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Mass spectra alignment using virtual lock-masses.

Brochu F, Plante PL, Drouin A, Gagnon D, Richard D, Durocher F, Diorio C, Marchand M, Corbeil J, Laviolette F.

Sci Rep. 2019 Jun 11;9(1):8469. doi: 10.1038/s41598-019-44923-8.


Culture-enriched human gut microbiomes reveal core and accessory resistance genes.

Raymond F, Boissinot M, Ouameur AA, Déraspe M, Plante PL, Kpanou SR, Bérubé È, Huletsky A, Roy PH, Ouellette M, Bergeron MG, Corbeil J.

Microbiome. 2019 Apr 5;7(1):56. doi: 10.1186/s40168-019-0669-7.


2017 Outbreak of Ebola Virus Disease in Northern Democratic Republic of Congo.

Nsio J, Kapetshi J, Makiala S, Raymond F, Tshapenda G, Boucher N, Corbeil J, Okitandjate A, Mbuyi G, Kiyele M, Mondonge V, Kikoo MJ, Van Herp M, Barboza P, Petrucci R, Benedetti G, Formenty P, Muyembe Muzinga B, Ilunga Kalenga O, Ahuka S, Fausther-Bovendo H, Ilunga BK, Kobinger GP, Muyembe JT.

J Infect Dis. 2019 Apr 3. pii: jiz107. doi: 10.1093/infdis/jiz107. [Epub ahead of print]


Predicting Ion Mobility Collision Cross-Sections Using a Deep Neural Network: DeepCCS.

Plante PL, Francovic-Fontaine É, May JC, McLean JA, Baker ES, Laviolette F, Marchand M, Corbeil J.

Anal Chem. 2019 Apr 16;91(8):5191-5199. doi: 10.1021/acs.analchem.8b05821. Epub 2019 Apr 1.


Interpretable genotype-to-phenotype classifiers with performance guarantees.

Drouin A, Letarte G, Raymond F, Marchand M, Corbeil J, Laviolette F.

Sci Rep. 2019 Mar 11;9(1):4071. doi: 10.1038/s41598-019-40561-2.


Complete Genome Sequence of Escherichia coli Siphophage BRET.

Ngazoa-Kakou S, Shao Y, Rousseau GM, Addablah AA, Tremblay DM, Hutinet G, Lemire N, Plante PL, Corbeil J, Koudou A, Soro BK, Coulibaly DN, Aoussi S, Dosso M, Moineau S.

Microbiol Resour Announc. 2019 Jan 31;8(5). pii: e01644-18. doi: 10.1128/MRA.01644-18. eCollection 2019 Jan.


Communities of Phytoplankton Viruses across the Transition Zone of the St. Lawrence Estuary.

Labbé M, Raymond F, Lévesque A, Thaler M, Mohit V, Audet M, Corbeil J, Culley A.

Viruses. 2018 Nov 27;10(12). pii: E672. doi: 10.3390/v10120672.


The EcoChip: A Wireless Multi-Sensor Platform for Comprehensive Environmental Monitoring.

Sylvain M, Lehoux F, Morency S, Faucher F, Bharucha E, Tremblay DM, Raymond F, Sarrazin D, Moineau S, Allard M, Corbeil J, Messaddeq Y, Gosselin B.

IEEE Trans Biomed Circuits Syst. 2018 Dec;12(6):1289-1300. doi: 10.1109/TBCAS.2018.2878404. Epub 2018 Oct 31.


Clostridium difficile: Investigating Transmission Patterns Between Infected and Colonized Patients Using Whole Genome Sequencing.

Kong LY, Eyre DW, Corbeil J, Raymond F, Walker AS, Wilcox MH, Crook DW, Michaud S, Toye B, Frost E, Dendukuri N, Schiller I, Bourgault AM, Dascal A, Oughton M, Longtin Y, Poirier L, Brassard P, Turgeon N, Gilca R, Loo VG.

Clin Infect Dis. 2019 Jan 7;68(2):204-209. doi: 10.1093/cid/ciy457.


Human viral pathogens are pervasive in wastewater treatment center aerosols.

Brisebois E, Veillette M, Dion-Dupont V, Lavoie J, Corbeil J, Culley A, Duchaine C.

