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Improved Performance Predicting Clarithromycin Resistance in Mycobacterium abscessus on an Independent Data Set.

Lipworth S, Hough N, Buchanan R, Smith EG, Robinson E, Alexander E, Peto T, Crook D, Walker T.

Antimicrob Agents Chemother. 2019 Jul 25;63(8). pii: e00400-19. doi: 10.1128/AAC.00400-19. Print 2019 Aug. No abstract available.


Playing to live: outcome evaluation of a community-based psychosocial expressive arts program for children during the Liberian Ebola epidemic.

Decosimo CA, Hanson J, Quinn M, Badu P, Smith EG.

Glob Ment Health (Camb). 2019 Apr 22;6:e3. doi: 10.1017/gmh.2019.1. eCollection 2019.


SymPortal: A novel analytical framework and platform for coral algal symbiont next-generation sequencing ITS2 profiling.

Hume BCC, Smith EG, Ziegler M, Warrington HJM, Burt JA, LaJeunesse TC, Wiedenmann J, Voolstra CR.

Mol Ecol Resour. 2019 Jul;19(4):1063-1080. doi: 10.1111/1755-0998.13004. Epub 2019 Apr 26.


An Opportunity to Report Closer-to-Efficacy Findings in a Study of Lamotrigine for Borderline Personality Disorder.

Smith EG.

Am J Psychiatry. 2018 Dec 1;175(12):1265. doi: 10.1176/appi.ajp.2018.18080991. No abstract available. Erratum in: Am J Psychiatry. 2019 Jan 1;176(1):81.


Whole-Genome Sequencing for Predicting Clarithromycin Resistance in Mycobacterium abscessus.

Lipworth S, Hough N, Leach L, Morgan M, Jeffery K, Andersson M, Robinson E, Smith EG, Crook D, Peto T, Walker T.

Antimicrob Agents Chemother. 2018 Dec 21;63(1). pii: e01204-18. doi: 10.1128/AAC.01204-18. Print 2019 Jan.


Prediction of Susceptibility to First-Line Tuberculosis Drugs by DNA Sequencing.

CRyPTIC Consortium and the 100,000 Genomes Project, Allix-Béguec C, Arandjelovic I, Bi L, Beckert P, Bonnet M, Bradley P, Cabibbe AM, Cancino-Muñoz I, Caulfield MJ, Chaiprasert A, Cirillo DM, Clifton DA, Comas I, Crook DW, De Filippo MR, de Neeling H, Diel R, Drobniewski FA, Faksri K, Farhat MR, Fleming J, Fowler P, Fowler TA, Gao Q, Gardy J, Gascoyne-Binzi D, Gibertoni-Cruz AL, Gil-Brusola A, Golubchik T, Gonzalo X, Grandjean L, He G, Guthrie JL, Hoosdally S, Hunt M, Iqbal Z, Ismail N, Johnston J, Khanzada FM, Khor CC, Kohl TA, Kong C, Lipworth S, Liu Q, Maphalala G, Martinez E, Mathys V, Merker M, Miotto P, Mistry N, Moore DAJ, Murray M, Niemann S, Omar SV, Ong RT, Peto TEA, Posey JE, Prammananan T, Pym A, Rodrigues C, Rodrigues M, Rodwell T, Rossolini GM, Sánchez Padilla E, Schito M, Shen X, Shendure J, Sintchenko V, Sloutsky A, Smith EG, Snyder M, Soetaert K, Starks AM, Supply P, Suriyapol P, Tahseen S, Tang P, Teo YY, Thuong TNT, Thwaites G, Tortoli E, van Soolingen D, Walker AS, Walker TM, Wilcox M, Wilson DJ, Wyllie D, Yang Y, Zhang H, Zhao Y, Zhu B.

N Engl J Med. 2018 Oct 11;379(15):1403-1415. doi: 10.1056/NEJMoa1800474. Epub 2018 Sep 26.


Identifying Mixed Mycobacterium tuberculosis Infection and Laboratory Cross-Contamination during Mycobacterial Sequencing Programs.

