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Genomics of antibiotic‐resistance prediction in Pseudomonas aeruginosa.
Published in:
Annals of the New York Academy of Sciences, 2019, v. 1435, n. 1, p. 5, doi. 10.1111/nyas.13358
By:
- Jeukens, Julie;
- Freschi, Luca;
- Kukavica‐Ibrulj, Irena;
- Emond‐Rheault, Jean‐Guillaume;
- Tucker, Nicholas P.;
- Levesque, Roger C.
Publication type:
Article
Prophage Integrase Typing Is a Useful Indicator of Genomic Diversity in Salmonella enterica.
Published in:
Frontiers in Microbiology, 2017, p. 1, doi. 10.3389/fmicb.2017.01283
By:
- Colavecchio, Anna;
- D'Souza, Yasmin;
- Tompkins, Elizabeth;
- Jeukens, Julie;
- Freschi, Luca;
- Emond-Rheault, Jean-Guillaume;
- Kukavica-Ibrulj, Irena;
- Boyle, Brian;
- Bekal, Sadjia;
- Tamber, Sandeep;
- Levesque, Roger C.;
- Goodridge, Lawrence D.
Publication type:
Article
A Syst-OMICS Approach to Ensuring Food Safety and Reducing the Economic Burden of Salmonellosis.
Published in:
Frontiers in Microbiology, 2017, p. 1, doi. 10.3389/fmicb.2017.00996
By:
- Emond-Rheault, Jean-Guillaume;
- Jeukens, Julie;
- Freschi, Luca;
- Kukavica-Ibrulj, Irena;
- Boyle, Brian;
- Dupont, Marie-Josée;
- Colavecchio, Anna;
- Barrere, Virginie;
- Cadieux, Brigitte;
- Arya, Gitanjali;
- Bekal, Sadjia;
- Berry, Chrystal;
- Burnett, Elton;
- Cavestri, Camille;
- Chapin, Travis K.;
- Crouse, Alanna;
- Daigle, France;
- Danyluk, Michelle D.;
- Delaquis, Pascal;
- Dewar, Ken
Publication type:
Article
A convolutional neural network highlights mutations relevant to antimicrobial resistance in Mycobacterium tuberculosis.
Published in:
Nature Communications, 2022, v. 13, n. 1, p. 1, doi. 10.1038/s41467-022-31236-0
By:
- Green, Anna G.;
- Yoon, Chang Ho;
- Chen, Michael L.;
- Ektefaie, Yasha;
- Fina, Mack;
- Freschi, Luca;
- Gröschel, Matthias I.;
- Kohane, Isaac;
- Beam, Andrew;
- Farhat, Maha
Publication type:
Article
In-host population dynamics of Mycobacterium tuberculosis complex during active disease.
Published in:
eLife, 2021, p. 1, doi. 10.7554/eLife.61805
By:
- Vargas, Roger;
- Freschi, Luca;
- Marin, Maximillian;
- Epperson, L. Elaine;
- Smith, Melissa;
- Oussenko, Irina;
- Durbin, David;
- Strong, Michael;
- Salfinger, Max;
- Farhat, Maha Reda
Publication type:
Article
Population structure, biogeography and transmissibility of Mycobacterium tuberculosis.
Published in:
Nature Communications, 2021, v. 12, n. 1, p. 1, doi. 10.1038/s41467-021-26248-1
By:
- Freschi, Luca;
- Vargas Jr., Roger;
- Husain, Ashaque;
- Kamal, S. M. Mostofa;
- Skrahina, Alena;
- Tahseen, Sabira;
- Ismail, Nazir;
- Barbova, Anna;
- Niemann, Stefan;
- Cirillo, Daniela Maria;
- Dean, Anna S.;
- Zignol, Matteo;
- Farhat, Maha Reda
Publication type:
Article
GenTB: A user-friendly genome-based predictor for tuberculosis resistance powered by machine learning.
Published in:
Genome Medicine, 2021, v. 13, n. 1, p. 1, doi. 10.1186/s13073-021-00953-4
By:
- Gröschel, Matthias I.;
- Owens, Martin;
- Freschi, Luca;
- Vargas Jr, Roger;
- Marin, Maximilian G.;
- Phelan, Jody;
- Iqbal, Zamin;
- Dixit, Avika;
- Farhat, Maha R.
Publication type:
Article
Increasing genomic diversity and evidence of constrained lifestyle evolution due to insertion sequences in Aeromonas salmonicida.
