PandemicStop-AI
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Publications

An overview of relevant publications by the PandemicStop-AI team

  • Yen IY, Whitfield GB, Rubinstein JL, Burrows LL, Brun YV, Howell PL. Conformational changes in the motor ATPase CpaF facilitate a rotary mechanism of Tad pilus assembly. Nat Commun. 2025;16(1):3839. doi:10.1038/s41467-025-59009-5
  • Jalali Y M AbdElFatah, T del Real Mata, C Hosseini, II, SG M, GA C, R S, H M, RS R, G VH, S Y, CP N, D M, S. QolorPhAST for ultra-rapid phenotypic antimicrobial susceptibility profiling directly from specimens. Accepted at Nature Nanotechnology. Published online 2025.
  • Delaby M, Yang L, Jacq M, Gallagher KA, Kysela DT, Hughes V, Pulido F, Veyrier FJ, VanNieuwenhze MS, Brun YV. Phenotypic plasticity in cell elongation among closely related bacterial species. Nat Commun. 2025;16(1):5099. doi:10.1038/s41467-025-60005-y
  • Bilodeau A, Beaupré F, Chabbert J, Bellavance JM, Lessard K, Deschênes A, Bernatchez R, De Koninck P, Gagné C, Lavoie-Cardinal F. A Self-Supervised Foundation Model for Robust and Generalizable Representation Learning in STED Microscopy. Bioinformatics. Preprint posted online June 6, 2025. doi:10.1101/2025.06.06.656993
  • Beaupré F, Bilodeau A, Wiesner T, Leclerc G, Lemieux M, Nadeau G, Castonguay K, Fan B, Labrecque S, Hložek R, De Koninck P, Gagné C, Lavoie-Cardinal F. Quantitative analysis of miniature synaptic calcium transients using positive unlabeled deep learning. Digital Discovery. 2025;4(1):105-119. doi:10.1039/D4DD00197D
  • Reszetnik G, Hammond K, Mahshid S, AbdElFatah T, Nguyen D, Corsini R, Caya C, Papenburg J, Cheng MP, Yansouni CP. Next-generation rapid phenotypic antimicrobial susceptibility testing. Nat Commun. 2024;15(1):9719. doi:10.1038/s41467-024-53930-x
  • Malet K, Faure E, Adam D, Donner J, Liu L, Pilon SJ, Fraser R, Jorth P, Newman DK, Brochiero E, Rousseau S, Nguyen D. Intracellular Pseudomonas aeruginosa within the Airway Epithelium of Cystic Fibrosis Lung Tissues. Am J Respir Crit Care Med. 2024;209(12):1453-1462. doi:10.1164/rccm.202308-1451OC
  • Heuillet M, Ahmad O, Durand A. Neural Active Learning Meets the Partial Monitoring Framework. In: Uncertainty in Artificial Intelligence. 2024:1621-1639. https://proceedings.mlr.press/v244/heuillet24a.html
  • Guo S, Chang Y, Brun YV, Howell PL, Burrows LL, Liu J. PilY1 regulates the dynamic architecture of the type IV pilus machine in Pseudomonas aeruginosa. Nat Commun. 2024;15(1):9382. doi:10.1038/s41467-024-53638-y
  • Farkas E, McKay GA, Hu LT, Nekouei M, Ho P, Moreira W, Chan CC, Dam LC, Auclair K, Gruenheid S, Whyte L, Dedon P, Nguyen D. Bioluminescent Pseudomonas aeruginosa and Escherichia coli for whole-cell screening of antibacterial and adjuvant compounds. Sci Rep. 2024;14(1):31039. doi:10.1038/s41598-024-81926-6
  • Bilodeau A, Michaud-Gagnon A, Chabbert J, Turcotte B, Heine J, Durand A, Lavoie-Cardinal F. Development of AI-assisted microscopy frameworks through realistic simulation with pySTED. Nat Mach Intell. 2024;6(10):1197-1215. doi:10.1038/s42256-024-00903-w
  • Sharon I, McKay GA, Nguyen D, Schmeing TM. Discovery of cyanophycin dipeptide hydrolase enzymes suggests widespread utility of the natural biopolymer cyanophycin. Proc Natl Acad Sci USA. 2023;120(8):e2216547120. doi:10.1073/pnas.2216547120
  • Bouchard C, Wiesner T, Deschênes A, Bilodeau A, Turcotte B, Gagné C, Lavoie-Cardinal F. Resolution enhancement with a task-assisted GAN to guide optical nanoscopy image analysis and acquisition. Nat Mach Intell. 2023;5(8):830-844. doi:10.1038/s42256-023-00689-3
