Luis Rueda, University of Windsor

Research

bioinformatics classification clustering computational biology data analytics deep learning genomics machine learning

Latest papers

A survey of contrastive learning methods in molecular representation.
Briefings in bioinformatics · 2026
PPISHES-an enhanced physicochemical approach for predicting protein interaction sites using graph neural networks.
Protein science : a publication of the Protein Society · 2025 · senior author
Ligand-receptor dynamics in heterophily-aware graph neural networks for enhanced cell type prediction from single-cell RNA-seq data.
Frontiers in molecular biosciences · 2025 · senior author

All 25 publications

Latest funding

NSERC I2I Phase Ia: An Intelligent Framework for Social Engineering Cyber Security Training
NSERC · 2021 · Principal investigator
$125,000
Multi-user in vivo animal imaging system
NSERC · 2020 · Co-investigator
$150,000
Market Assessment of an intelligent framework for social engineering cyber security training
NSERC · 2020 · Principal investigator
$15,000

All 9 grants and awards

25 publications.

01

A survey of contrastive learning methods in molecular representation.

Forooghi A, Sadeghi S, Rueda L, Ngom A

Briefings in bioinformatics2026

DOI: 10.1093/bib/bbaf731 PMID: 41671347

02

PPISHES-an enhanced physicochemical approach for predicting protein interaction sites using graph neural networks.

Khanna D, Shaikh AAS, Rueda L

Protein science : a publication of the Protein Society2025Senior author

DOI: 10.1002/pro.70349 PMID: 41158105

03

Ligand-receptor dynamics in heterophily-aware graph neural networks for enhanced cell type prediction from single-cell RNA-seq data.

Duan L, Hashemi M, Ngom A, Rueda L

Frontiers in molecular biosciences2025Senior author

DOI: 10.3389/fmolb.2025.1547231 PMID: 40421418

04

PPPCT: Privacy-Preserving framework for Parallel Clustering Transcriptomics data.

Tadi AA, Alhadidi D, Rueda L

Computers in biology and medicine2024Senior author

DOI: 10.1016/j.compbiomed.2024.108351 PMID: 38520921

05

SEGCECO: Subgraph Embedding of Gene expression matrix for prediction of CEll-cell COmmunication.

Vasighizaker A, Hora S, Zeng R, Rueda L

Briefings in bioinformatics2024Senior author

DOI: 10.1093/bib/bbae160 PMID: 38605638

06

A Fecal-Microbial-Extracellular-Vesicles-Based Metabolomics Machine Learning Framework and Biomarker Discovery for Predicting Colorectal Cancer Patients.

Yagin FH, Alkhateeb A, Colak C, Azzeh M, Yagin B, Rueda L

Metabolites2023Senior author

DOI: 10.3390/metabo13050589 PMID: 37233630

07

Cell Type Annotation Model Selection: General-Purpose vs. Pattern-Aware Feature Gene Selection in Single-Cell RNA-Seq Data.

Vasighizaker A, Trivedi Y, Rueda L

Genes2023Senior author

DOI: 10.3390/genes14030596 PMID: 36980868

08

Computationally repurposing drugs for breast cancer subtypes using a network-based approach.

Firoozbakht F, Rezaeian I, Rueda L, Ngom A

BMC bioinformatics2022

DOI: 10.1186/s12859-022-04662-6 PMID: 35443626

09

Discovering cell types using manifold learning and enhanced visualization of single-cell RNA-Seq data.

Vasighizaker A, Danda S, Rueda L

Scientific reports2022Senior author

DOI: 10.1038/s41598-021-03613-0 PMID: 34996927

10

The Circadian Clock Gene, Bmal1, Regulates Intestinal Stem Cell Signaling and Represses Tumor Initiation

Stokes K, Nunes M, Trombley C, Flôres DEFL, Wu G, Taleb Z, Alkhateeb A, Banskota S, Harris C, Love OP

Cellular and Molecular Gastroenterology and Hepatology (CMGH)2021102 citationsOpen Access

DOI: 10.1016/j.jcmgh.2021.08.001 PMID: W3199086925

NSERC I2I Phase Ia: An Intelligent Framework for Social Engineering Cyber Security Training

Principal investigatorNSERC2021Idea to Innovation

Principal investigators: Rueda, Luis

$125,000

Multi-user in vivo animal imaging system

Co-investigatorNSERC2020Research Tools and Instruments

Principal investigators: Rahim, MirMunir

$150,000

Market Assessment of an intelligent framework for social engineering cyber security training

Principal investigatorNSERC2020Idea to Innovation

Principal investigators: Rueda, Luis

$15,000

Integrative Machine Learning Models for Discovery and Validation of Biological Knowledge

Principal investigatorNSERC2019Discovery Grants Program - Individual

Principal investigators: Rueda, Luis

Keywords: machine learning; bioinformatics; computational biology; deep learning; clustering; classification; data analytics; genomics; transcriptomics; systems biology

$238,000

An intelligent system that supports additive manufacturing and machining

Principal investigatorNSERC2016Engage Grants Program

Principal investigators: Rueda, Luis

$25,000

ICS IG 2014 Computational Biology Undergraduate Summer Student Health Research award - Design and implementation of algorithms for finding short motifs in protein-protein interactions associated with prostate cancer.

SupervisorCIHR2014Undergraduate: Summer Studentship Award - Institute Community Support

Principal investigators: Deschamps, Anthony

Keywords: Computational Biology

$5,000

Integrative machine learning methods for prediction of protein-protein interactions and analysis of the dynamics of interactomes

Principal investigatorNSERC2014Discovery Grants Program - Individual

Principal investigators: Rueda, Luis

$130,000

Efficient linear dimensionality reduction and optimal multi-dimensional clustering

Principal investigatorNSERC2009Discovery Grants Program - Individual

Principal investigators: Rueda, Luis

$120,000

Novel linear classification techniques and efficient adaptive encoding schemes

Principal investigatorNSERC2003Discovery Grants Program - Individual

Principal investigators: Rueda, Luis

$46,114

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

Computer Science, School of
Biological Sciences
Mechanical, Automotive and Materials Engineering (MAME)
School of Computer Science
Pathology & Molecular Medicine

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

Alioune Ngom

Computer Science, School of

9 shared papers, latest 2026

Waguih ElMaraghy

Mechanical, Automotive and Materials Engineering (MAME)

2 shared papers, latest 2019

Dima Alhadidi

School of Computer Science

1 shared papers, latest 2024

Waliul Khan

Pathology & Molecular Medicine

1 shared papers, latest 2021

Lisa Porter

Biological Sciences

1 shared papers, latest 2017

Phillip Karpowicz

Biological Sciences

1 shared papers, latest 2021

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 2021

Subject: Prospective PhD student: bioinformatics Dear Professor Rueda, 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 "A survey of contrastive learning methods in molecular representation." (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 "NSERC I2I Phase Ia: An Intelligent Framework for Social Engineering Cyber Security Training" (2021), 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]