Wyllie DH, Robinson E, Peto T, Crook DW, Ajileye A, Rathod P, Allen R, Jarrett L, Smith EG, Walker AS.

J Clin Microbiol. 2018 Oct 25;56(11). pii: e00923-18. doi: 10.1128/JCM.00923-18. Print 2018 Nov.


Validation of the binary designation Symbiodinium thermophilum (Dinophyceae).

Hume BCC, D'Angelo C, Smith EG, Stevens JR, Burt JA, Wiedenmann J.

J Phycol. 2018 Oct;54(5):762-764. doi: 10.1111/jpy.12764. Epub 2018 Aug 23.


Control of Artifactual Variation in Reported Intersample Relatedness during Clinical Use of a Mycobacterium tuberculosis Sequencing Pipeline.

Wyllie DH, Sanderson N, Myers R, Peto T, Robinson E, Crook DW, Smith EG, Walker AS.

J Clin Microbiol. 2018 Jul 26;56(8). pii: e00104-18. doi: 10.1128/JCM.00104-18. Print 2018 Aug.


Mycobacterium chimaera infection following cardiac surgery in the United Kingdom: clinical features and outcome of the first 30 cases.

Scriven JE, Scobie A, Verlander NQ, Houston A, Collyns T, Cajic V, Kon OM, Mitchell T, Rahama O, Robinson A, Withama S, Wilson P, Maxwell D, Agranoff D, Davies E, Llewelyn M, Soo SS, Sahota A, Cooper MA, Hunter M, Tomlins J, Tiberi S, Kendall S, Dedicoat M, Alexander E, Fenech T, Zambon M, Lamagni T, Smith EG, Chand M.

Clin Microbiol Infect. 2018 Nov;24(11):1164-1170. doi: 10.1016/j.cmi.2018.04.027. Epub 2018 May 25.


Canine recommended breed weight ranges are not a good predictor of an ideal body condition score.

Smith EG, Davis K, Sulsh L, Harvey SC, Fowler KE.

J Anim Physiol Anim Nutr (Berl). 2018 Aug;102(4):1088-1090. doi: 10.1111/jpn.12919. Epub 2018 May 8.


Machine learning for classifying tuberculosis drug-resistance from DNA sequencing data.

Yang Y, Niehaus KE, Walker TM, Iqbal Z, Walker AS, Wilson DJ, Peto TEA, Crook DW, Smith EG, Zhu T, Clifton DA.

Bioinformatics. 2018 May 15;34(10):1666-1671. doi: 10.1093/bioinformatics/btx801.


Evaluation of Whole-Genome Sequencing for Mycobacterial Species Identification and Drug Susceptibility Testing in a Clinical Setting: a Large-Scale Prospective Assessment of Performance against Line Probe Assays and Phenotyping.

Quan TP, Bawa Z, Foster D, Walker T, Del Ojo Elias C, Rathod P; MMM Informatics Group, Iqbal Z, Bradley P, Mowbray J, Walker AS, Crook DW, Wyllie DH, Peto TEA, Smith EG.

J Clin Microbiol. 2018 Jan 24;56(2). pii: e01480-17. doi: 10.1128/JCM.01480-17. Print 2018 Feb.


Global outbreak of severe Mycobacterium chimaera disease after cardiac surgery: a molecular epidemiological study.

van Ingen J, Kohl TA, Kranzer K, Hasse B, Keller PM, Katarzyna Szafrańska A, Hillemann D, Chand M, Schreiber PW, Sommerstein R, Berger C, Genoni M, Rüegg C, Troillet N, Widmer AF, Becker SL, Herrmann M, Eckmanns T, Haller S, Höller C, Debast SB, Wolfhagen MJ, Hopman J, Kluytmans J, Langelaar M, Notermans DW, Ten Oever J, van den Barselaar P, Vonk ABA, Vos MC, Ahmed N, Brown T, Crook D, Lamagni T, Phin N, Smith EG, Zambon M, Serr A, Götting T, Ebner W, Thürmer A, Utpatel C, Spröer C, Bunk B, Nübel U, Bloemberg GV, Böttger EC, Niemann S, Wagner D, Sax H.

