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Luca Freschi - Publications

Affiliations: 
2009-2014 Département de biologie Université Laval, Québec, Ville de Québec, Québec, Canada 
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25/48 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Hebert FO, Freschi L, Blackburn G, Béliveau C, Dewar K, Boyle B, Gundersen-Rindal DE, Sparks ME, Cusson M, Hamelin RC, Levesque RC. Expansion of LINEs and species-specific DNA repeats drives genome expansion in Asian Gypsy Moths. Scientific Reports. 9: 16413. PMID 31712581 DOI: 10.1038/S41598-019-52840-Z  0.33
2019 Farhat MR, Freschi L, Calderon R, Ioerger T, Snyder M, Meehan CJ, de Jong B, Rigouts L, Sloutsky A, Kaur D, Sunyaev S, van Soolingen D, Shendure J, Sacchettini J, Murray M. GWAS for quantitative resistance phenotypes in Mycobacterium tuberculosis reveals resistance genes and regulatory regions. Nature Communications. 10: 2128. PMID 31086182 DOI: 10.1038/S41467-019-10110-6  0.323
2019 Dixit A, Freschi L, Vargas R, Calderon R, Sacchettini J, Drobniewski F, Galea JT, Contreras C, Yataco R, Zhang Z, Lecca L, Kolokotronis SO, Mathema B, Farhat MR. Whole genome sequencing identifies bacterial factors affecting transmission of multidrug-resistant tuberculosis in a high-prevalence setting. Scientific Reports. 9: 5602. PMID 30944370 DOI: 10.1038/S41598-019-41967-8  0.314
2018 Freschi L, Vincent AT, Jeukens J, Emond-Rheault JG, Kukavica-Ibrulj I, Dupont MJ, Charette SJ, Boyle B, Levesque RC. The Pseudomonas aeruginosa pan-genome provides new insights on its population structure, horizontal gene transfer and pathogenicity. Genome Biology and Evolution. PMID 30496396 DOI: 10.1093/Gbe/Evy259  0.378
2018 Freschi L, Bertelli C, Jeukens J, Moore MP, Kukavica-Ibrulj I, Emond-Rheault JG, Hamel J, Fothergill JL, Tucker NP, McClean S, Klockgether J, de Soyza A, Brinkman FSL, Levesque RC, Winstanley C. Genomic characterisation of an international Pseudomonas aeruginosa reference panel indicates that the two major groups draw upon distinct mobile gene pools. Fems Microbiology Letters. PMID 29897457 DOI: 10.1093/Femsle/Fny120  0.373
2018 Mottawea W, Duceppe MO, Dupras AA, Usongo V, Jeukens J, Freschi L, Emond-Rheault JG, Hamel J, Kukavica-Ibrulj I, Boyle B, Gill A, Burnett E, Franz E, Arya G, Weadge JT, et al. Prophage Sequence Profiles Reflect Genome Diversity and Can Be Used for High Discrimination Subtyping. Frontiers in Microbiology. 9: 836. PMID 29780368 DOI: 10.3389/Fmicb.2018.00836  0.343
2018 Jeukens J, Kukavica-Ibrulj I, Emond-Rheault JG, Freschi L, Levesque RC. Comparative genomics of a drug-resistant Pseudomonas aeruginosa panel and the challenges of antimicrobial resistance prediction from genomes. Fems Microbiology Letters. 364. PMID 28922838 DOI: 10.1093/Femsle/Fnx161  0.36
2017 Vincent AT, Freschi L, Jeukens J, Kukavica-Ibrulj I, Emond-Rheault JG, Leduc A, Boyle B, Jean-Pierre F, Groleau MC, Déziel E, Barbeau J, Charette SJ, Levesque RC. Genomic characterisation of environmental Pseudomonas aeruginosa isolated from dental unit waterlines revealed the insertion sequence ISPa11 as a chaotropic element. Fems Microbiology Ecology. 93. PMID 28934400 DOI: 10.1093/Femsec/Fix106  0.344
2017 Colavecchio A, D'Souza Y, Tompkins E, Jeukens J, Freschi L, Emond-Rheault JG, Kukavica-Ibrulj I, Boyle B, Bekal S, Tamber S, Levesque RC, Goodridge LD. Prophage Integrase Typing Is a Useful Indicator of Genomic Diversity in Salmonella enterica. Frontiers in Microbiology. 8: 1283. PMID 28740489 DOI: 10.3389/Fmicb.2017.01283  0.345
