Gregory Butler, Concordia University

Latest papers

Ion channel classification through machine learning and protein language model embeddings.
Journal of integrative bioinformatics · 2024 · senior author
SPOT: A machine learning model that predicts specific substrates for transport proteins.
PLoS biology · 2024
Comparative genomic analysis of thermophilic fungi reveals convergent evolutionary adaptations and gene losses.
Communications biology · 2024

All 15 publications

Latest funding

Challenges in biomolecular network reconstruction
NSERC · 2018 · Principal investigator
$140,000
Knowledge-based bioinformatics
NSERC · 2009 · Principal investigator
$120,000
Development of enzymatic pulp and paper applications
NSERC · 2006 · Co-investigator
$561,514

All 12 grants and awards

15 publications.

01

Ion channel classification through machine learning and protein language model embeddings.

Ghazikhani H, Butler G

Journal of integrative bioinformatics2024Senior author

DOI: 10.1515/jib-2023-0047 PMID: 39572876

02

SPOT: A machine learning model that predicts specific substrates for transport proteins.

Kroll A, Niebuhr N, Butler G, Lercher MJ

PLoS biology2024

DOI: 10.1371/journal.pbio.3002807 PMID: 39325691

03

Comparative genomic analysis of thermophilic fungi reveals convergent evolutionary adaptations and gene losses.

Steindorff AS, Aguilar-Pontes MV, Robinson AJ, Andreopoulos B, LaButti K, Kuo A, Mondo S, Riley R, Otillar R, Haridas S, Lipzen A, Grimwood J, Schmutz J, Clum A, Reid ID, Moisan MC, Butler G, Nguyen TTM, Dewar K, Conant G, Drula E, Henrissat B, Hansel C, Singer S, Hutchinson MI, de Vries RP, Natvig DO, Powell AJ, Tsang A, Grigoriev IV

Communications biology2024

DOI: 10.1038/s42003-024-06681-w PMID: 39266695

04

Exploiting protein language models for the precise classification of ion channels and ion transporters.

Ghazikhani H, Butler G

Proteins2024Senior author

DOI: 10.1002/prot.26694 PMID: 38656743

05

Enhanced identification of membrane transport proteins: a hybrid approach combining ProtBERT-BFD and convolutional neural networks.

Ghazikhani H, Butler G

Journal of integrative bioinformatics2023Senior author

DOI: 10.1515/jib-2022-0055 PMID: 37497772

06

Integrative approach for detecting membrane proteins.

Alballa M, Butler G

BMC bioinformatics2020Senior author

DOI: 10.1186/s12859-020-03891-x PMID: 33349234

07

BENIN: Biologically enhanced network inference.

Wonkap SK, Butler G

Journal of bioinformatics and computational biology2020Senior author

DOI: 10.1142/s0219720020400077 PMID: 32698722

08

TooT-T: discrimination of transport proteins from non-transport proteins.

Alballa M, Butler G

BMC bioinformatics2020Senior author

DOI: 10.1186/s12859-019-3311-6 PMID: 32321420

09

TranCEP: Predicting the substrate class of transmembrane transport proteins using compositional, evolutionary, and positional information.

Alballa M, Aplop F, Butler G

PloS one2020Senior author

DOI: 10.1371/journal.pone.0227683 PMID: 31935244

10

An Adaptive Defect Weighted Sampling Algorithm to Design Pseudoknotted RNA Secondary Structures.

Zandi K, Butler G, Kharma N

Frontiers in genetics2016

DOI: 10.3389/fgene.2016.00129 PMID: 27499762

Challenges in biomolecular network reconstruction

Principal investigatorNSERC2018Discovery Grants Program - Individual

Principal investigators: Butler, Gregory

$140,000

Knowledge-based bioinformatics

Principal investigatorNSERC2009Discovery Grants Program - Individual

Principal investigators: Butler, Gregory

$120,000

Development of enzymatic pulp and paper applications

Co-investigatorNSERC2006Strategic Projects - Group

Principal investigators: Tsang, Adrian

$561,514

Knowledge-based bioinformatics

Principal investigatorNSERC2004Discovery Grants Program - Individual

Principal investigators: Butler, Gregory

$148,500

Gene Discovery and Expression Analysis in Aspergillus niger

Co-investigatorNSERC2000Genomics Projects

Principal investigators: Storms, Reginald

$500,000

Frameworks and databases with applications to bioinformatics

Principal investigatorNSERC2000Discovery Grants Program - Individual

Principal investigators: Butler, Gregory

$113,192

Software architectures, algorithms, and databases for computer algebra

Principal investigatorNSERC1996Discovery Grants Program - Individual

Principal investigators: Butler, Gregory

$104,248

Upgrade for CICMA computing laboratory

Co-investigatorNSERC1995Research Tools and Instruments - Category 1 (<$150,000)

Principal investigators: Lam, Clement

$60,000

Centre interuniversitaire en calcul mathématique algébrique

Co-investigatorNSERC1994Research Tools and Instruments - Category 1 (<$150,000)

Principal investigators: Cummins, Christopher

$30,926

Workstation

Principal investigatorNSERC1993Research Tools and Instruments - Category 1 (<$150,000)

Principal investigators: Butler, Gregory

$17,350

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

Nawwaf Kharma

Electrical & Computer Engineering

1 shared papers, latest 2016

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Subject: Prospective PhD student Dear Professor Butler, 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 "Ion channel classification through machine learning and protein language model embeddings." (2024), and it connects closely to my own work on [your research topic]. [One or two sentences on what you did and what you learned.] 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]