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Rapid inference of antibiotic resistance and susceptibility by genomic neighbour typing.

Břinda K, Callendrello A, Ma KC, MacFadden DR, Charalampous T, Lee RS, Cowley L, Wadsworth CB, Grad YH, Kucherov G, O'Grady J, Baym M, Hanage WP.

Nat Microbiol. 2020 Feb 10. doi: 10.1038/s41564-019-0656-6. [Epub ahead of print]


Optimizing DNA extraction methods for Nanopore sequencing of Neisseria gonorrhoeae direct from urine samples.

Street TL, Barker L, Sanderson ND, Kavanagh J, Hoosdally S, Cole K, Newnham R, Selvaratnam M, Andersson M, Llewelyn MJ, O'Grady J, Crook DW, Eyre DW; GonFast Investigators Group.

J Clin Microbiol. 2019 Dec 18. pii: JCM.01822-19. doi: 10.1128/JCM.01822-19. [Epub ahead of print]


Metagenomic identification of severe pneumonia pathogens in mechanically-ventilated patients: a feasibility and clinical validity study.

Yang L, Haidar G, Zia H, Nettles R, Qin S, Wang X, Shah F, Rapport SF, Charalampous T, Methé B, Fitch A, Morris A, McVerry BJ, O'Grady J, Kitsios GD.

Respir Res. 2019 Nov 27;20(1):265. doi: 10.1186/s12931-019-1218-4.


Modern Outcomes Following Treatment of Hepatocellular Carcinoma in Hereditary Hemochromatosis: A Matched Cohort Study.

McPhail MJW, Khorsandi SE, Abbott L, Al-Kadhimi G, Kane P, Karani J, O'Grady J, Heaton N, Bomford A, Suddle A.

Am J Clin Oncol. 2019 Dec;42(12):918-923. doi: 10.1097/COC.0000000000000583.


Determining the appropriateness of requests for outpatient magnetic resonance imaging of the hip

Manta A, O’Grady J, Bleakney R, Theodoropoulos J.

Can J Surg. 2019 Aug 1;62(4):224-226.


Improved Survival in Liver Transplant Patients Receiving Prolonged-release Tacrolimus-based Immunosuppression in the European Liver Transplant Registry (ELTR): An Extension Study.

Adam R, Karam V, Cailliez V, Trunečka P, Samuel D, Tisone G, Němec P, Soubrane O, Schneeberger S, Gridelli B, Bechstein WO, Risaliti A, Line PD, Vivarelli M, Rossi M, Pirenne J, Klempnauer JL, Rummo A, Di Benedetto F, Zieniewicz K, Troisi R, Paul A, Vali T, Kollmar O, Boudjema K, Hoti E, Colledan M, Pratschke J, Lang H, Popescu I, Ericzon BG, Strupas K, De Simone P, Kochs E, Heyd B, Gugenheim J, Pinna AD, Bennet W, Kazimi M, Bachellier P, Wigmore SJ, Rasmussen A, Clavien PA, Hidalgo E, O'Grady JG, Zamboni F, Kilic M, Duvoux C; all contributing centers ( and the European Liver and Intestine Transplant Association (ELITA).

Transplantation. 2019 Sep;103(9):1844-1862. doi: 10.1097/TP.0000000000002700.


Elevated Insulin and Insulin Resistance are Associated with Altered Myelin in Cognitively Unimpaired Middle-Aged Adults.

O'Grady JP, Dean DC 3rd, Yang KL, Canda CM, Hoscheidt SM, Starks EJ, Merluzzi A, Hurley S, Davenport NJ, Okonkwo OC, Anderson RM, Asthana S, Johnson SC, Alexander AL, Bendlin BB.

Obesity (Silver Spring). 2019 Sep;27(9):1464-1471. doi: 10.1002/oby.22558. Epub 2019 Jul 17.


The co-design, implementation and evaluation of a serious board game 'PlayDecide patient safety' to educate junior doctors about patient safety and the importance of reporting safety concerns.

Ward M, Ní Shé É, De Brún A, Korpos C, Hamza M, Burke E, Duffy A, Egan K, Geary U, Holland C, O'Grady J, Robinson K, Smith A, Watson A, McAuliffe E.