2017 Emond-Rheault JG, Jeukens J, Freschi L, Kukavica-Ibrulj I, Boyle B, Dupont MJ, Colavecchio A, Barrere V, Cadieux B, Arya G, Bekal S, Berry C, Burnett E, Cavestri C, Chapin TK, et al. A Syst-OMICS Approach to Ensuring Food Safety and Reducing the Economic Burden of Salmonellosis. Frontiers in Microbiology. 8: 996. PMID 28626454 DOI: 10.3389/Fmicb.2017.00996  0.351
2017 Jeukens J, Freschi L, Kukavica-Ibrulj I, Emond-Rheault JG, Tucker NP, Levesque RC. Genomics of antibiotic-resistance prediction in Pseudomonas aeruginosa. Annals of the New York Academy of Sciences. PMID 28574575 DOI: 10.1111/Nyas.13358  0.301
2017 Colavecchio A, Jeukens J, Freschi L, Edmond Rheault JG, Kukavica-Ibrulj I, Levesque RC, LeJeune J, Goodridge L. Complete Genome Sequences of Two Phage-Like Plasmids Carrying the CTX-M-15 Extended-Spectrum β-Lactamase Gene. Genome Announcements. 5. PMID 28495759 DOI: 10.1128/Genomea.00102-17  0.322
2017 Jeukens J, Freschi L, Vincent AT, Emond-Rheault JG, Kukavica-Ibrulj I, Charette SJ, Levesque RC. A Pan-Genomic Approach to Understand the Basis of Host Adaptation in Achromobacter. Genome Biology and Evolution. 9: 1030-1046. PMID 28383665 DOI: 10.1093/Gbe/Evx061  0.391
2016 Vincent AT, Trudel MV, Freschi L, Nagar V, Gagné-Thivierge C, Levesque RC, Charette SJ. Increasing genomic diversity and evidence of constrained lifestyle evolution due to insertion sequences in Aeromonas salmonicida. Bmc Genomics. 17: 44. PMID 26753691 DOI: 10.1186/S12864-016-2381-3  0.378
2015 Freschi L, Jeukens J, Kukavica-Ibrulj I, Boyle B, Dupont MJ, Laroche J, Larose S, Maaroufi H, Fothergill JL, Moore M, Winsor GL, Aaron SD, Barbeau J, Bell SC, Burns JL, et al. Clinical utilization of genomics data produced by the international Pseudomonas aeruginosa consortium. Frontiers in Microbiology. 6: 1036. PMID 26483767 DOI: 10.3389/Fmicb.2015.01036  0.345
2015 Thrane SW, Taylor VL, Freschi L, Kukavica-Ibrulj I, Boyle B, Laroche J, Pirnay JP, Lévesque RC, Lam JS, Jelsbak L. The Widespread Multidrug-Resistant Serotype O12 Pseudomonas aeruginosa Clone Emerged through Concomitant Horizontal Transfer of Serotype Antigen and Antibiotic Resistance Gene Clusters. Mbio. 6. PMID 26396243 DOI: 10.1128/Mbio.01396-15  0.308
2015 Jeukens J, Freschi L, Kukavica-Ibrulj I, Nguyen D, Levesque RC. Draft Genome Sequence of Triclosan-Resistant Cystic Fibrosis Isolate Achromobacter xylosoxidans CF304. Genome Announcements. 3. PMID 26227609 DOI: 10.1128/Genomea.00865-15  0.307
2014 Landry CR, Freschi L, Zarin T, Moses AM. Turnover of protein phosphorylation evolving under stabilizing selection. Frontiers in Genetics. 5: 245. PMID 25101120 DOI: 10.3389/Fgene.2014.00245  0.592
2014 Freschi L, Osseni M, Landry CR. Functional divergence and evolutionary turnover in mammalian phosphoproteomes. Plos Genetics. 10: e1004062. PMID 24465218 DOI: 10.1371/Journal.Pgen.1004062  0.603
2013 Diss G, Filteau M, Freschi L, Leducq JB, Rochette S, Torres-Quiroz F, Landry CR. Integrative avenues for exploring the dynamics and evolution of protein interaction networks. Current Opinion in Biotechnology. 24: 775-83. PMID 23571097 DOI: 10.1016/J.Copbio.2013.02.023  0.666
2013 Freschi L, Torres-Quiroz F, Dubé AK, Landry CR. qPCA: a scalable assay to measure the perturbation of protein-protein interactions in living cells. Molecular Biosystems. 9: 36-43. PMID 23099892 DOI: 10.1039/C2Mb25265A  0.576
2012 Diss G, Freschi L, Landry CR. Where do phosphosites come from and where do they go after gene duplication? International Journal of Evolutionary Biology. 2012: 843167. PMID 22779031 DOI: 10.1155/2012/843167  0.677
2012 Lee S, Thebault P, Freschi L, Beaufils S, Blundell TL, Landry CR, Bolanos-Garcia VM, Elowe S. Characterization of spindle checkpoint kinase Mps1 reveals domain with functional and structural similarities to tetratricopeptide repeat motifs of Bub1 and BubR1 checkpoint kinases. The Journal of Biological Chemistry. 287: 5988-6001. PMID 22187426 DOI: 10.1074/Jbc.M111.307355  0.549
