of gene expression Protein translation dynamics Ribosome Ribosome evolution

Latest papers

Cryo-EM analysis of cooperative conformational changes in the SARS-CoV-2 spike protein trimer.
IUCrJ · 2026 · senior author
Fast and interpretable quantification of biological shape heterogeneity via stratified Wasserstein kernel.
PLoS computational biology · 2026 · senior author
Advanced coarse-grained model for fast simulation of nascent polypeptide chain dynamics within the ribosome.
Biophysical journal · 2026 · senior author

All 18 publications

Latest funding

Closing the Gap in Agricultural Climate Action: Harmonizing Data, Enhancing Emission Models, and Empowering Canadian Farmers
NSERC · 2025 · Principal investigator
$1,409,007
Unraveling the biophysical mechanisms of antibiotic resistance in Mycobacteria from Atomic Force Microscopy image data
NSERC · 2023 · Principal investigator
$25,000
Digital Solutions for Advancing Agroecological Transitions
SSHRC · 2021 · Co-investigator
$237,786

All 6 grants and awards

18 publications.

01

Cryo-EM analysis of cooperative conformational changes in the SARS-CoV-2 spike protein trimer.

Wang Q, Cholak S, Woollard G, Subramaniam S, Dao Duc K

IUCrJ2026Senior author

DOI: 10.1107/s2052252526004513 PMID: 42345087

02

Fast and interpretable quantification of biological shape heterogeneity via stratified Wasserstein kernel.

Zhao W, Sutherland DJ, Dao Duc K

PLoS computational biology2026Senior author

DOI: 10.1371/journal.pcbi.1014254 PMID: 42096490

03

Advanced coarse-grained model for fast simulation of nascent polypeptide chain dynamics within the ribosome.

Yu S, Kushner A, Teasell E, Zhao W, Srebnik S, Dao Duc K

Biophysical journal2026Senior author

DOI: 10.1016/j.bpj.2025.10.044 PMID: 41194472

04

Transport-based transfer learning on Electronic Health Records: application to detection of treatment disparities.

Li W, Ahmed S, Park YP, Dao Duc K

Journal of the American Medical Informatics Association : JAMIA2026Senior author

DOI: 10.1093/jamia/ocaf134 PMID: 40901720

05

The Inaugural Flatiron Institute Cryo-EM Conformational Heterogeneity Challenge.

Astore MA, Woollard G, Silva-Sánchez D, Zhou W, Kopylov M, Dao Duc K, Lederman RR, Li Y, Zhou Y, Yuan J, Ye F, Gu Q, Vuillemot R, Jonic S, Dang L, Ludtke SJ, Bridges H, Liu S, McLean M, Peretroukhin V, Schwab J, Cruz-Chú ER, Schwander P, Aurèle Gilles M, Singer A, Herreros D, Carazo JM, Sorzano COS, Feathers JR, Zhong ED, Grigorie N, Cossio P, Hanson SM

bioRxiv : the preprint server for biology2025

DOI: 10.1101/2025.07.18.665582 PMID: 41280101

06

Struc2mapGAN: improving synthetic cryogenic electron microscopy density maps with generative adversarial networks.

Zhang C, Condon A, Dao Duc K

Bioinformatics advances2025Senior author

DOI: 10.1093/bioadv/vbaf179 PMID: 40831760

07

A comprehensive survey and benchmark of deep learning-based methods for atomic model building from cryo-electron microscopy density maps.

Zhang C, Condon A, Dao Duc K

Briefings in bioinformatics2025Senior author

DOI: 10.1093/bib/bbaf322 PMID: 40645653

08

InstaMap: instant-NGP for cryo-EM density maps.

Woollard G, Zhou W, Thiede EH, Lin C, Grigorieff N, Cossio P, Dao Duc K, Hanson SM

Acta crystallographica. Section D, Structural biology2025

DOI: 10.1107/s2059798325002025 PMID: 40135651

09

Optimal control of ribosome population for gene expression under periodic nutrient intake.

Soubrier C, Foxall E, Ciandrini L, Dao Duc K

Journal of the Royal Society, Interface2024Senior author

DOI: 10.1098/rsif.2023.0652 PMID: 38442858

10

CAT PETR: a graphical user interface for differential analysis of phosphorylation and expression data.

