Luca Freschi

Luca Freschi

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Luca Freschi

Luca Freschi

Publications by authors named "Luca Freschi"

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Beyond multidrug resistance: Leveraging rare variants with machine and statistical learning models in Mycobacterium tuberculosis resistance prediction.

EBioMedicine 2019 May 29;43:356-369. Epub 2019 Apr 29.

Department of Biomedical Informatics, Harvard Medical School, Boston, MA, United States of America; Division of Pulmonary & Critical Care, Massachusetts General Hospital, Boston, MA, United States of America. Electronic address:

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http://dx.doi.org/10.1016/j.ebiom.2019.04.016DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6557804PMC
May 2019

Major Release of 161 Whole-Genome Sequences from the International Consortium Database.

Microbiol Resour Announc 2019 Mar 28;8(13). Epub 2019 Mar 28.

Institut de biologie intégrative et des systèmes (IBIS), Université Laval, Québec, QC, Canada

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http://dx.doi.org/10.1128/MRA.00013-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6439239PMC
March 2019

Genomics of antibiotic-resistance prediction in Pseudomonas aeruginosa.

Ann N Y Acad Sci 2019 Jan 2;1435(1):5-17. Epub 2017 Jun 2.

Institut de biologie intégrative et des systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada.

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http://dx.doi.org/10.1111/nyas.13358DOI Listing
January 2019

The Pseudomonas aeruginosa Pan-Genome Provides New Insights on Its Population Structure, Horizontal Gene Transfer, and Pathogenicity.

Genome Biol Evol 2019 01 1;11(1):109-120. Epub 2019 Jan 1.

Département de microbiologie-infectiologie et immunologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, Quebec, Canada.

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https://academic.oup.com/gbe/article/11/1/109/5215156
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http://dx.doi.org/10.1093/gbe/evy259DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6328365PMC
January 2019

Genomic characterisation of environmental Pseudomonas aeruginosa isolated from dental unit waterlines revealed the insertion sequence ISPa11 as a chaotropic element.

FEMS Microbiol Ecol 2017 09;93(9)

Institut de biologie intégrative et des systèmes (IBIS), Pavillon Charles-Eugène-Marchand, 1030 avenue de la Médecine, Université Laval, Quebec City G1V 0A6, Canada.

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http://dx.doi.org/10.1093/femsec/fix106DOI Listing
September 2017

Complete Genome Sequences of Two Phage-Like Plasmids Carrying the CTX-M-15 Extended-Spectrum β-Lactamase Gene.

Genome Announc 2017 May 11;5(19). Epub 2017 May 11.

Department of Food Science and Agricultural Chemistry, Food Safety and Quality Program, McGill University, Ste-Anne-de-Bellevue, Canada

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http://dx.doi.org/10.1128/genomeA.00102-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5427194PMC
May 2017

AnCo3, a New Member of the Emerging Family of Phage-Like Plasmids.

Genome Announc 2017 May 11;5(19). Epub 2017 May 11.

Department of Food Science and Agricultural Chemistry, Food Safety and Quality Program, McGill University, Ste-Anne-de-Bellevue, Canada

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http://dx.doi.org/10.1128/genomeA.00110-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5427195PMC
May 2017

Increasing genomic diversity and evidence of constrained lifestyle evolution due to insertion sequences in Aeromonas salmonicida.

BMC Genomics 2016 Jan 12;17:44. Epub 2016 Jan 12.

Institut de biologie intégrative et des systèmes, Pavillon Charles-Eugène-Marchand, Université Laval, 1030 avenue de la Médecine, Quebec City, G1V 0A6, QC, Canada.

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http://dx.doi.org/10.1186/s12864-016-2381-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4709979PMC
January 2016

Comparative genomics and biological characterization of sequential Pseudomonas aeruginosa isolates from persistent airways infection.

BMC Genomics 2015 Dec 29;16:1105. Epub 2015 Dec 29.

Infections and Cystic Fibrosis Unit, Division of Immunology, Transplantation and Infectious Diseases, San Raffaele Scientific Institute, Milano, Italy.

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http://dx.doi.org/10.1186/s12864-015-2276-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4696338PMC
December 2015

Draft Genome Sequences of Two Lipopeptide-Producing Strains of Bacillus methylotrophicus.

Genome Announc 2015 Oct 8;3(5). Epub 2015 Oct 8.

Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada.

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http://dx.doi.org/10.1128/genomeA.01176-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4599100PMC
October 2015

Draft Genome Sequence of Triclosan-Resistant Cystic Fibrosis Isolate Achromobacter xylosoxidans CF304.

Genome Announc 2015 Jul 30;3(4). Epub 2015 Jul 30.

Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada

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http://dx.doi.org/10.1128/genomeA.00865-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4520907PMC
July 2015

Turnover of protein phosphorylation evolving under stabilizing selection.

Front Genet 2014 23;5:245. Epub 2014 Jul 23.

Department of Cell and Systems Biology, University of Toronto Toronto, ON, Canada ; Department of Ecology and Evolutionary Biology, University of Toronto Toronto, ON, Canada ; Center for Analysis of Genome Evolution and Function, University of Toronto Toronto, ON, Canada.

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http://dx.doi.org/10.3389/fgene.2014.00245DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4107968PMC
August 2014

Functional divergence and evolutionary turnover in mammalian phosphoproteomes.

PLoS Genet 2014 Jan 23;10(1):e1004062. Epub 2014 Jan 23.

Département de Biologie, Université Laval, Québec, Canada ; Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada ; PROTEO, The Quebec Research Network on Protein Function, Structure and Engineering, Université Laval, Québec, Canada.

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http://dx.doi.org/10.1371/journal.pgen.1004062DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3900387PMC
January 2014

Integrative avenues for exploring the dynamics and evolution of protein interaction networks.

Curr Opin Biotechnol 2013 Aug 7;24(4):775-83. Epub 2013 Apr 7.

Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), PROTEO, Université Laval, Québec, Canada G1V 0A6.

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http://dx.doi.org/10.1016/j.copbio.2013.02.023DOI Listing
August 2013

qPCA: a scalable assay to measure the perturbation of protein-protein interactions in living cells.

Mol Biosyst 2013 Jan 25;9(1):36-43. Epub 2012 Oct 25.

Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada.

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http://dx.doi.org/10.1039/c2mb25265aDOI Listing
January 2013

Where do phosphosites come from and where do they go after gene duplication?

Int J Evol Biol 2012 20;2012:843167. Epub 2012 Jun 20.

Département de Biologie, PROTEO and Institut de Biologie Intégrative et des Systèmes, Université Laval, Pavillon Charles-Eugène-Marchand, 1030, Avenue de la Médecine, Québec, QC, Canada G1V 0A6.

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http://dx.doi.org/10.1155/2012/843167DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3388353PMC
August 2012

Phosphorylation network rewiring by gene duplication.

Mol Syst Biol 2011 Jul 5;7:504. Epub 2011 Jul 5.

Département de Biologie, Université Laval, Québec, Canada.

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http://dx.doi.org/10.1038/msb.2011.43DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159966PMC
July 2011

Biodiversity matters in a changing world.

Biol Lett 2011 Feb 21;7(1):4-6. Epub 2010 Jul 21.

PROTEO, Université Laval, , Pavillon Charles-Eugène-Marchand, 1030, Avenue de la Médecine, Québec, Canada , G1V 0A6.

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http://dx.doi.org/10.1098/rsbl.2010.0567DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3030889PMC
February 2011