BMC Med Educ. 2019 Jun 25;19(1):232. doi: 10.1186/s12909-019-1655-2.


Nanopore metagenomics enables rapid clinical diagnosis of bacterial lower respiratory infection.

Charalampous T, Kay GL, Richardson H, Aydin A, Baldan R, Jeanes C, Rae D, Grundy S, Turner DJ, Wain J, Leggett RM, Livermore DM, O'Grady J.

Nat Biotechnol. 2019 Jul;37(7):783-792. doi: 10.1038/s41587-019-0156-5. Epub 2019 Jun 24.


Integrating informatics tools and portable sequencing technology for rapid detection of resistance to anti-tuberculous drugs.

Phelan JE, O'Sullivan DM, Machado D, Ramos J, Oppong YEA, Campino S, O'Grady J, McNerney R, Hibberd ML, Viveiros M, Huggett JF, Clark TG.

Genome Med. 2019 Jun 24;11(1):41. doi: 10.1186/s13073-019-0650-x.


The application of CRISPR-Cas for single species identification from environmental DNA.

Williams MA, O'Grady J, Ball B, Carlsson J, de Eyto E, McGinnity P, Jennings E, Regan F, Parle-McDermott A.

Mol Ecol Resour. 2019 Sep;19(5):1106-1114. doi: 10.1111/1755-0998.13045. Epub 2019 Jul 18.


Implicit Measures of Receptive Vocabulary Knowledge in Individuals With Level 3 Autism.

Coderre EL, Chernenok M, O'Grady J, Bosley L, Gordon B, Ledoux K.

Cogn Behav Neurol. 2019 Jun;32(2):95-119. doi: 10.1097/WNN.0000000000000194.


Essential Office Procedures for Medicare Patients in Primary Care: Comparison With Family Medicine Residency Training.

Poulin EA, Swartz AW, O'Grady JS, Kersten MPM, Angstman KB.

Fam Med. 2019 Jul;51(7):574-577. doi: 10.22454/FamMed.2019.659478. Epub 2019 May 21.


Bifidobacteriumbreve Bif195 Protects Against Small-Intestinal Damage Caused by Acetylsalicylic Acid in Healthy Volunteers.

Mortensen B, Murphy C, O'Grady J, Lucey M, Elsafi G, Barry L, Westphal V, Wellejus A, Lukjancenko O, Eklund AC, Nielsen HB, Baker A, Damholt A, van Hylckama Vlieg JET, Shanahan F, Buckley M.

Gastroenterology. 2019 Sep;157(3):637-646.e4. doi: 10.1053/j.gastro.2019.05.008. Epub 2019 May 13.


Recent and emerging technologies for the rapid diagnosis of infection and antimicrobial resistance.

Trotter AJ, Aydin A, Strinden MJ, O'Grady J.

Curr Opin Microbiol. 2019 Oct;51:39-45. doi: 10.1016/j.mib.2019.03.001. Epub 2019 May 9. Review.


Outcomes of liver transplantation for non-alcoholic steatohepatitis: A European Liver Transplant Registry study.

Haldar D, Kern B, Hodson J, Armstrong MJ, Adam R, Berlakovich G, Fritz J, Feurstein B, Popp W, Karam V, Muiesan P, O'Grady J, Jamieson N, Wigmore SJ, Pirenne J, Malek-Hosseini SA, Hidalgo E, Tokat Y, Paul A, Pratschke J, Bartels M, Trunecka P, Settmacher U, Pinzani M, Duvoux C, Newsome PN, Schneeberger S; European Liver and Intestine Transplant Association (ELITA).

J Hepatol. 2019 Aug;71(2):313-322. doi: 10.1016/j.jhep.2019.04.011. Epub 2019 May 7.


Letter: dietary fibre benefits for the oesophagus-physical rather than metabolic action? Authors' reply.

O'Grady J, Shanahan F.

Aliment Pharmacol Ther. 2019 May;49(10):1368-1369. doi: 10.1111/apt.15238. No abstract available.


Population-Based Incidence of Potentially Life-Threatening Complications of Hypocalcemia and the Role of Vitamin D Deficiency.

Aul AJ, Fischer PR, O'Grady JS, Mara KC, Maxson JA, Meek AM, Petterson TM, Thacher TD.

