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L. Freschi · SciRah

Researcher profile · Semantic Scholar

L. Freschi

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L. Freschi — researcher profile on SciRah

h-index: 29
Works: 64
Citations: 2,216

Most-cited papers

The Pseudomonas aeruginosa Pan-Genome Provides New Insights on Its Population Structure, Horizontal Gene Transfer, and Pathogenicity
L. Freschi, A. T. Vincent, Julie Jeukens, Jean‐Guillaume Emond‐Rheault +5 more
2018Genome Biology and Evolution268 citations Open access
Semantic Scholar
GWAS for quantitative resistance phenotypes in Mycobacterium tuberculosis reveals resistance genes and regulatory regions
M. Farhat, L. Freschi, R. Calderón, T. Ioerger +11 more
2019Nature Communications160 citations Open access
Semantic Scholar
Clinical utilization of genomics data produced by the international Pseudomonas aeruginosa consortium
L. Freschi, Julie Jeukens, I. Kukavica-Ibrulj, B. Boyle +54 more
2015Frontiers in Microbiology159 citations Open access
Semantic Scholar
Delay-induced oscillatory dynamics of tumour-immune system interaction
A. d'Onofrio, F. Gatti, P. Cerrai, L. Freschi
2010Mathematical and computer modelling111 citations Open access
Semantic Scholar
Beyond multidrug resistance: Leveraging rare variants with machine and statistical learning models in Mycobacterium tuberculosis resistance prediction
Michael L. Chen, A. Doddi, Jimmy Royer, L. Freschi +5 more
2019EBioMedicine96 citations Open access
Semantic Scholar
Genomic characterisation of an international Pseudomonas aeruginosa reference panel indicates that the two major groups draw upon distinct mobile gene pools
L. Freschi, C. Bertelli, Julie Jeukens, Matthew P. Moore +11 more
2018FEMS Microbiology Letters72 citations Open access
Semantic Scholar
A convolutional neural network highlights mutations relevant to antimicrobial resistance in Mycobacterium tuberculosis
Anna G. Green, C. H. Yoon, Michael L. Chen, Yasha Ektefaie +6 more
2022Nature Communications71 citations Open access
Semantic Scholar
GenTB: A user-friendly genome-based predictor for tuberculosis resistance powered by machine learning
M. Gröschel, Martin Owens, L. Freschi, R. Vargas +5 more
2021Genome Medicine71 citations Open access
Semantic Scholar
Genomics of antibiotic‐resistance prediction in Pseudomonas aeruginosa
Julie Jeukens, L. Freschi, I. Kukavica-Ibrulj, Jean‐Guillaume Emond‐Rheault +2 more
2017Annals of the New York Academy of Sciences70 citations Open access
Semantic Scholar
The Widespread Multidrug-Resistant Serotype O12 Pseudomonas aeruginosa Clone Emerged through Concomitant Horizontal Transfer of Serotype Antigen and Antibiotic Resistance Gene Clusters
S. Thrane, Véronique L. Taylor, L. Freschi, I. Kukavica-Ibrulj +6 more
2015mBio61 citations Open access
Semantic Scholar
Role of Epistasis in Amikacin, Kanamycin, Bedaquiline, and Clofazimine Resistance in Mycobacterium tuberculosis Complex
R. Vargas, L. Freschi, A. Spitaleri, S. Tahseen +6 more
2021bioRxiv59 citations Open access
Semantic Scholar
Increasing genomic diversity and evidence of constrained lifestyle evolution due to insertion sequences in Aeromonas salmonicida
A. T. Vincent, M. Trudel, L. Freschi, V. Nagar +3 more
2016BMC Genomics55 citations Open access
Semantic Scholar
In-host population dynamics of Mycobacterium tuberculosis complex during active disease
R. Vargas, L. Freschi, Maximillian G. Marin, L. E. Epperson +6 more
2021eLife53 citations Open access
Semantic Scholar
Salmonella enterica Prophage Sequence Profiles Reflect Genome Diversity and Can Be Used for High Discrimination Subtyping
Walid Mottawea, Marc-Olivier Duceppe, A. A. Dupras, V. Usongo +20 more
2018Frontiers in Microbiology52 citations Open access
Semantic Scholar
A Pan-Genomic Approach to Understand the Basis of Host Adaptation in Achromobacter
Julie Jeukens, L. Freschi, A. T. Vincent, Jean‐Guillaume Emond‐Rheault +3 more
2017Genome Biology and Evolution52 citations Open access
Semantic Scholar
Turnover of protein phosphorylation evolving under stabilizing selection