J Environ Sci (China). 2018 May;67:45-53. doi: 10.1016/j.jes.2017.07.015. Epub 2017 Jul 29.


Draft Genome Sequence of a Sporulating and Motile Strain of Lachnotalea glycerini Isolated from Water in Québec City, Canada.

Maheux AF, Boudreau DK, Bérubé È, Boissinot M, Raymond F, Brodeur S, Corbeil J, Isabel S, Omar RF, Bergeron MG.

Genome Announc. 2017 Oct 19;5(42). pii: e01059-17. doi: 10.1128/genomeA.01059-17.


Draft Genome Sequence of Romboutsia maritimum sp. nov. Strain CCRI-22766T, Isolated from Coastal Estuarine Mud.

Maheux AF, Boudreau DK, Bérubé È, Boissinot M, Raymond F, Brodeur S, Corbeil J, Brightwell G, Broda D, Omar RF, Bergeron MG.

Genome Announc. 2017 Oct 12;5(41). pii: e01044-17. doi: 10.1128/genomeA.01044-17.


Draft Genome Sequence of Romboutsia weinsteinii sp. nov. Strain CCRI-19649T Isolated from Surface Water.

Maheux AF, Boudreau DK, Bérubé È, Boissinot M, Cantin P, Raymond F, Corbeil J, Omar RF, Bergeron MG.

Genome Announc. 2017 Oct 5;5(40). pii: e00901-17. doi: 10.1128/genomeA.00901-17.


Phenetic Comparison of Prokaryotic Genomes Using k-mers.

Déraspe M, Raymond F, Boisvert S, Culley A, Roy PH, Laviolette F, Corbeil J.

Mol Biol Evol. 2017 Oct 1;34(10):2716-2729. doi: 10.1093/molbev/msx200.


Global Mapping of the Macrophage-HIV-1 Transcriptome Reveals that Productive Infection Induces Remodeling of Host Cell DNA and Chromatin.

Deshiere A, Joly-Beauparlant C, Breton Y, Ouellet M, Raymond F, Lodge R, Barat C, Roy MA, Corbeil J, Tremblay MJ.

Sci Rep. 2017 Jul 12;7(1):5238. doi: 10.1038/s41598-017-05566-9.


Genome-Wide Screen for Haploinsufficient Cell Size Genes in the Opportunistic Yeast Candida albicans.

Chaillot J, Cook MA, Corbeil J, Sellam A.

G3 (Bethesda). 2017 Feb 9;7(2):355-360. doi: 10.1534/g3.116.037986.


Assessment of in vivo systemic toxicity and biodistribution of iron-doped silica nanoshells.

Mendez N, Liberman A, Corbeil J, Barback C, Viveros R, Wang J, Wang-Rodriguez J, Blair SL, Mattrey R, Vera D, Trogler W, Kummel AC.

Nanomedicine. 2017 Apr;13(3):933-942. doi: 10.1016/j.nano.2016.10.018. Epub 2016 Nov 11.


Draft genome of the American Eel (Anguilla rostrata).

Pavey SA, Laporte M, Normandeau E, Gaudin J, Letourneau L, Boisvert S, Corbeil J, Audet C, Bernatchez L.

Mol Ecol Resour. 2017 Jul;17(4):806-811. doi: 10.1111/1755-0998.12608. Epub 2016 Nov 14.


Predictive computational phenotyping and biomarker discovery using reference-free genome comparisons.

Drouin A, Giguère S, Déraspe M, Marchand M, Tyers M, Loo VG, Bourgault AM, Laviolette F, Corbeil J.

BMC Genomics. 2016 Sep 26;17(1):754.


Draft Genome Sequence of Criibacterium bergeronii gen. nov., sp. nov., Strain CCRI-22567T, Isolated from a Vaginal Sample from a Woman with Bacterial Vaginosis.

Maheux AF, Bérubé È, Boudreau DK, Raymond F, Corbeil J, Roy PH, Boissinot M, Omar RF.

Genome Announc. 2016 Sep 1;4(5). pii: e00959-16. doi: 10.1128/genomeA.00959-16.


Partial recovery of microbiomes after antibiotic treatment.

Raymond F, Déraspe M, Boissinot M, Bergeron MG, Corbeil J.

