Martin Ester, Simon Fraser University

Research

biomedical applications causal discovery and inference Machine learning precision medicine transfer learning

Latest papers

Deep docking, part 2: an amplified DDU platform for ultra-large virtual screening.
Chemical science · 2026
A scalable reinforcement learning approach for screening large peptide libraries for bioactive peptide discovery.
Nature communications · 2025
scMUSCL: multi-source transfer learning for clustering scRNA-seq data.
Bioinformatics (Oxford, England) · 2025 · senior author

All 29 publications

Latest funding

Transfer learning and causal models for biomedical data
NSERC · 2023 · Principal investigator
$118,000
Data Mining in Heterogeneous Information Networks with Attributes
NSERC · 2017 · Principal investigator
$252,000
Anomaly detection on smart mobile devices using probabilistic graphical models
NSERC · 2014 · Principal investigator
$25,000

All 11 grants and awards

29 publications.

01

Deep docking, part 2: an amplified DDU platform for ultra-large virtual screening.

Pandey M, Sajed T, Semenov I, Zhang R, Ban F, Manskaia E, Ester M, Cherkasov A

Chemical science2026

DOI: 10.1039/d5sc09599a PMID: 42254487

02

A scalable reinforcement learning approach for screening large peptide libraries for bioactive peptide discovery.

Pandey M, Foo J, Massah S, Alford MA, Mslati H, Subbaraj G, Saba M, Gentile F, Lallous N, Haney EF, Hancock REW, Ester M, Cherkasov A

Nature communications2025

DOI: 10.1038/s41467-025-66748-y PMID: 41309621

03

scMUSCL: multi-source transfer learning for clustering scRNA-seq data.

Khoeini A, Sar F, Lin YY, Collins C, Ester M

Bioinformatics (Oxford, England)2025Senior author

DOI: 10.1093/bioinformatics/btaf137 PMID: 40152244

04

Machine learning model identifies genetic predictors of cisplatin-induced ototoxicity in CERS6 and TLR4.

Arab A, Kashani B, Cordova-Delgado M, Scott EN, Alemi K, Trueman J, Groeneweg G, Chang WC, Loucks CM, Ross CJD, Carleton BC, Ester M

Computers in biology and medicine2024Senior author

DOI: 10.1016/j.compbiomed.2024.109324 PMID: 39488053

05

Identifying Synergistic Components of Botanical Fungicide Formulations Using Interpretable Graph Neural Networks.

Snow O, Kazemi A, Bhanshali F, Nasiri A, Rozek A, Ester M

Journal of chemical information and modeling2024Senior author

DOI: 10.1021/acs.jcim.4c00128 PMID: 39031079

06

Phenotype prediction from single-cell RNA-seq data using attention-based neural networks.

Mao Y, Lin YY, Wong NKY, Volik S, Sar F, Collins C, Ester M

Bioinformatics (Oxford, England)2024Senior author

DOI: 10.1093/bioinformatics/btae067 PMID: 38390963

07

Multi-treatment Effect Estimation from Biomedical Data.

Aoki R, Chen Y, Ester M

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing2023Senior author

PMID: 36540986

08

Ligand Binding Prediction Using Protein Structure Graphs and Residual Graph Attention Networks.

Pandey M, Radaeva M, Mslati H, Garland O, Fernandez M, Ester M, Cherkasov A

Molecules (Basel, Switzerland)2022

DOI: 10.3390/molecules27165114 PMID: 36014351

09

Healthy memory aging - the benefits of regular daily activities increase with age.

Krakovska O, Christie GJ, Farzan F, Sixsmith A, Ester M, Moreno S

Aging2021

DOI: 10.18632/aging.203753 PMID: 34915450

10

Drug sensitivity prediction from cell line-based pharmacogenomics data: guidelines for developing machine learning models.

Sharifi-Noghabi H, Jahangiri-Tazehkand S, Smirnov P, Hon C, Mammoliti A, Nair SK, Mer AS, Ester M, Haibe-Kains B

Briefings in bioinformatics2021

DOI: 10.1093/bib/bbab294 PMID: 34382071