2011 Freschi L, Courcelles M, Thibault P, Michnick SW, Landry CR. Phosphorylation network rewiring by gene duplication. Molecular Systems Biology. 7: 504. PMID 21734643 DOI: 10.1038/Msb.2011.43  0.637
2011 Di Poi C, Diss G, Freschi L. Biodiversity matters in a changing world. Biology Letters. 7: 4-6. PMID 20659919 DOI: 10.1098/Rsbl.2010.0567  0.637
Low-probability matches (unlikely to be authored by this person)
2015 Bianconi I, Jeukens J, Freschi L, Alcalá-Franco B, Facchini M, Boyle B, Molinaro A, Kukavica-Ibrulj I, Tümmler B, Levesque RC, Bragonzi A. Comparative genomics and biological characterization of sequential Pseudomonas aeruginosa isolates from persistent airways infection. Bmc Genomics. 16: 1105. PMID 26714629 DOI: 10.1186/S12864-015-2276-8  0.285
2015 Jeukens J, Kukavica-Ibrulj I, Freschi L, Jabaji S, Levesque RC. Draft Genome Sequences of Two Lipopeptide-Producing Strains of Bacillus methylotrophicus. Genome Announcements. 3. PMID 26450741 DOI: 10.1128/Genomea.01176-15  0.281
2019 Scott A, Pottenger S, Timofte D, Moore M, Wright L, Kukavica-Ibrulj I, Jeukens J, Levesque RC, Freschi L, Pinchbeck GL, Schmidt VM, McEwan N, Radford AD, Fothergill JL. Reservoirs of resistance: polymyxin resistance in veterinary-associated companion animal isolates of . The Veterinary Record. PMID 31239295 DOI: 10.1136/Vr.105075  0.271
2017 Colavecchio A, Jeukens J, Freschi L, Edmond Rheault JG, Kukavica-Ibrulj I, Levesque R, Goodridge L. AnCo3, a New Member of the Emerging Family of Phage-Like Plasmids. Genome Announcements. 5. PMID 28495760 DOI: 10.1128/Genomea.00110-17  0.27
2017 Djoumad A, Nisole A, Zahiri R, Freschi L, Picq S, Gundersen-Rindal DE, Sparks ME, Dewar K, Stewart D, Maaroufi H, Levesque RC, Hamelin RC, Cusson M. Comparative analysis of mitochondrial genomes of geographic variants of the gypsy moth, Lymantria dispar, reveals a previously undescribed genotypic entity. Scientific Reports. 7: 14245. PMID 29079798 DOI: 10.1038/S41598-017-14530-6  0.266
2016 Stewart D, Zahiri R, Djoumad A, Freschi L, Lamarche J, Holden D, Cervantes S, Ojeda DI, Potvin A, Nisole A, Béliveau C, Capron A, Kimoto T, Day B, Yueh H, et al. 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. Plos One. 11: e0160878. PMID 27513667 DOI: 10.1371/Journal.Pone.0160878  0.26
2019 Chen ML, Doddi A, Royer J, Freschi L, Schito M, Ezewudo M, Kohane IS, Beam A, Farhat M. Beyond multidrug resistance: Leveraging rare variants with machine and statistical learning models in Mycobacterium tuberculosis resistance prediction. Ebiomedicine. PMID 31047860 DOI: 10.1016/J.Ebiom.2019.04.016  0.259
2018 Cadieux B, Colavecchio A, Jeukens J, Freschi L, Emond-Rheault J, Kukavica-Ibrulj I, Levesque RC, Bekal S, Chandler JC, Coleman SM, Bisha B, Goodridge LD. Prophage induction reduces Shiga toxin producing Escherichia coli (STEC) and Salmonella enterica on tomatoes and spinach: A model study Food Control. 89: 250-259. DOI: 10.1016/J.Foodcont.2018.02.001  0.237
2013 Cangelosi D, Fabbiano S, Felicioli C, Freschi L, Marangoni R. Quick Direct-method Controlled (QDC): a simulator of metabolic experiments Embnet.Journal. 19: 39-42. DOI: 10.14806/Ej.19.1.505  0.229
2021 Moore MP, Lamont IL, Williams D, Paterson S, Kukavica-Ibrulj I, Tucker NP, Kenna DTD, Turton JF, Jeukens J, Freschi L, Wee BA, Loman NJ, Holden S, Manzoor S, Hawkey P, et al. Transmission, adaptation and geographical spread of the Liverpool epidemic strain. Microbial Genomics. PMID 33720817 DOI: 10.1099/mgen.0.000511  0.227
2020 Emond-Rheault JG, Hamel J, Jeukens J, Freschi L, Kukavica-Ibrulj I, Boyle B, Tamber S, Malo D, Franz E, Burnett E, Daigle F, Arya G, Sanderson K, Wiedmann M, Slawson RM, et al. The Plasmidome as a Reservoir of Antibiotic Resistance. Microorganisms. 8. PMID 32650601 DOI: 10.3390/microorganisms8071016  0.225