Gut Microbes. 2016 Sep 2;7(5):428-34. doi: 10.1080/19490976.2016.1216747. Epub 2016 Aug 5.


Characterization of frataxin gene network in Friedreich's ataxia fibroblasts using the RNA-Seq technique.

Sanchez N, Chapdelaine P, Rousseau J, Raymond F, Corbeil J, Tremblay JP.

Mitochondrion. 2016 Sep;30:59-66. doi: 10.1016/j.mito.2016.06.003. Epub 2016 Jun 25. No abstract available.


Targeted Proteomics of Human Metapneumovirus in Clinical Samples and Viral Cultures.

Foster MW, Gerhardt G, Robitaille L, Plante PL, Boivin G, Corbeil J, Moseley MA.

Anal Chem. 2015 Oct 20;87(20):10247-54. doi: 10.1021/acs.analchem.5b01544. Epub 2015 Sep 29.


The initial state of the human gut microbiome determines its reshaping by antibiotics.

Raymond F, Ouameur AA, Déraspe M, Iqbal N, Gingras H, Dridi B, Leprohon P, Plante PL, Giroux R, Bérubé È, Frenette J, Boudreau DK, Simard JL, Chabot I, Domingo MC, Trottier S, Boissinot M, Huletsky A, Roy PH, Ouellette M, Bergeron MG, Corbeil J.

ISME J. 2016 Mar;10(3):707-20. doi: 10.1038/ismej.2015.148. Epub 2015 Sep 11.


Complete Genome Sequence of Streptococcus thermophilus SMQ-301, a Model Strain for Phage-Host Interactions.

Labrie SJ, Tremblay DM, Plante PL, Wasserscheid J, Dewar K, Corbeil J, Moineau S.

Genome Announc. 2015 May 21;3(3). pii: e00480-15. doi: 10.1128/genomeA.00480-15.


Machine learning assisted design of highly active peptides for drug discovery.

Giguère S, Laviolette F, Marchand M, Tremblay D, Moineau S, Liang X, Biron É, Corbeil J.

PLoS Comput Biol. 2015 Apr 7;11(4):e1004074. doi: 10.1371/journal.pcbi.1004074. eCollection 2015 Apr.


The resistome of Pseudomonas aeruginosa in relationship to phenotypic susceptibility.

Kos VN, Déraspe M, McLaughlin RE, Whiteaker JD, Roy PH, Alm RA, Corbeil J, Gardner H.

Antimicrob Agents Chemother. 2015 Jan;59(1):427-36. doi: 10.1128/AAC.03954-14. Epub 2014 Nov 3.


A new Microviridae phage isolated from a failed biotechnological process driven by Escherichia coli.

Labrie SJ, Dupuis MÈ, Tremblay DM, Plante PL, Corbeil J, Moineau S.

Appl Environ Microbiol. 2014 Nov;80(22):6992-7000. doi: 10.1128/AEM.01365-14. Epub 2014 Sep 5.


Evolution of oseltamivir resistance mutations in Influenza A(H1N1) and A(H3N2) viruses during selection in experimentally infected mice.

Pizzorno A, Abed Y, Plante PL, Carbonneau J, Baz M, Hamelin MÈ, Corbeil J, Boivin G.

Antimicrob Agents Chemother. 2014 Nov;58(11):6398-405. doi: 10.1128/AAC.02956-14. Epub 2014 Aug 11.


Genomic characterization of a large outbreak of Legionella pneumophila serogroup 1 strains in Quebec City, 2012.

Lévesque S, Plante PL, Mendis N, Cantin P, Marchand G, Charest H, Raymond F, Huot C, Goupil-Sormany I, Desbiens F, Faucher SP, Corbeil J, Tremblay C.

PLoS One. 2014 Aug 8;9(8):e103852. doi: 10.1371/journal.pone.0103852. eCollection 2014.


Epitope mapping of the 2009 pandemic and the A/Brisbane/59/2007 seasonal (H1N1) influenza virus haemagglutinins using mAbs and escape mutants.

Retamal M, Abed Y, Corbeil J, Boivin G.

J Gen Virol. 2014 Nov;95(Pt 11):2377-89. doi: 10.1099/vir.0.067819-0. Epub 2014 Jul 30.


