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Items: 1 to 20 of 53

1.

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.

Version 2. F1000Res. 2018 Apr 13 [revised 2018 Jan 1];7. pii: ISCB Comm J-459. doi: 10.12688/f1000research.14509.2. eCollection 2018.

2.

Leprosy at the edge of Europe-Biomolecular, isotopic and osteoarchaeological findings from medieval Ireland.

Taylor GM, Murphy EM, Mendum TA, Pike AWG, Linscott B, Wu H, O'Grady J, Richardson H, O'Donovan E, Troy C, Stewart GR.

PLoS One. 2018 Dec 26;13(12):e0209495. doi: 10.1371/journal.pone.0209495. eCollection 2018.

3.

Nanopore sequencing and assembly of a human genome with ultra-long reads.

Jain M, Koren S, Miga KH, Quick J, Rand AC, Sasani TA, Tyson JR, Beggs AD, Dilthey AT, Fiddes IT, Malla S, Marriott H, Nieto T, O'Grady J, Olsen HE, Pedersen BS, Rhie A, Richardson H, Quinlan AR, Snutch TP, Tee L, Paten B, Phillippy AM, Simpson JT, Loman NJ, Loose M.

Nat Biotechnol. 2018 Apr;36(4):338-345. doi: 10.1038/nbt.4060. Epub 2018 Jan 29.

4.

Diagnosing antimicrobial resistance.

Burnham CD, Leeds J, Nordmann P, O'Grady J, Patel J.

Nat Rev Microbiol. 2017 Oct 12;15(11):697-703. doi: 10.1038/nrmicro.2017.103. Review.

PMID:
29021600
5.

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.

F1000Res. 2017 May 31;6:760. doi: 10.12688/f1000research.11354.1. eCollection 2017.

6.

Performance of the Xpert MTB/RIF assay in the diagnosis of tuberculosis in formalin-fixed, paraffin-embedded tissues.

Polepole P, Kabwe M, Kasonde M, Tembo J, Shibemba A, O'Grady J, Kapata N, Zumla A, Bates M.

Int J Mycobacteriol. 2017 Jan-Mar;6(1):87-93. doi: 10.4103/2212-5531.201892.

7.

Application of highly portable MinION nanopore sequencing technology for the monitoring of nosocomial tuberculosis infection.

Bates M, Polepole P, Kapata N, Loose M, O'Grady J.

Int J Mycobacteriol. 2016 Dec;5 Suppl 1:S24. doi: 10.1016/j.ijmyco.2016.10.035. Epub 2016 Nov 23.

8.

The variability and reproducibility of whole genome sequencing technology for detecting resistance to anti-tuberculous drugs.

Phelan J, O'Sullivan DM, Machado D, Ramos J, Whale AS, O'Grady J, Dheda K, Campino S, McNerney R, Viveiros M, Huggett JF, Clark TG.

Genome Med. 2016 Dec 22;8(1):132. doi: 10.1186/s13073-016-0385-x.

9.

Diagnosing tuberculosis in the 21st century - Dawn of a genomics revolution?

Jeanes C, O'Grady J.

Int J Mycobacteriol. 2016 Dec;5(4):384-391. doi: 10.1016/j.ijmyco.2016.11.028. Review.

10.

qPCR, dPCR, NGS - A journey.

Huggett JF, O'Grady J, Bustin S.

Biomol Detect Quantif. 2015 Jan 15;3:A1-5. doi: 10.1016/j.bdq.2015.01.001. eCollection 2015 Mar. No abstract available.

11.

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.

F1000Res. 2015 Oct 15;4:1075. doi: 10.12688/f1000research.7201.1. eCollection 2015.

12.

Performance of urine lipoarabinomannan assays for paediatric tuberculosis in Tanzania.

Kroidl I, Clowes P, Reither K, Mtafya B, Rojas-Ponce G, Ntinginya EN, Kalomo M, Minja LT, Kowuor D, Saathoff E, Kroidl A, Heinrich N, Maboko L, Bates M, O'Grady J, Zumla A, Hoelscher M, Rachow A.

Eur Respir J. 2015 Sep;46(3):761-70. doi: 10.1183/09031936.00003315. Epub 2015 Jun 25.

13.

Emerging commercial molecular tests for the diagnosis of bloodstream infection.

Mwaigwisya S, Assiri RA, O'Grady J.

Expert Rev Mol Diagn. 2015 May;15(5):681-92. doi: 10.1586/14737159.2015.1029459. Epub 2015 Apr 12. Review.

PMID:
25866124
14.

Ancient DNA analysis - An established technique in charting the evolution of tuberculosis and leprosy.

Donoghue HD, Spigelman M, O'Grady J, Szikossy I, Pap I, Lee OY, Wu HH, Besra GS, Minnikin DE.

Tuberculosis (Edinb). 2015 Jun;95 Suppl 1:S140-4. doi: 10.1016/j.tube.2015.02.020. Epub 2015 Feb 13.

PMID:
25773651
15.

Extra-pulmonary tuberculosis and Xpert® MTB/RIF: all about meta-analyses?

O'Grady J, Kik SV, Ferrara G.

Int J Tuberc Lung Dis. 2015 Mar;19(3):254. doi: 10.5588/ijtld.15.0040. No abstract available.

PMID:
25686127
16.

A migration-driven model for the historical spread of leprosy in medieval Eastern and Central Europe.

Donoghue HD, Michael Taylor G, Marcsik A, Molnár E, Pálfi G, Pap I, Teschler-Nicola M, Pinhasi R, Erdal YS, Velemínsky P, Likovsky J, Belcastro MG, Mariotti V, Riga A, Rubini M, Zaio P, Besra GS, Lee OY, Wu HH, Minnikin DE, Bull ID, O'Grady J, Spigelman M.

Infect Genet Evol. 2015 Apr;31:250-6. doi: 10.1016/j.meegid.2015.02.001. Epub 2015 Feb 11.

PMID:
25680828
17.

MinION nanopore sequencing identifies the position and structure of a bacterial antibiotic resistance island.

Ashton PM, Nair S, Dallman T, Rubino S, Rabsch W, Mwaigwisya S, Wain J, O'Grady J.

Nat Biotechnol. 2015 Mar;33(3):296-300. doi: 10.1038/nbt.3103. Epub 2014 Dec 8.

PMID:
25485618
18.

How to make Mathematics Biology's next and better microscope.

Huggett J, O'Grady J, Bustin S.

Biomol Detect Quantif. 2014 Sep 10;1(1):A1-A3. eCollection 2014 Sep. No abstract available.

19.

Use of the Xpert(®) MTB/RIF assay for diagnosing pulmonary tuberculosis comorbidity and multidrug-resistant TB in obstetrics and gynaecology inpatient wards at the University Teaching Hospital, Lusaka, Zambia.

Bates M, Ahmed Y, Chilukutu L, Tembo J, Cheelo B, Sinyangwe S, Kapata N, Maeurer M, O'Grady J, Mwaba P, Zumla A.

Trop Med Int Health. 2013 Sep;18(9):1134-1140. doi: 10.1111/tmi.12145. Epub 2013 Jul 3.

20.

Advances in multiparametric molecular diagnostics technologies for respiratory tract infections.

Reddington K, Tuite N, Barry T, O'Grady J, Zumla A.

Curr Opin Pulm Med. 2013 May;19(3):298-304. doi: 10.1097/MCP.0b013e32835f1b32. Review.

PMID:
23425918

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