Lancet Infect Dis. 2017 Oct;17(10):1033-1041. doi: 10.1016/S1473-3099(17)30324-9. Epub 2017 Jul 12.


Acclimatization of symbiotic corals to mesophotic light environments through wavelength transformation by fluorescent protein pigments.

Smith EG, D'Angelo C, Sharon Y, Tchernov D, Wiedenmann J.

Proc Biol Sci. 2017 Jul 12;284(1858). pii: 20170320. doi: 10.1098/rspb.2017.0320.


Genetic structure of coral-Symbiodinium symbioses on the world's warmest reefs.

Smith EG, Hume BCC, Delaney P, Wiedenmann J, Burt JA.

PLoS One. 2017 Jun 30;12(6):e0180169. doi: 10.1371/journal.pone.0180169. eCollection 2017.


Symbiont community stability through severe coral bleaching in a thermally extreme lagoon.

Smith EG, Vaughan GO, Ketchum RN, McParland D, Burt JA.

Sci Rep. 2017 May 25;7(1):2428. doi: 10.1038/s41598-017-01569-8.


Animal models to improve our understanding and treatment of suicidal behavior.

Gould TD, Georgiou P, Brenner LA, Brundin L, Can A, Courtet P, Donaldson ZR, Dwivedi Y, Guillaume S, Gottesman II, Kanekar S, Lowry CA, Renshaw PF, Rujescu D, Smith EG, Turecki G, Zanos P, Zarate CA Jr, Zunszain PA, Postolache TT.

Transl Psychiatry. 2017 Apr 11;7(4):e1092. doi: 10.1038/tp.2017.50. Review.


Off-Label Prescribing of Second-Generation Antipsychotics to Elderly Veterans with Posttraumatic Stress Disorder and Dementia.

Semla TP, Lee A, Gurrera R, Bajor L, Li M, Miller DR, Smith EG, Wang C, Wan Y, Kazis LE, Bauer MS.

J Am Geriatr Soc. 2017 Aug;65(8):1789-1795. doi: 10.1111/jgs.14897. Epub 2017 Apr 3.


Associations Between Medication Class and Subsequent Augmentation of Depression Treatment in Privately Insured US Adults.

Ameli O, Soria-Saucedo R, Smith EG, Cabral HJ, Soley-Bori M, Kazis LE.

J Clin Psychopharmacol. 2017 Jun;37(3):323-331. doi: 10.1097/JCP.0000000000000687.


Tuberculosis is changing.

Walker TM, Cruz ALG, Peto TE, Smith EG, Esmail H, Crook DW.

Lancet Infect Dis. 2017 Apr;17(4):359-361. doi: 10.1016/S1473-3099(17)30123-8. Epub 2017 Mar 13. No abstract available.


Same-Day Diagnostic and Surveillance Data for Tuberculosis via Whole-Genome Sequencing of Direct Respiratory Samples.

Votintseva AA, Bradley P, Pankhurst L, Del Ojo Elias C, Loose M, Nilgiriwala K, Chatterjee A, Smith EG, Sanderson N, Walker TM, Morgan MR, Wyllie DH, Walker AS, Peto TEA, Crook DW, Iqbal Z.

J Clin Microbiol. 2017 May;55(5):1285-1298. doi: 10.1128/JCM.02483-16. Epub 2017 Mar 8.


Host specificity of Symbiodinium variants revealed by an ITS2 metahaplotype approach.

Smith EG, Ketchum RN, Burt JA.

ISME J. 2017 Jun;11(6):1500-1503. doi: 10.1038/ismej.2016.206. Epub 2017 Feb 17.


Some Synonymous and Nonsynonymous gyrA Mutations in Mycobacterium tuberculosis Lead to Systematic False-Positive Fluoroquinolone Resistance Results with the Hain GenoType MTBDRsl Assays.