Improving the safety of Staphylococcus aureus polyvalent phages by their production on a Staphylococcus xylosus strain.

El Haddad L, Ben Abdallah N, Plante PL, Dumaresq J, Katsarava R, Labrie S, Corbeil J, St-Gelais D, Moineau S.

PLoS One. 2014 Jul 25;9(7):e102600. doi: 10.1371/journal.pone.0102600. eCollection 2014.


First Complete Genome Sequence of Staphylococcus xylosus, a Meat Starter Culture and a Host to Propagate Staphylococcus aureus Phages.

Labrie SJ, El Haddad L, Tremblay DM, Plante PL, Wasserscheid J, Dumaresq J, Dewar K, Corbeil J, Moineau S.

Genome Announc. 2014 Jul 10;2(4). pii: e00671-14. doi: 10.1128/genomeA.00671-14.


Genome-wide stochastic adaptive DNA amplification at direct and inverted DNA repeats in the parasite Leishmania.

Ubeda JM, Raymond F, Mukherjee A, Plourde M, Gingras H, Roy G, Lapointe A, Leprohon P, Papadopoulou B, Corbeil J, Ouellette M.

PLoS Biol. 2014 May 20;12(5):e1001868. doi: 10.1371/journal.pbio.1001868. eCollection 2014 May.


Human Analysts at Superhuman Scales: What Has Friendly Software To Do?

Godzaridis É, Boisvert S, Xia F, Kandel M, Behling S, Long B, Sosa CP, Laviolette F, Corbeil J.

Big Data. 2013 Dec;1(4):227-36. doi: 10.1089/big.2013.0031.


Gene amplification and point mutations in pyrimidine metabolic genes in 5-fluorouracil resistant Leishmania infantum.

Ritt JF, Raymond F, Leprohon P, Légaré D, Corbeil J, Ouellette M.

PLoS Negl Trop Dis. 2013 Nov 21;7(11):e2564. doi: 10.1371/journal.pntd.0002564. eCollection 2013 Nov.


MHC-NP: predicting peptides naturally processed by the MHC.

Giguère S, Drouin A, Lacoste A, Marchand M, Corbeil J, Laviolette F.

J Immunol Methods. 2013 Dec 31;400-401:30-6. doi: 10.1016/j.jim.2013.10.003. Epub 2013 Oct 18.


Serotyping of Streptococcus pneumoniae based on capsular genes polymorphisms.

Raymond F, Boucher N, Allary R, Robitaille L, Lefebvre B, Tremblay C, Corbeil J, Gervaix A.

PLoS One. 2013 Sep 24;8(9):e76197. doi: 10.1371/journal.pone.0076197. eCollection 2013.


Correlation between Clostridium difficile bacterial load, commercial real-time PCR cycle thresholds, and results of diagnostic tests based on enzyme immunoassay and cell culture cytotoxicity assay.

Dionne LL, Raymond F, Corbeil J, Longtin J, Gervais P, Longtin Y.

J Clin Microbiol. 2013 Nov;51(11):3624-30. doi: 10.1128/JCM.01444-13. Epub 2013 Aug 21.


Nasopharyngeal carriage of individual Streptococcus pneumoniae serotypes during pediatric radiologically confirmed community acquired pneumonia following PCV7 introduction in Switzerland.

Chappuy H, Keitel K, Gehri M, Tabin R, Robitaille L, Raymond F, Corbeil J, Maspoli V, Bouazza N, Alcoba G, Lacroix L, Manzano S, Galetto-Lacour A, Gervaix A.

BMC Infect Dis. 2013 Jul 31;13:357. doi: 10.1186/1471-2334-13-357.


Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species.