2021 Vargas R, Freschi L, Marin M, Epperson LE, Smith M, Oussenko I, Durbin D, Strong M, Salfinger M, Farhat MR. In-host population dynamics of complex during active disease. Elife. 10. PMID 33522489 DOI: 10.7554/eLife.61805  0.22
2019 Jeukens J, Freschi L, Kukavica-Ibrulj I, Emond-Rheault JG, Allard C, Barbeau J, Cantin A, Charette SJ, Déziel E, Malouin F, Milot J, Nguyen D, Popa C, Boyle B, Levesque RC. The population among Cystic Fibrosis patients in Quebec, Canada: a disease hotspot without known epidemic isolates. Journal of Clinical Microbiology. PMID 30944192 DOI: 10.1128/Jcm.02019-18  0.212
2023 Green AG, Vargas R, Marin MG, Freschi L, Xie J, Farhat MR. Analysis of genome-wide mutational dependence in naturally evolving Mycobacterium tuberculosis populations. Molecular Biology and Evolution. PMID 37352142 DOI: 10.1093/molbev/msad131  0.206
2022 Green AG, Yoon CH, Chen ML, Ektefaie Y, Fina M, Freschi L, Gröschel MI, Kohane I, Beam A, Farhat M. A convolutional neural network highlights mutations relevant to antimicrobial resistance in Mycobacterium tuberculosis. Nature Communications. 13: 3817. PMID 35780211 DOI: 10.1038/s41467-022-31236-0  0.199
2019 Jeukens J, Emond-Rheault JG, Freschi L, Kukavica-Ibrulj I, Levesque RC. Major Release of 161 Whole-Genome Sequences from the International Consortium Database. Microbiology Resource Announcements. 8. PMID 30923236 DOI: 10.1128/MRA.00013-19  0.176
2021 Ektefaie Y, Dixit A, Freschi L, Farhat MR. Globally diverse resistance acquisition: a retrospective geographical and temporal analysis of whole genome sequences. The Lancet. Microbe. 2: e96-e104. PMID 33912853 DOI: 10.1016/s2666-5247(20)30195-6  0.17
2021 Vargas R, Freschi L, Spitaleri A, Tahseen S, Barilar I, Niemann S, Miotto P, Cirillo DM, Köser CU, Farhat MR. The role of epistasis in amikacin, kanamycin, bedaquiline, and clofazimine resistance in complex. Antimicrobial Agents and Chemotherapy. AAC0116421. PMID 34460306 DOI: 10.1128/AAC.01164-21  0.163
2023 Vargas R, Luna MJ, Freschi L, Marin M, Froom R, Murphy KC, Campbell EA, Ioerger TR, Sassetti CM, Farhat MR. Phase variation as a major mechanism of adaptation in complex. Proceedings of the National Academy of Sciences of the United States of America. 120: e2301394120. PMID 37399390 DOI: 10.1073/pnas.2301394120  0.154
2021 Freschi L, Vargas R, Husain A, Kamal SMM, Skrahina A, Tahseen S, Ismail N, Barbova A, Niemann S, Cirillo DM, Dean AS, Zignol M, Farhat MR. Population structure, biogeography and transmissibility of Mycobacterium tuberculosis. Nature Communications. 12: 6099. PMID 34671035 DOI: 10.1038/s41467-021-26248-1  0.153
2022 Cadieux B, Lawal OU, Emond-Rheault JG, Jeukens J, Freschi L, Kukavica-Ibrulj I, Levesque RC, Austin JW, Goodridge L. Draft Genome Sequences of Two Clostridium botulinum Group II Strains Carrying Phage-Like Plasmids. Microbiology Resource Announcements. e0009122. PMID 35583330 DOI: 10.1128/mra.00091-22  0.153
2024 Dixit A, Freschi L, Vargas R, Gröschel MI, Nakhoul M, Tahseen S, Alam SMM, Kamal SMM, Skrahina A, Basilio RP, Lim DR, Ismail N, Farhat MR. Estimation of country-specific tuberculosis resistance antibiograms using pathogen genomics and machine learning. Bmj Global Health. 9. PMID 38548342 DOI: 10.1136/bmjgh-2023-013532  0.142
2021 Gröschel MI, Owens M, Freschi L, Vargas R, Marin MG, Phelan J, Iqbal Z, Dixit A, Farhat MR. GenTB: A user-friendly genome-based predictor for tuberculosis resistance powered by machine learning. Genome Medicine. 13: 138. PMID 34461978 DOI: 10.1186/s13073-021-00953-4  0.114
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