C. Landry, L. Freschi, Taraneh Zarin, Alan M. Moses
2014Frontiers in Genetics51 citations Open access
Semantic Scholar
Globally diverse Mycobacterium tuberculosis resistance acquisition: a retrospective geographical and temporal analysis of whole genome sequences
Yasha Ektefaie, Avika Dixit, L. Freschi, M. Farhat
2021The Lancet Microbe48 citations Open access
Semantic Scholar
Comparative genomics and biological characterization of sequential Pseudomonas aeruginosa isolates from persistent airways infection
I. Bianconi, Julie Jeukens, L. Freschi, B. Alcalá-Franco +7 more
2015BMC Genomics48 citations Open access
Semantic Scholar
Functional Divergence and Evolutionary Turnover in Mammalian Phosphoproteomes
L. Freschi, M. Osseni, C. Landry
2014PLoS Genetics47 citations Open access
Semantic Scholar
Comparative genomics of a drug-resistant Pseudomonas aeruginosa panel and the challenges of antimicrobial resistance prediction from genomes
Julie Jeukens, I. Kukavica-Ibrulj, Jean‐Guillaume Emond‐Rheault, L. Freschi +1 more
2017FEMS Microbiology Letters44 citations
Semantic Scholar
Comparative analysis of mitochondrial genomes of geographic variants of the gypsy moth, Lymantria dispar, reveals a previously undescribed genotypic entity
A. Djoumad, A. Nisole, R. Zahiri, L. Freschi +9 more
2017Scientific Reports43 citations Open access
Semantic Scholar
A Syst-OMICS Approach to Ensuring Food Safety and Reducing the Economic Burden of Salmonellosis
Jean‐Guillaume Emond‐Rheault, Julie Jeukens, L. Freschi, I. Kukavica-Ibrulj +67 more
2017Frontiers in Microbiology40 citations Open access
Semantic Scholar
qPCA: a scalable assay to measure the perturbation of protein-protein interactions in living cells.
L. Freschi, Francisco Torres-Quiroz, A. K. Dubé, C. Landry
2013Molecular Biosystems40 citations
Semantic Scholar
Characterization of Spindle Checkpoint Kinase Mps1 Reveals Domain with Functional and Structural Similarities to Tetratricopeptide Repeat Motifs of Bub1 and BubR1 Checkpoint Kinases
Se-Min Lee, P. Thebault, L. Freschi, S. Beaufils +4 more
2011Journal of Biological Chemistry38 citations Open access
Semantic Scholar
Whole genome sequencing identifies bacterial factors affecting transmission of multidrug-resistant tuberculosis in a high-prevalence setting
Avika Dixit, L. Freschi, R. Vargas, R. Calderón +10 more
2019Scientific Reports35 citations Open access
Semantic Scholar
Phosphorylation network rewiring by gene duplication
L. Freschi, M. Courcelles, P. Thibault, S. Michnick +1 more
2011Molecular Systems Biology35 citations Open access
Semantic Scholar
Phase variation as a major mechanism of adaptation in Mycobacterium tuberculosis complex
R. Vargas, Michael J. Luna, L. Freschi, Maximillian Marin +6 more
2023Proceedings of the National Academy of Sciences of the United States of America34 citations Open access
Semantic Scholar
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
Don Stewart, R. Zahiri, A. Djoumad, L. Freschi +15 more
2016PLoS ONE34 citations Open access
Semantic Scholar
Prophage Integrase Typing Is a Useful Indicator of Genomic Diversity in Salmonella enterica
Anna Colavecchio, Y. D'Souza, Elizabeth Tompkins, Julie Jeukens +8 more
2017Frontiers in Microbiology30 citations Open access
Semantic Scholar
Deep learning predicts tuberculosis drug resistance status from genome sequencing data
Michael L. Chen, A. Doddi, Jimmy Royer, L. Freschi +5 more
2018bioRxiv29 citations Open access
Semantic Scholar
The Salmonella enterica Plasmidome as a Reservoir of Antibiotic Resistance
Jean‐Guillaume Emond‐Rheault, Jérémie Hamel, Julie Jeukens, L. Freschi +17 more
2020Microorganisms28 citations Open access
Semantic Scholar
Genomic characterisation of environmental Pseudomonas aeruginosa isolated from dental unit waterlines revealed the insertion sequence ISPa11 as a chaotropic element
A. T. Vincent, L. Freschi, Julie Jeukens, I. Kukavica-Ibrulj +9 more
2017FEMS Microbiology Ecology23 citations Open access
Semantic Scholar
Reservoirs of resistance: polymyxin resistance in veterinary-associated companion animal isolates of Pseudomonas aeruginosa