J Pediatr. 2019 Aug;211:98-104.e4. doi: 10.1016/j.jpeds.2019.02.018. Epub 2019 Apr 4.


A powerful, non-invasive test to rule out infection.

O'Grady J.

Nat Microbiol. 2019 Apr;4(4):554-555. doi: 10.1038/s41564-019-0424-7. No abstract available.


Review article: dietary fibre in the era of microbiome science.

O'Grady J, O'Connor EM, Shanahan F.

Aliment Pharmacol Ther. 2019 Mar;49(5):506-515. doi: 10.1111/apt.15129. Review.


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. Review.


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.


Response to "Is the hub-and-spoke model of care delivery a possible answer to geographical variation in liver transplant outcomes?"

Webb GJ, Hodson J, Chauhan A, O'Grady J, Neuberger JM, Hirschfield GM, Ferguson JW.

Am J Transplant. 2019 Apr;19(4):1248-1249. doi: 10.1111/ajt.15226. Epub 2019 Jan 22. No abstract available.


Review of the role of abdominal imaging in irritable bowel syndrome.

Kavanagh RG, O'Grady J, Carey BW, O'Connor OJ, Maher MM.

World J Radiol. 2018 Nov 28;10(11):143-149. doi: 10.4329/wjr.v10.i11.143. Review.


Low-Dose Computed Tomography for the Optimization of Radiation Dose Exposure in Patients with Crohn's Disease.

Kavanagh RG, O'Grady J, Carey BW, McLaughlin PD, O'Neill SB, Maher MM, O'Connor OJ.

Gastroenterol Res Pract. 2018 Oct 31;2018:1768716. doi: 10.1155/2018/1768716. eCollection 2018. Review.


Evaluation of multiplex tandem PCR (MT-PCR) assays for the detection of bacterial resistance genes among Enterobacteriaceae in clinical urines.

Schmidt K, Stanley KK, Hale R, Smith L, Wain J, O'Grady J, Livermore DM.

J Antimicrob Chemother. 2019 Feb 1;74(2):349-356. doi: 10.1093/jac/dky419.


Gathering momentum for the way ahead: fifth report of the Lancet Standing Commission on Liver Disease in the UK.

Williams R, Alexander G, Aspinall R, Batterham R, Bhala N, Bosanquet N, Severi K, Burton A, Burton R, Cramp ME, Day N, Dhawan A, Dillon J, Drummond C, Dyson J, Ferguson J, Foster GR, Gilmore I, Greenberg J, Henn C, Hudson M, Jarvis H, Kelly D, Mann J, McDougall N, McKee M, Moriarty K, Morling J, Newsome P, O'Grady J, Rolfe L, Rice P, Rutter H, Sheron N, Thorburn D, Verne J, Vohra J, Wass J, Yeoman A.

Lancet. 2018 Dec 1;392(10162):2398-2412. doi: 10.1016/S0140-6736(18)32561-3. Epub 2018 Nov 22.


Dietary Fiber and Gastrointestinal Disease: an Evolving Story.

O'Grady J, Shanahan F.

Curr Gastroenterol Rep. 2018 Nov 8;20(12):59. doi: 10.1007/s11894-018-0667-0. Review. No abstract available.


Management of Recurrent and De Novo NAFLD/NASH After Liver Transplantation.

Germani G, Laryea M, Rubbia-Brandt L, Egawa H, Burra P, OʼGrady J, Watt KD.

Transplantation. 2019 Jan;103(1):57-67. doi: 10.1097/TP.0000000000002485. Review.


A Model to Predict 1-Month Risk of Transplant or Death in Hepatitis A-Related Acute Liver Failure.

Kim JD, Cho EJ, Ahn C, Park SK, Choi JY, Lee HC, Kim DY, Choi MS, Wang HJ, Kim IH, Yeon JE, Seo YS, Tak WY, Kim MY, Lee HJ, Kim YS, Jun DW, Sohn JH, Kwon SY, Park SH, Heo J, Jeong SH, Lee JH, Nakayama N, Mochida S, Ido A, Tsubouchi H, Takikawa H, Shalimar, Acharya SK, Bernal W, O'Grady J, Kim YJ.