Ajileye A, Alvarez N, Merker M, Walker TM, Akter S, Brown K, Moradigaravand D, Schön T, Andres S, Schleusener V, Omar SV, Coll F, Huang H, Diel R, Ismail N, Parkhill J, de Jong BC, Peto TE, Crook DW, Niemann S, Robledo J, Smith EG, Peacock SJ, Köser CU.

Antimicrob Agents Chemother. 2017 Mar 24;61(4). pii: e02169-16. doi: 10.1128/AAC.02169-16. Print 2017 Apr.


Insidious Risk of Severe Mycobacterium chimaera Infection in Cardiac Surgery Patients.

Chand M, Lamagni T, Kranzer K, Hedge J, Moore G, Parks S, Collins S, Del Ojo Elias C, Ahmed N, Brown T, Smith EG, Hoffman P, Kirwan P, Mason B, Smith-Palmer A, Veal P, Lalor MK, Bennett A, Walker J, Yeap A, Isidro Carrion Martin A, Dolan G, Bhatt S, Skingsley A, Charlett A, Pearce D, Russell K, Kendall S, Klein AA, Robins S, Schelenz S, Newsholme W, Thomas S, Collyns T, Davies E, McMenamin J, Doherty L, Peto TE, Crook D, Zambon M, Phin N.

Clin Infect Dis. 2017 Feb 1;64(3):335-342. doi: 10.1093/cid/ciw754. Epub 2016 Dec 7. Erratum in: Clin Infect Dis. 2017 Sep 1;65(5):875.


The Business Case for Expanded Clozapine Utilization.

Gören JL, Rose AJ, Smith EG, Ney JP.

Psychiatr Serv. 2016 Nov 1;67(11):1197-1205. Epub 2016 Jun 15.


Organizational Characteristics of Veterans Affairs Clinics With High and Low Utilization of Clozapine.

Gören JL, Rose AJ, Engle RL, Smith EG, Christopher ML, Rickles NM, Semla TP, McCullough MB.

Psychiatr Serv. 2016 Nov 1;67(11):1189-1196. Epub 2016 Jun 15.


Programmatic utility of tuberculosis cluster investigation using a social network approach in Birmingham, United Kingdom.

Munang ML, Browne C, Evans JT, Smith EG, Hawkey PM, Welch SB, Kaur H, Dedicoat MJ.

Int J Tuberc Lung Dis. 2016 Oct;20(10):1300-1305.


Antidepressant Medication Treatment and Risk of Death.

Zivin K, Kim HM, Yosef M, Maust DT, Valenstein M, Smith EG, Davydow DS.

J Clin Psychopharmacol. 2016 Oct;36(5):445-52. doi: 10.1097/JCP.0000000000000545.


Identifying lineage effects when controlling for population structure improves power in bacterial association studies.

Earle SG, Wu CH, Charlesworth J, Stoesser N, Gordon NC, Walker TM, Spencer CCA, Iqbal Z, Clifton DA, Hopkins KL, Woodford N, Smith EG, Ismail N, Llewelyn MJ, Peto TE, Crook DW, McVean G, Walker AS, Wilson DJ.

Nat Microbiol. 2016 Apr 4;1:16041. doi: 10.1038/nmicrobiol.2016.41.


Development and Validation of a Computerized-Adaptive Test for PTSD (P-CAT).

Eisen SV, Schultz MR, Ni P, Haley SM, Smith EG, Spiro A, Osei-Bonsu PE, Nordberg S, Jette AM.

Psychiatr Serv. 2016 Oct 1;67(10):1116-1123. Epub 2016 Jun 1.


Intervening at the Setting Level to Prevent Behavioral Incidents in Residential Child Care: Efficacy of the CARE Program Model.

Izzo CV, Smith EG, Holden MJ, Norton CI, Nunno MA, Sellers DE.

Prev Sci. 2016 Jul;17(5):554-64. doi: 10.1007/s11121-016-0649-0.