Bradnam KR, Fass JN, Alexandrov A, Baranay P, Bechner M, Birol I, Boisvert S, Chapman JA, Chapuis G, Chikhi R, Chitsaz H, Chou WC, Corbeil J, Del Fabbro C, Docking TR, Durbin R, Earl D, Emrich S, Fedotov P, Fonseca NA, Ganapathy G, Gibbs RA, Gnerre S, Godzaridis E, Goldstein S, Haimel M, Hall G, Haussler D, Hiatt JB, Ho IY, Howard J, Hunt M, Jackman SD, Jaffe DB, Jarvis ED, Jiang H, Kazakov S, Kersey PJ, Kitzman JO, Knight JR, Koren S, Lam TW, Lavenier D, Laviolette F, Li Y, Li Z, Liu B, Liu Y, Luo R, Maccallum I, Macmanes MD, Maillet N, Melnikov S, Naquin D, Ning Z, Otto TD, Paten B, Paulo OS, Phillippy AM, Pina-Martins F, Place M, Przybylski D, Qin X, Qu C, Ribeiro FJ, Richards S, Rokhsar DS, Ruby JG, Scalabrin S, Schatz MC, Schwartz DC, Sergushichev A, Sharpe T, Shaw TI, Shendure J, Shi Y, Simpson JT, Song H, Tsarev F, Vezzi F, Vicedomini R, Vieira BM, Wang J, Worley KC, Yin S, Yiu SM, Yuan J, Zhang G, Zhang H, Zhou S, Korf IF.

Gigascience. 2013 Jul 22;2(1):10. doi: 10.1186/2047-217X-2-10.


Gene expression modulation and the molecular mechanisms involved in Nelfinavir resistance in Leishmania donovani axenic amastigotes.

Kumar P, Lodge R, Raymond F, Ritt JF, Jalaguier P, Corbeil J, Ouellette M, Tremblay MJ.

Mol Microbiol. 2013 Aug;89(3):565-82. doi: 10.1111/mmi.12298. Epub 2013 Jul 5.


Learning a peptide-protein binding affinity predictor with kernel ridge regression.

Giguère S, Marchand M, Laviolette F, Drouin A, Corbeil J.

BMC Bioinformatics. 2013 Mar 5;14:82. doi: 10.1186/1471-2105-14-82.


Telomeric gene deletion and intrachromosomal amplification in antimony-resistant Leishmania.

Mukherjee A, Boisvert S, Monte-Neto RL, Coelho AC, Raymond F, Mukhopadhyay R, Corbeil J, Ouellette M.

Mol Microbiol. 2013 Apr;88(1):189-202. doi: 10.1111/mmi.12178. Epub 2013 Mar 6.


Simian immunodeficiency virus infects follicular helper CD4 T cells in lymphoid tissues during pathogenic infection of pigtail macaques.

Xu Y, Weatherall C, Bailey M, Alcantara S, De Rose R, Estaquier J, Wilson K, Suzuki K, Corbeil J, Cooper DA, Kent SJ, Kelleher AD, Zaunders J.

J Virol. 2013 Apr;87(7):3760-73. doi: 10.1128/JVI.02497-12. Epub 2013 Jan 16.


HIV downregulates interferon-stimulated genes in primary macrophages.

Wie SH, Du P, Luong TQ, Rought SE, Beliakova-Bethell N, Lozach J, Corbeil J, Kornbluth RS, Richman DD, Woelk CH.

J Interferon Cytokine Res. 2013 Feb;33(2):90-5. doi: 10.1089/jir.2012.0052. Epub 2012 Dec 31.


Ray Meta: scalable de novo metagenome assembly and profiling.

Boisvert S, Raymond F, Godzaridis E, Laviolette F, Corbeil J.

Genome Biol. 2012 Dec 22;13(12):R122. doi: 10.1186/gb-2012-13-12-r122.


Assessment of cortical bone with clinical and ultrashort echo time sequences.

Du J, Hermida JC, Diaz E, Corbeil J, Znamirowski R, D'Lima DD, Bydder GM.

Magn Reson Med. 2013 Sep;70(3):697-704. doi: 10.1002/mrm.24497. Epub 2012 Sep 21.


Dentists' views on fearful patients. Problems and promises.

Brahm CO, Lundgren J, Carlsson SG, Nilsson P, Corbeil J, Hägglin C.

Swed Dent J. 2012;36(2):79-89.


Bacterial meningitis and pneumococcal serotype distribution in children in cameroon.

Gervaix A, Taguebue J, Bescher BN, Corbeil J, Raymond F, Alcoba G, Kobela M, Tetanye E.

Pediatr Infect Dis J. 2012 Oct;31(10):1084-7. doi: 10.1097/INF.0b013e318260552d.


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