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The challenges of designing a benchmark strategy for bioinformatics pipelines in the identification of antimicrobial resistance determinants using next generation sequencing technologies.
Angers-Loustau A, Petrillo M, Bengtsson-Palme J, Berendonk T, Blais B, Chan KG, Coque TM, Hammer P, Heß S, Kagkli DM, Krumbiegel C, Lanza VF, Madec JY, Naas T, O'Grady J, Paracchini V, Rossen JWA, Ruppé E, Vamathevan J, Venturi V, Van den Eede G. Angers-Loustau A, et al. F1000Res. 2018 Apr 13;7:ISCB Comm J-459. doi: 10.12688/f1000research.14509.2. eCollection 2018. F1000Res. 2018. PMID: 30026930 Free PMC article. Review.
Diagnosing antimicrobial resistance.
Burnham CD, Leeds J, Nordmann P, O'Grady J, Patel J. Burnham CD, et al. Nat Rev Microbiol. 2017 Oct 12;15(11):697-703. doi: 10.1038/nrmicro.2017.103. Nat Rev Microbiol. 2017. PMID: 29021600 Free article. Review.
Clinical Metagenomic Sequencing for Species Identification and Antimicrobial Resistance Prediction in Orthopedic Device Infection.
Street TL, Sanderson ND, Kolenda C, Kavanagh J, Pickford H, Hoosdally S, Cregan J, Taunt C, Jones E, Oakley S, Atkins BL, Dudareva M, McNally MA, O'Grady J, Crook DW, Eyre DW. Street TL, et al. J Clin Microbiol. 2022 Apr 20;60(4):e0215621. doi: 10.1128/jcm.02156-21. Epub 2022 Mar 31. J Clin Microbiol. 2022. PMID: 35354286 Free PMC article.
MinION Analysis and Reference Consortium: Phase 2 data release and analysis of R9.0 chemistry.
Jain M, Tyson JR, Loose M, Ip CLC, Eccles DA, O'Grady J, Malla S, Leggett RM, Wallerman O, Jansen HJ, Zalunin V, Birney E, Brown BL, Snutch TP, Olsen HE; MinION Analysis and Reference Consortium. Jain M, et al. F1000Res. 2017 May 31;6:760. doi: 10.12688/f1000research.11354.1. eCollection 2017. F1000Res. 2017. PMID: 28794860 Free PMC article.
MinION Analysis and Reference Consortium: Phase 1 data release and analysis.
Ip CLC, Loose M, Tyson JR, de Cesare M, Brown BL, Jain M, Leggett RM, Eccles DA, Zalunin V, Urban JM, Piazza P, Bowden RJ, Paten B, Mwaigwisya S, Batty EM, Simpson JT, Snutch TP, Birney E, Buck D, Goodwin S, Jansen HJ, O'Grady J, Olsen HE; MinION Analysis and Reference Consortium. Ip CLC, et al. F1000Res. 2015 Oct 15;4:1075. doi: 10.12688/f1000research.7201.1. eCollection 2015. F1000Res. 2015. PMID: 26834992 Free PMC article.
CoronaHiT: high-throughput sequencing of SARS-CoV-2 genomes.
Baker DJ, Aydin A, Le-Viet T, Kay GL, Rudder S, de Oliveira Martins L, Tedim AP, Kolyva A, Diaz M, Alikhan NF, Meadows L, Bell A, Gutierrez AV, Trotter AJ, Thomson NM, Gilroy R, Griffith L, Adriaenssens EM, Stanley R, Charles IG, Elumogo N, Wain J, Prakash R, Meader E, Mather AE, Webber MA, Dervisevic S, Page AJ, O'Grady J. Baker DJ, et al. Genome Med. 2021 Feb 9;13(1):21. doi: 10.1186/s13073-021-00839-5. Genome Med. 2021. PMID: 33563320 Free PMC article.
788 results