Corrigendum: Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis.

Bradley P, Gordon NC, Walker TM, Dunn L, Heys S, Huang B, Earle S, Pankhurst LJ, Anson L, de Cesare M, Piazza P, Votintseva AA, Golubchik T, Wilson DJ, Wyllie DH, Diel R, Niemann S, Feuerriegel S, Kohl TA, Ismail N, Omar SV, Smith EG, Buck D, McVean G, Walker AS, Peto TE, Crook DW, Iqbal Z.

Nat Commun. 2016 Apr 20;7:11465. doi: 10.1038/ncomms11465. No abstract available.


Long-term effects of lithium on renal function.

Smith EG.

Lancet. 2015 Nov 14;386(10007):1943. doi: 10.1016/S0140-6736(15)00832-6. Epub 2015 Nov 13. No abstract available.


Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis.

Bradley P, Gordon NC, Walker TM, Dunn L, Heys S, Huang B, Earle S, Pankhurst LJ, Anson L, de Cesare M, Piazza P, Votintseva AA, Golubchik T, Wilson DJ, Wyllie DH, Diel R, Niemann S, Feuerriegel S, Kohl TA, Ismail N, Omar SV, Smith EG, Buck D, McVean G, Walker AS, Peto TE, Crook DW, Iqbal Z.

Nat Commun. 2015 Dec 21;6:10063. doi: 10.1038/ncomms10063. Erratum in: Nat Commun. 2016;7:11465.


Rapid, comprehensive, and affordable mycobacterial diagnosis with whole-genome sequencing: a prospective study.

Pankhurst LJ, Del Ojo Elias C, Votintseva AA, Walker TM, Cole K, Davies J, Fermont JM, Gascoyne-Binzi DM, Kohl TA, Kong C, Lemaitre N, Niemann S, Paul J, Rogers TR, Roycroft E, Smith EG, Supply P, Tang P, Wilcox MH, Wordsworth S, Wyllie D, Xu L, Crook DW; COMPASS-TB Study Group.

Lancet Respir Med. 2016 Jan;4(1):49-58. doi: 10.1016/S2213-2600(15)00466-X. Epub 2015 Dec 4.


The Ascendancy of Second-Generation Antipsychotics as Frontline Antimanic Agents.

Miller CJ, Li M, Penfold RB, Lee AF, Smith EG, Nordberg SS, Osser DN, Bajor L, Zhang F, Bauer MS.

J Clin Psychopharmacol. 2015 Dec;35(6):645-53. doi: 10.1097/JCP.0000000000000405.


Brief CBT and Suicide Risk: Ruling Out Nonspecific Effects of Individual Therapy.

Stankiewicz BW, Smith EG, Herz L.

Am J Psychiatry. 2015 Oct;172(10):1022. doi: 10.1176/appi.ajp.2015.15060774. No abstract available.


An assessment of Qatar's coral communities in a regional context.

Burt JA, Smith EG, Warren C, Dupont J.

Mar Pollut Bull. 2016 Apr 30;105(2):473-9. doi: 10.1016/j.marpolbul.2015.09.025. Epub 2015 Sep 26.


Whole-genome sequencing for prediction of Mycobacterium tuberculosis drug susceptibility and resistance: a retrospective cohort study.

Walker TM, Kohl TA, Omar SV, Hedge J, Del Ojo Elias C, Bradley P, Iqbal Z, Feuerriegel S, Niehaus KE, Wilson DJ, Clifton DA, Kapatai G, Ip CLC, Bowden R, Drobniewski FA, Allix-Béguec C, Gaudin C, Parkhill J, Diel R, Supply P, Crook DW, Smith EG, Walker AS, Ismail N, Niemann S, Peto TEA; Modernizing Medical Microbiology (MMM) Informatics Group.

Lancet Infect Dis. 2015 Oct;15(10):1193-1202. doi: 10.1016/S1473-3099(15)00062-6. Epub 2015 Jun 23. Erratum in: Lancet Infect Dis. 2017 Nov 21;:.


