PandemicStop-AI
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Publications

An overview of relevant publications by the PandemicStop-AI team

  • Delaby, M, L Yang, M Jacq, KA Gallagher, DT Kysela, V Hughes, F Pulido, FJ Veyrier, MS VanNieuwenhze, YV Brun. 2025. Phenotypic plasticity in bacterial elongation among closely related species. Nature Comm, 16: 5099.
  • Ian Y Yen, Gregory B Whitfield, John L Rubinstein, Lori L Burrows, Yves V Brun, P Lynne Howell*. Conformational changes in the motor ATPase CpaF facilitate a rotary mechanism of Tad pilus assembly. 2025. Nat Comm 16, 3839.
  • Guo S, Chang Y, Brun YV, Howell PL, Burrows LL, Liu J. 2024. PilY1 regulates the dynamic architecture of the type IV pilus machine in Pseudomonas aeruginosa. Nat Commun, 15:9382.
  • Berne, C, S Zappa, YV Brun. 2023. eDNA-stimulated cell dispersion from Caulobacter crescentus biofilms upon oxygen limitation is dependent on a toxin-antitoxin system. eLife, doi: 10.7554/eLife.80808.
  • Chepkwony, NK et YV Brun, 2021. A polysaccharide deacetylase enhances bacterial adhesion in high ionic strength environments, iScience, 24, 103071.
  • Caccamo, P.D., M. Jacq, M.S. VanNieuwenhze et Y.V. Brun. 2020. A Division of Labor in the Recruitment and Topological Organization of a Bacterial Morphogenic Complex. Current Biology, 30:3908-3922.
  • Snyder, R.A., C.K. Ellison, G.B. Severin, G.B. Whitfield, C.M. Waters et Y.V. Brun. 2020. Surface Sensing Stimulates Cellular Differentiation in Caulobacter crescentus. PNAS, 117:17984-17991
  • Hsu, YP, E Hall, G. Booher, B Murphy, AD Radkov, J Yablonowski, C Mulcahey, L Alvarez, F Cava, YV Brun, E Kuru, MS VanNieuwenhze. 2020. Fluorogenic D-amino acids enable real-time monitoring of peptidoglycan biosynthesis and high-throughput transpeptidation assays. Nature Chemistry, 11:335-341.
  • Culp EJ, N Waglechner, W Wang, AA Fiebig-Comyn, YP Hsu, K Koteva, D Sychantha, BK Coombes, MS VanNieuwenhze, YV Brun et GD Wright. 2020. Evolution-guided discovery of antibiotics with a novel mode of action. Nature, 578(7796):582-587.
  • Ducret, A., E.M. Quardokus et Y.V. Brun. 2016. MicrobeJ, a tool for high throughput bacterial cell detection and quantitative analysis. Nature Microbiology, 1, 16077. doi:10.1038/nmicrobiol.2016.77
  • Bilodeau, A., Beaupré, F., Chabbert, J., Bellavance, J. M., Lessard, K., Deschênes, A., … & Lavoie-Cardinal, F. (2025). A Self-Supervised Foundation Model for Robust and Generalizable Representation Learning in STED Microscopy. bioRxiv, 2025-06.
  • Beaupré, F., Bilodeau, A., Wiesner, T., Leclerc, G., Lemieux, M., Nadeau, G., … & Lavoie-Cardinal, F. (2025). Quantitative analysis of miniature synaptic calcium transients using positive unlabeled deep learning. Digital Discovery, 4(1), 105-119.
  • Bilodeau, A., Michaud-Gagnon, A., Chabbert, J., Turcotte, B., Heine, J., Durand, A., & Lavoie-Cardinal, F. (2024). Development of AI-assisted microscopy frameworks through realistic simulation with pySTED. Nature Machine Intelligence, 6(10), 1197-1215.
  • Bouchard, C., Wiesner, T., Deschênes, A., Bilodeau, A., Turcotte, B., Gagné, C., & Lavoie-Cardinal, F. (2023). Resolution enhancement with a task-assisted GAN to guide optical nanoscopy image analysis and acquisition. Nature Machine Intelligence, 5(8), 830-844.
  • Bilodeau, A., Delmas, C. V., Parent, M., De Koninck, P., Durand, A., & Lavoie-Cardinal, F. (2022). Microscopy analysis neural network to solve detection, enumeration and segmentation from image-level annotations. Nature Machine Intelligence, 4(5), 455-466.
  • Wiesner, T., Bilodeau, A., Bernatchez, R., Deschênes, A., Raulier, B., De Koninck, P., & Lavoie-Cardinal, F. (2020). Activity-dependent remodeling of synaptic protein organization revealed by high throughput analysis of STED nanoscopy images. Frontiers in neural circuits, 14, 57.
  • Durand, A., Wiesner, T., Gardner, M.A., Robitaille, L.É., Bilodeau, A., Gagné, C., De Koninck, P. and Lavoie-Cardinal, F., 2018. A machine learning approach for online automated optimization of super-resolution optical microscopy. Nature communications, 9(1), p.5247.
  • Heuillet, M., Ahmad, O., & Durand, A. (2024). Neural Active Learning Meets the Partial Monitoring Framework. In Uncertainty in Artificial Intelligence (pp. 1621-1639).
  • Jalali M, AbdElFatah T, del Real Mata C, Hosseini II, Yedire SG, McKay GA, Corsini R, Shieh H, Moakhar RS, Reszetnik G, Vahid Hamidi S, Yansouni CP, Nguyen D, Mahshid S*. QolorPhAST for ultra-rapid phenotypic antimicrobial susceptibility profiling directly from specimens. Accepted Nature Nanotechnology.
  • 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 Dec 28;14(1):31039. PMID: 39730767.
  • Reszetnik G, Hammond K, Mahshid S, Abdelwahab T, Nguyen D, Corsini R, Caya C, Papenburg J, Cheng MP, Yansouni CP. Next-generation rapid phenotypic antimicrobial susceptibility testing. Nat Commun 2024 Nov, 15 (9719).
  • 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. Amer. J. Resp. Crit. Care Med. 2024 Jun 15; 209(12):1453-1462. PMID: 38324627.
  • Sharon I., Mckay GA, Nguyen D, Schmeing M. Discovery of cyanophycin dipeptide hydrolase enzymes suggests widespread utility of the natural biopolymer cyanophycin. PNAS 2023 Feb 21; 120(8):e2216547120. PMID 36800389.
  • Paquette A, Payne A, McKay G, Kammili A, Bernal F, Mah T.F, Gruenheid S, Nguyen D. Boddy C. RpoN-based stapled peptides with improved DNA binding suppress Pseudomonas aeruginosa virulence. RSC Medicinal Chemistry 2022, 13:445-455.
  • Gallique M, Wei K, Maisuria VB, Okshevsky M, McKay G, Nguyen D, Tufenkji N. Cranberry-Derived Proanthocyanidins Potentiate β-Lactam Antibiotics against Resistant Bacteria. Appl Environ Microbiol. 2021 Apr 27;87(10):e00127-21. PMID: 33712420.
  • Martins D, McKay G, English AM, Nguyen D*. Sublethal paraquat confers multidrug tolerance in Pseudomonas aeruginosa by inducing superoxide dismutase activity and lowering envelope permeability. Frontiers Microbiology. 2020 Sept 25; 11:576708. PMID: 33101252.
  • Martins D, McKay G, Sampathkumar G, Khakimova M, English AM, Nguyen D*. Superoxide dismutase confers antibiotic tolerance to stationary phase Pseudomonas aeruginosa and requires (p)ppGpp signaling. PNAS Sep 2018; 115(39):9797-9802. PMID 30201715.