  • Berne C, Zappa S, Brun YV. eDNA-stimulated cell dispersion from Caulobacter crescentus biofilms upon oxygen limitation is dependent on a toxin–antitoxin system. eLife. 2023;12:e80808. doi:10.7554/eLife.80808
  • Paquette AR, Payne SR, McKay GA, Brazeau-Henrie JT, Darnowski MG, Kammili A, Bernal F, Mah TF, Gruenheid S, Nguyen D, Boddy CN. RpoN-Based stapled peptides with improved DNA binding suppress Pseudomonas aeruginosa virulence. RSC Med Chem. 2022;13(4):445-455. doi:10.1039/D1MD00371B
  • Bilodeau A, Delmas CVL, Parent M, De Koninck P, Durand A, Lavoie-Cardinal F. Microscopy analysis neural network to solve detection, enumeration and segmentation from image-level annotations. Nat Mach Intell. 2022;4(5):455-466. doi:10.1038/s42256-022-00472-w
  • Gallique M, Wei K, Maisuria VB, Okshevsky M, McKay G, Nguyen D, Tufenkji N. Cranberry-Derived Proanthocyanidins Potentiate β-Lactam Antibiotics against Resistant Bacteria. McBain AJ, ed. Appl Environ Microbiol. 2021;87(10):e00127-21. doi:10.1128/AEM.00127-21
  • Chepkwony NK, Brun YV. A polysaccharide deacetylase enhances bacterial adhesion in high-ionic-strength environments. iScience. 2021;24(9):103071. doi:10.1016/j.isci.2021.103071
  • Wiesner T, Bilodeau A, Bernatchez R, Deschênes A, Raulier B, De Koninck P, Lavoie-Cardinal F. Activity-Dependent Remodeling of Synaptic Protein Organization Revealed by High Throughput Analysis of STED Nanoscopy Images. Front Neural Circuits. 2020;14:57. doi:10.3389/fncir.2020.00057
  • Snyder RA, Ellison CK, Severin GB, Whitfield GB, Waters CM, Brun YV. Surface sensing stimulates cellular differentiation in Caulobacter crescentus. Proc Natl Acad Sci USA. 2020;117(30):17984-17991. doi:10.1073/pnas.1920291117
  • Martins D, McKay GA, English AM, Nguyen D. Sublethal Paraquat Confers Multidrug Tolerance in Pseudomonas aeruginosa by Inducing Superoxide Dismutase Activity and Lowering Envelope Permeability. Front Microbiol. 2020;11:576708. doi:10.3389/fmicb.2020.576708
  • Culp EJ, Waglechner N, Wang W, Fiebig-Comyn AA, Hsu YP, Koteva K, Sychantha D, Coombes BK, Van Nieuwenhze MS, Brun YV, Wright GD. Evolution-guided discovery of antibiotics that inhibit peptidoglycan remodelling. Nature. 2020;578(7796):582-587. doi:10.1038/s41586-020-1990-9
  • Caccamo PD, Jacq M, VanNieuwenhze MS, Brun YV. A Division of Labor in the Recruitment and Topological Organization of a Bacterial Morphogenic Complex. Current Biology. 2020;30(20):3908-3922.e4. doi:10.1016/j.cub.2020.07.063
  • Hsu YP, Hall E, Booher G, Murphy B, Radkov AD, Yablonowski J, Mulcahey C, Alvarez L, Cava F, Brun YV, Kuru E, VanNieuwenhze MS. Fluorogenic d-amino acids enable real-time monitoring of peptidoglycan biosynthesis and high-throughput transpeptidation assays. Nat Chem. 2019;11(4):335-341. doi:10.1038/s41557-019-0217-x
  • Martins D, McKay G, Sampathkumar G, Khakimova M, English AM, Nguyen D. Superoxide dismutase activity confers (p)ppGpp-mediated antibiotic tolerance to stationary-phase Pseudomonas aeruginosa. Proc Natl Acad Sci USA. 2018;115(39):9797-9802. doi:10.1073/pnas.1804525115
  • Durand A, Wiesner T, Gardner MA, Robitaille LÉ, Bilodeau A, Gagné C, De Koninck P, Lavoie-Cardinal F. A machine learning approach for online automated optimization of super-resolution optical microscopy. Nat Commun. 2018;9(1):5247. doi:10.1038/s41467-018-07668-y
  • Ducret A, Quardokus EM, Brun YV. MicrobeJ, a tool for high throughput bacterial cell detection and quantitative analysis. Nat Microbiol. 2016;1(7):16077. doi:10.1038/nmicrobiol.2016.77