Hepatology. 2019 Aug;70(2):621-629. doi: 10.1002/hep.30262. Epub 2019 Feb 17.


A multicentre, benchmarking study of rectal cancer management in provincial New Zealand hospitals.

O'Grady MJ, O'Grady J, Shine R, Bonnet G, Eglington T.

N Z Med J. 2018 Aug 17;131(1480):23-31.


Long-term Challenges After Solid Organ Transplantation: Summary of Expert Presentations From the Sandoz 5th Standalone Transplantation Meeting, 2017.

Legendre C, Viebahn R, Fehrman-Ekholm I, Masnou N, Berenguer M, Potena L, Wennberg L, O'Grady J, Epailly E, Diekmann F, Binet I, Schwenger V, Kuypers D, Guthoff M.

Transplantation. 2018 Sep;102(9S Suppl 1):S1-S14. doi: 10.1097/TP.0000000000002316. No abstract available.


Predictive Factors for Survival in Children Receiving Liver Transplants for Wilson's Disease: A Cohort Study Using European Liver Transplant Registry Data.

Pfister ED, Karch A, Adam R, Polak WG, Karam V, Mirza D, O'Grady J, Klempnauer J, Reding R, Kalicinski P, Coker A, Trunecka P, Astarcioglu I, Jacquemin E, Pratschke J, Paul A, Popescu I, Schneeberger S, Boillot O, Fischer L, Mikolajczyk RT, Baumann U, Duvoux C; for all European Liver Transplant Registry contributing centers and the European Liver Intestine Transplant Association.

Liver Transpl. 2018 Sep;24(9):1186-1198. doi: 10.1002/lt.25308.


Proximity to transplant center and outcome among liver transplant patients.

Webb GJ, Hodson J, Chauhan A, O'Grady J, Neuberger JM, Hirschfield GM, Ferguson JW.

Am J Transplant. 2019 Jan;19(1):208-220. doi: 10.1111/ajt.15004. Epub 2018 Aug 3.


Corticosteroids Reduce Risk of Death Within 28 Days for Patients With Severe Alcoholic Hepatitis, Compared With Pentoxifylline or Placebo-a Meta-analysis of Individual Data From Controlled Trials.

Louvet A, Thursz MR, Kim DJ, Labreuche J, Atkinson SR, Sidhu SS, O'Grady JG, Akriviadis E, Sinakos E, Carithers RL Jr, Ramond MJ, Maddrey WC, Morgan TR, Duhamel A, Mathurin P.

Gastroenterology. 2018 Aug;155(2):458-468.e8. doi: 10.1053/j.gastro.2018.05.011. Epub 2018 May 5.


Vascular invasion and survival after liver transplantation for hepatocellular carcinoma: a study from the European Liver Transplant Registry.

Pommergaard HC, Rostved AA, Adam R, Thygesen LC, Salizzoni M, Gómez Bravo MA, Cherqui D, Filipponi F, Boudjema K, Mazzaferro V, Soubrane O, García-Valdecasas JC, Prous JF, Pinna AD, O'Grady J, Karam V, Duvoux C, Rasmussen A; European Liver and Intestine Transplant Association (ELITA).

HPB (Oxford). 2018 Aug;20(8):768-775. doi: 10.1016/j.hpb.2018.03.002. Epub 2018 Apr 3.


International Liver Transplantation Society Consensus Statement on Immunosuppression in Liver Transplant Recipients.

Charlton M, Levitsky J, Aqel B, OʼGrady J, Hemibach J, Rinella M, Fung J, Ghabril M, Thomason R, Burra P, Little EC, Berenguer M, Shaked A, Trotter J, Roberts J, Rodriguez-Davalos M, Rela M, Pomfret E, Heyrend C, Gallegos-Orozco J, Saliba F.

Transplantation. 2018 May;102(5):727-743. doi: 10.1097/TP.0000000000002147. Review. Erratum in: Transplantation. 2019 Jan;103(1):e37.


Histopathology of 460 liver allografts removed at retransplantation: A shift in disease patterns over 27 years.

Neves Souza L, de Martino RB, Sanchez-Fueyo A, Rela M, Dhawan A, O'Grady J, Heaton N, Quaglia A.