Andrea Scott, Sian Pottenger, D. Timofte, Matthew P. Moore +10 more
2019The Veterinary Record19 citations
Semantic Scholar
Transmission, adaptation and geographical spread of the Pseudomonas aeruginosa Liverpool epidemic strain
Matthew P. Moore, I. Lamont, David Williams, S. Paterson +16 more
2021Microbial Genomics18 citations Open access
Semantic Scholar
Complete Genome Sequences of Two Phage-Like Plasmids Carrying the CTX-M-15 Extended-Spectrum β-Lactamase Gene
Anna Colavecchio, Julie Jeukens, L. Freschi, Jean-Guillaume Edmond Rheault +4 more
2017Genome Announcements17 citations Open access
Semantic Scholar
Integrative avenues for exploring the dynamics and evolution of protein interaction networks.
G. Diss, Marie Filteau, L. Freschi, Jean-Baptiste Leducq +3 more
2013Current Opinion in Biotechnology17 citations
Semantic Scholar
Analysis of Genome-Wide Mutational Dependence in Naturally Evolving Mycobacterium tuberculosis Populations
Anna G. Green, R. Vargas, Maximillian G. Marin, L. Freschi +2 more
2023Molecular biology and evolution12 citations Open access
Semantic Scholar
In-host population dynamics of M. tuberculosis during treatment failure
R. Vargas, L. Freschi, Maximillian G. Marin, L. E. Epperson +6 more
2019bioRxiv11 citations Open access
Semantic Scholar
Expansion of LINEs and species-specific DNA repeats drives genome expansion in Asian Gypsy Moths
F. Hebert, L. Freschi, Gwylim S. Blackburn, C. Béliveau +7 more
2019Scientific Reports11 citations Open access
Semantic Scholar
Prophage induction reduces Shiga toxin producing Escherichia coli (STEC) and Salmonella enterica on tomatoes and spinach: A model study
Brigitte Cadieux, Anna Colavecchio, Julie Jeukens, L. Freschi +8 more
2018Food Control10 citations Open access
Semantic Scholar
Draft Genome Sequences of Two Lipopeptide-Producing Strains of Bacillus methylotrophicus
Julie Jeukens, I. Kukavica-Ibrulj, L. Freschi, S. Jabaji +1 more
2015Genome Announcements7 citations Open access
Semantic Scholar
Biodiversity matters in a changing world
C. Di Poi, Guillaume Diss, L. Freschi
2011Biology Letters7 citations Open access
Semantic Scholar
1397. Modern Lineages of Mycobacterium tuberculosis Were Recently Introduced in Western India and Demonstrate Increased Transmissibility
Avika Dixit, A. Kagal, Yasha Ektefaie, L. Freschi +15 more
2021medRxiv4 citations Open access
Semantic Scholar
Tuberculosis resistance acquisition in space and time: an analysis of globally diverse M. tuberculosis whole genome sequences
Yasha Ektefaie, Avika Dixit, L. Freschi, M. Farhat
20194 citations Open access
Semantic Scholar
Major Release of 161 Whole-Genome Sequences from the International Pseudomonas Consortium Database
Julie Jeukens, Jean‐Guillaume Emond‐Rheault, L. Freschi, I. Kukavica-Ibrulj +1 more
2019Microbiology Resource Announcements4 citations Open access
Semantic Scholar
Genome wide association with quantitative resistance phenotypes in Mycobacterium tuberculosis reveals novel resistance genes and regulatory regions
M. Farhat, L. Freschi, R. Calderón, T. Ioerger +11 more
2018bioRxiv4 citations Open access
Semantic Scholar
Draft Genome Sequence of Triclosan-Resistant Cystic Fibrosis Isolate Achromobacter xylosoxidans CF304
Julie Jeukens, L. Freschi, I. Kukavica-Ibrulj, Dao Nguyen +1 more
2015Genome Announcements4 citations Open access
Semantic Scholar
Where Do Phosphosites Come from and Where Do They Go after Gene Duplication?
G. Diss, L. Freschi, C. Landry
2012International Journal of Evolutionary Biology4 citations Open access
Semantic Scholar
AnCo3, a New Member of the Emerging Family of Phage-Like Plasmids
Anna Colavecchio, Julie Jeukens, L. Freschi, Jean-Guillaume Edmond Rheault +3 more
2017Genome Announcements3 citations Open access
Semantic Scholar
Phase variation as a major mechanism of adaptation in Mycobacterium tuberculosis complex
R. Vargas, Michael J. Luna, L. Freschi, Kenan C. Murphy +3 more
2022bioRxiv2 citations Open access
Semantic Scholar

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