Flanagan K, Pelech S, Av-Gay Y, Dao Duc K

Statistical applications in genetics and molecular biology2023Senior author

DOI: 10.1515/sagmb-2023-0017 PMID: 37592851

Closing the Gap in Agricultural Climate Action: Harmonizing Data, Enhancing Emission Models, and Empowering Canadian Farmers

Principal investigatorNSERC2025Society

Principal investigators: Dao Duc, Khanh

Keywords: Agriculture and primary food production; Environment

$1,409,007

Unraveling the biophysical mechanisms of antibiotic resistance in Mycobacteria from Atomic Force Microscopy image data

Principal investigatorNSERC2023Alliance Grants

Principal investigators: Dao Duc, Khanh K

Keywords: Antibiotic resistance; Atomic Force Microscopy; Bacterial morphology; Cell heterogeneity; Cell shape; Computational Geometry; Image Analysis; Machine Learning

$25,000

Digital Solutions for Advancing Agroecological Transitions

Co-investigatorSSHRC2021New Frontiers in Research Fund - Special Call

Principal investigators: Wittman, Hannah

Keywords: agroecology citizen science food soveriengty agroforestry digital technology for agriculture

$237,786

Investigating the properties of the ribosomes and their impact on translation dynamics across scales and systems

Principal investigatorNSERC2020Discovery Grants Program - Individual

Principal investigators: Dao Duc, Khanh

Keywords: ribosome; protein translation dynamics; biophysical modeling and analysis; mrna transport; ribosome structure and assembly; ribosome evolution; endoplasmic reticulum; optimization of gene expression; mathematical modeling

$185,000

Investigating the properties of the ribosomes and their impact on translation dynamics across scales and systems

Principal investigatorNSERC2020Discovery Launch Supplement

Principal investigators: Dao Duc, Khanh

$12,500

Beyond structure determination: Developing new algorithms for characterization of protein conformational heterogeneity and energy landscape inference from Cryo-EM data

Principal investigatorSSHRC2019New Frontiers in Research Fund - Exploration

Principal investigators: Dao Duc, Khanh

$273,175

From CIHR, NSERC and SSHRC funding decisions: CIHR since 2008, NSERC since 1991 and SSHRC since 1998, including their latest published competition results.

Frequent collaborators

Mathematics
Computer Science at UBC
Chemical and Biological Engineering
Okanagan - Computer Science, Mathematics, Physics and Statistics
Biochemistry and Molecular Biology
Department of Microbiology and Immunology

Co-authors at University of British Columbia, colored by department. Thicker lines mean more shared papers; select anyone to open their profile and their own map.

Simcha Srebnik

Chemical and Biological Engineering

2 shared papers, latest 2026

Anne Condon

Computer Science at UBC

2 shared papers, latest 2025

Eric Foxall

Okanagan - Computer Science, Mathematics, Physics and Statistics

1 shared papers, latest 2024

Yossef Av-Gay

Department of Microbiology and Immunology

1 shared papers, latest 2023

Sriram Subramaniam

Biochemistry and Molecular Biology

1 shared papers, latest 2026

Write to this professor

A short, specific email works best. This draft uses one of their recent papers; replace the parts in brackets with your own details before sending.

Applying for

Paper to mentionMention their NSERC grant from 2025

Subject: Prospective PhD student: Biophysical modeling and analysis Dear Professor Dao Duc, My name is [your name], and I am a [your current degree or role] at [your institution]. I am applying for a PhD position starting in [term and year]. I read your paper "Cryo-EM analysis of cooperative conformational changes in the SARS-CoV-2 spike protein trimer." (2026), and it connects closely to my own work on [your research topic]. [One or two sentences on what you did and what you learned.] I also saw your NSERC-funded project "Closing the Gap in Agricultural Climate Action: Harmonizing Data, Enhancing Emission Models, and Empowering Canadian Farmers" (2025), and I would be glad to contribute to work in that direction. Are you accepting new PhD students for [term and year]? I have attached my CV and transcripts, and I would be glad to talk at a time that suits you. Thank you for your time. Kind regards, [your name]