Published in:
BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2381-3
By:
- Vincent, Antony T.;
- Trudel, Mélanie V.;
- Freschi, Luca;
- Nagar, Vandan;
- Gagné-Thivierge, Cynthia;
- Levesque, Roger C.;
- Charette, Steve J.
Publication type:
Article
Comparative genomics and biological characterization of sequential Pseudomonas aeruginosa isolates from persistent airways infection.
Published in:
BMC Genomics, 2015, v. 16, p. 1, doi. 10.1186/s12864-015-2276-8
By:
- Bianconi, Irene;
- Jeukens, Julie;
- Freschi, Luca;
- Alcalá-Franco, Beatriz;
- Facchini, Marcella;
- Boyle, Brian;
- Molinaro, Antonio;
- Kukavica-Ibrulj, Irena;
- Tümmler, Burkhard;
- Levesque, Roger C.;
- Bragonzi, Alessandra
Publication type:
Article
Turnover of protein phosphorylation evolving under stabilizing selection.
Published in:
Frontiers in Genetics, 2014, v. 5, p. 1, doi. 10.3389/fgene.2014.00245
By:
- Landry, Christian R.;
- Freschi, Luca;
- Zarin, Taraneh;
- Moses, Alan M.
Publication type:
Article
GWAS for quantitative resistance phenotypes in Mycobacterium tuberculosis reveals resistance genes and regulatory regions.
Published in:
Nature Communications, 2019, v. 10, n. 1, p. N.PAG, doi. 10.1038/s41467-019-10110-6
By:
- Farhat, Maha R.;
- Freschi, Luca;
- Calderon, Roger;
- Ioerger, Thomas;
- Snyder, Matthew;
- Meehan, Conor J.;
- de Jong, Bouke;
- Rigouts, Leen;
- Sloutsky, Alex;
- Kaur, Devinder;
- Sunyaev, Shamil;
- van Soolingen, Dick;
- Shendure, Jay;
- Sacchettini, Jim;
- Murray, Megan
Publication type:
Article
Analysis of Genome-Wide Mutational Dependence in Naturally Evolving Mycobacterium tuberculosis Populations.
Published in:
Molecular Biology & Evolution, 2023, v. 40, n. 6, p. 1, doi. 10.1093/molbev/msad131
By:
- Green, Anna G;
- Vargas, Roger;
- Marin, Maximillian G;
- Freschi, Luca;
- Xie, Jiaqi;
- Farhat, Maha R
Publication type:
Article
The Salmonella enterica Plasmidome as a Reservoir of Antibiotic Resistance.
Published in:
Microorganisms, 2020, v. 8, n. 7, p. 1016, doi. 10.3390/microorganisms8071016
By:
- Emond-Rheault, Jean-Guillaume;
- Hamel, Jérémie;
- Jeukens, Julie;
- Freschi, Luca;
- Kukavica-Ibrulj, Irena;
- Boyle, Brian;
- Tamber, Sandeep;
- Malo, Danielle;
- Franz, Eelco;
- Burnett, Elton;
- Daigle, France;
- Arya, Gitanjali;
- Sanderson, Kenneth;
- Wiedmann, Martin;
- Slawson, Robin M.;
- Weadge, Joel T.;
- Stephan, Roger;
- Bekal, Sadjia;
- Gruenheid, Samantha;
- Goodridge, Lawrence D.
Publication type:
Article
Expansion of LINEs and species-specific DNA repeats drives genome expansion in Asian Gypsy Moths.
Published in:
Scientific Reports, 2019, v. 9, n. 1, p. N.PAG, doi. 10.1038/s41598-019-52840-z
By:
- Hebert, Francois Olivier;
- Freschi, Luca;
- Blackburn, Gwylim;
- Béliveau, Catherine;
- Dewar, Ken;
- Boyle, Brian;
- Gundersen-Rindal, Dawn E.;
- Sparks, Michael E.;
- Cusson, Michel;
- Hamelin, Richard C.;
- Levesque, Roger C.
Publication type:
Article
Phosphorylation network rewiring by gene duplication.
Published in:
Molecular Systems Biology, 2011, v. 7, n. 1, p. 1, doi. 10.1038/msb.2011.43
By:
- Freschi, Luca;
- Courcelles, Mathieu;
- Thibault, Pierre;
- Michnick, Stephen W;
- Landry, Christian R
Publication type:
Article
The Pseudomonas aeruginosa Pan-Genome Provides New Insights on Its Population Structure, Horizontal Gene Transfer, and Pathogenicity.