Clin Transplant. 2018 Apr;32(4):e13227. doi: 10.1111/ctr.13227. Epub 2018 Mar 23.


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.


Locoregional treatments before liver transplantation for hepatocellular carcinoma: a study from the European Liver Transplant Registry.

Pommergaard HC, Rostved AA, Adam R, Thygesen LC, Salizzoni M, Gómez Bravo MA, Cherqui D, De Simone P, Boudjema K, Mazzaferro V, Soubrane O, García-Valdecasas JC, Fabregat Prous J, Pinna AD, O'Grady J, Karam V, Duvoux C, Rasmussen A; European Liver and Intestine Transplant Association (ELITA).

Transpl Int. 2018 May;31(5):531-539. doi: 10.1111/tri.13123. Epub 2018 Feb 21.


Relaxing access to liver transplantation with living donation: A foolish move or a time to change?

O'Grady JG.

J Hepatol. 2018 May;68(5):893-894. doi: 10.1016/j.jhep.2017.11.033. Epub 2017 Dec 5. No abstract available.


Disease burden and costs from excess alcohol consumption, obesity, and viral hepatitis: fourth report of the Lancet Standing Commission on Liver Disease in the UK.

Williams R, Alexander G, Armstrong I, Baker A, Bhala N, Camps-Walsh G, Cramp ME, de Lusignan S, Day N, Dhawan A, Dillon J, Drummond C, Dyson J, Foster G, Gilmore I, Hudson M, Kelly D, Langford A, McDougall N, Meier P, Moriarty K, Newsome P, O'Grady J, Pryke R, Rolfe L, Rice P, Rutter H, Sheron N, Taylor A, Thompson J, Thorburn D, Verne J, Wass J, Yeoman A.

Lancet. 2018 Mar 17;391(10125):1097-1107. doi: 10.1016/S0140-6736(17)32866-0. Epub 2017 Nov 29. Erratum in: Lancet. 2017 Dec 7;:.


A retrospective analysis of post-transplant lymphoproliferative disorder following liver transplantation.

Fararjeh FA, Mahmood S, Tachtatzis P, Yallop D, Devereux S, Patten P, Agrawal K, Suddle A, O'Grady J, Heaton N, Marcus R, Kassam S.

Eur J Haematol. 2018 Jan;100(1):98-103. doi: 10.1111/ejh.12988. Epub 2017 Dec 4.


The Unyvero P55 'sample-in, answer-out' pneumonia assay: A performance evaluation.

Ozongwu C, Personne Y, Platt G, Jeanes C, Aydin S, Kozato N, Gant V, O'Grady J, Enne VI.

Biomol Detect Quantif. 2017 Jun 28;13:1-6. doi: 10.1016/j.bdq.2017.06.001. eCollection 2017 Sep.


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.


Validation of artificial neural networks as a methodology for donor-recipient matching for liver transplantation.

Ayllón MD, Ciria R, Cruz-Ramírez M, Pérez-Ortiz M, Gómez I, Valente R, O'Grady J, de la Mata M, Hervás-Martínez C, Heaton ND, Briceño J.

Liver Transpl. 2018 Feb;24(2):192-203. doi: 10.1002/lt.24870.


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.


Developing a donation after cardiac death risk index for adult and pediatric liver transplantation.

Khorsandi SE, Giorgakis E, Vilca-Melendez H, O'Grady J, Heneghan M, Aluvihare V, Suddle A, Agarwal K, Menon K, Prachalias A, Srinivasan P, Rela M, Jassem W, Heaton N.

World J Transplant. 2017 Jun 24;7(3):203-212. doi: 10.5500/wjt.v7.i3.203.


Death With Low MELD Scores and Possible Implications for Organ Allocation.

O'Grady JG, Lake J.

Am J Transplant. 2017 Sep;17(9):2238-2239. doi: 10.1111/ajt.14414. Epub 2017 Jul 27. No abstract available.


Affinity Proteomics for Fast, Sensitive, Quantitative Analysis of Proteins in Plasma.

O'Grady JP, Meyer KW, Poe DN.

Methods Mol Biol. 2017;1619:55-61. doi: 10.1007/978-1-4939-7057-5_5.


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