Local adaptation constrains the distribution potential of heat-tolerant Symbiodinium from the Persian/Arabian Gulf.

D'Angelo C, Hume BC, Burt J, Smith EG, Achterberg EP, Wiedenmann J.

ISME J. 2015 Dec;9(12):2551-60. doi: 10.1038/ismej.2015.80. Epub 2015 May 19.


Mortality associated with lithium and valproate treatment of US Veterans Health Administration patients with mental disorders.

Smith EG, Austin KL, Kim HM, Eisen SV, Kilbourne AM, Miller DR, Zivin K, Hannemann C, Sauer BC, Valenstein M.

Br J Psychiatry. 2015 Jul;207(1):55-63. doi: 10.1192/bjp.bp.113.138685. Epub 2015 May 7.


Symbiodinium thermophilum sp. nov., a thermotolerant symbiotic alga prevalent in corals of the world's hottest sea, the Persian/Arabian Gulf.

Hume BC, D'Angelo C, Smith EG, Stevens JR, Burt J, Wiedenmann J.

Sci Rep. 2015 Feb 27;5:8562. doi: 10.1038/srep08562.


Tuberculosis microepidemics among dispersed migrants, Birmingham, UK, 2004-2013.

Munang ML, Browne C, Khanom S, Evans JT, Smith EG, Hawkey PM, Kunst H, Welch SB, Dedicoat MJ.

Emerg Infect Dis. 2015 Mar;21(3):524-7. doi: 10.3201/eid2103.140209.


The ACCE method: an approach for obtaining quantitative or qualitative estimates of residual confounding that includes unmeasured confounding.

Smith EG.

Version 2. F1000Res. 2014 Aug 11 [revised 2015 Jan 1];3:187. doi: 10.12688/f1000research.4801.2. eCollection 2014.


Suicide risk in Veterans Health Administration patients with mental health diagnoses initiating lithium or valproate: a historical prospective cohort study.

Smith EG, Austin KL, Kim HM, Miller DR, Eisen SV, Christiansen CL, Kilbourne AM, Sauer BC, McCarthy JF, Valenstein M.

BMC Psychiatry. 2014 Dec 17;14:357. doi: 10.1186/s12888-014-0357-x.


Patterns of initiation of second generation antipsychotics for bipolar disorder: a month-by-month analysis of provider behavior.

Miller CJ, Li M, Penfold RB, Lee AF, Smith EG, Osser DN, Bajor L, Bauer MS.

BMC Psychiatry. 2014 Nov 30;14:339. doi: 10.1186/s12888-014-0339-z.


Assessment of Mycobacterium tuberculosis transmission in Oxfordshire, UK, 2007-12, with whole pathogen genome sequences: an observational study.

Walker TM, Lalor MK, Broda A, Ortega LS, Morgan M, Parker L, Churchill S, Bennett K, Golubchik T, Giess AP, Del Ojo Elias C, Jeffery KJ, Bowler ICJW, Laurenson IF, Barrett A, Drobniewski F, McCarthy ND, Anderson LF, Abubakar I, Thomas HL, Monk P, Smith EG, Walker AS, Crook DW, Peto TEA, Conlon CP.

Lancet Respir Med. 2014 Apr;2(4):285-292. doi: 10.1016/S2213-2600(14)70027-X. Epub 2014 Mar 4.


Income inequality and child maltreatment in the United States.

Eckenrode J, Smith EG, McCarthy ME, Dineen M.

Pediatrics. 2014 Mar;133(3):454-61. doi: 10.1542/peds.2013-1707. Epub 2014 Feb 10.


Antidepressant augmentation using the N-methyl-D-aspartate antagonist memantine: a randomized, double-blind, placebo-controlled trial.

Smith EG, Deligiannidis KM, Ulbricht CM, Landolin CS, Patel JK, Rothschild AJ.

J Clin Psychiatry. 2013 Oct;74(10):966-73. doi: 10.4088/JCP.12m08252.

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