Published in:
Genome Biology & Evolution, 2019, v. 11, n. 1, p. 109, doi. 10.1093/gbe/evy259
By:
- Freschi, Luca;
- Vincent, Antony T;
- Jeukens, Julie;
- Emond-Rheault, Jean-Guillaume;
- Kukavica-Ibrulj, Irena;
- Dupont, Marie-Josée;
- Charette, Steve J;
- Boyle, Brian;
- Levesque, Roger C
Publication type:
Article
A Pan-Genomic Approach to Understand the Basis of Host Adaptation in Achromobacter.
Published in:
Genome Biology & Evolution, 2017, v. 9, n. 4, p. 1030, doi. 10.1093/gbe/evx061
By:
- Jeukens, Julie;
- Freschi, Luca;
- Vincent, Antony T.;
- Emond-Rheault, Jean-Guillaume;
- Kukavica-Ibrulj, Irena;
- Charette, Steve J.;
- Levesque, Roger C.
Publication type:
Article
A Multi-Species TaqMan PCR Assay for the Identification of Asian Gypsy Moths (Lymantria spp.) and Other Invasive Lymantriines of Biosecurity Concern to North America.
Published in:
PLoS ONE, 2016, v. 11, n. 8, p. 1, doi. 10.1371/journal.pone.0160878
By:
- Stewart, Donald;
- Zahiri, Reza;
- Djoumad, Abdelmadjid;
- Freschi, Luca;
- Lamarche, Josyanne;
- Holden, Dave;
- Cervantes, Sandra;
- Ojeda, Dario I.;
- Potvin, Amélie;
- Nisole, Audrey;
- Béliveau, Catherine;
- Capron, Arnaud;
- Kimoto, Troy;
- Day, Brittany;
- Yueh, Hesther;
- Duff, Cameron;
- Levesque, Roger C.;
- Hamelin, Richard C.;
- Cusson, Michel
Publication type:
Article
Reservoirs of resistance: polymyxin resistance in veterinary-associated companion animal isolates of Pseudomonas aeruginosa.
Published in:
Veterinary Record: Journal of the British Veterinary Association, 2019, v. 185, n. 7, p. 1, doi. 10.1136/vr.105075
By:
- Scott, Andrea;
- Pottenger, Sian;
- Timofte, Dorina;
- Moore, Matthew;
- Wright, Laura;
- Kukavica-Ibrulj, Irena;
- Jeukens, Julie;
- Levesque, Roger C.;
- Freschi, Luca;
- Pinchbeck, Gina L.;
- Schmidt, Vanessa M.;
- McEwan, Neil;
- Radford, Alan D.;
- Fothergill, Joanne L.
Publication type:
Article
Functional Divergence and Evolutionary Turnover in Mammalian Phosphoproteomes.
Published in:
PLoS Genetics, 2014, v. 10, n. 1, p. 1, doi. 10.1371/journal.pgen.1004062
By:
- Freschi, Luca;
- Osseni, Mazid;
- Landry, Christian R.
Publication type:
Article
Clinical utilization of genomics data produced by the international Pseudomonas aeruginosa consortium.
Published in:
Frontiers in Microbiology, 2015, p. 1, doi. 10.3389/fmicb.2015.01036
By:
- Freschi, Luca;
- Jeukens, Julie;
- Kukavica-Ibrulj, Irena;
- Boyle, Brian;
- Dupont, Marie-Josée;
- Laroche, Jérôme;
- Larose, Stéphane;
- Maaroufi, Halim;
- Fothergill, Joanne L.;
- Moore, Matthew;
- Winsor, Geoffrey L.;
- Aaron, Shawn D.;
- Barbeau, Jean;
- Bell, Scott C.;
- Burns, Jane L.;
- Camara, Miguel;
- Cantin, André;
- Charette, Steve J.;
- Dewar, Ken;
- Déziel, #201;ric
Publication type:
Article
Where Do Phosphosites Come fromand Where Do They Go after Gene Duplication?
Published in:
International Journal of Evolutionary Biology, 2012, p. 1, doi. 10.1155/2012/843167
By:
- Diss, Guillaume;
- Freschi, Luca;
- Landry, Christian R.
Publication type:
Article

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