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Items: 1 to 50 of 64

1.

Reply to 'Errors in long-read assemblies can critically affect protein prediction'.

Koren S, Phillippy AM, Simpson JT, Loman NJ, Loose M.

Nat Biotechnol. 2019 Feb;37(2):127-128. doi: 10.1038/s41587-018-0005-y. No abstract available.

PMID:
30670797
2.

An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar.

Grubaugh ND, Gangavarapu K, Quick J, Matteson NL, De Jesus JG, Main BJ, Tan AL, Paul LM, Brackney DE, Grewal S, Gurfield N, Van Rompay KKA, Isern S, Michael SF, Coffey LL, Loman NJ, Andersen KG.

Genome Biol. 2019 Jan 8;20(1):8. doi: 10.1186/s13059-018-1618-7.

3.

Genomic and epidemiological monitoring of yellow fever virus transmission potential.

Faria NR, Kraemer MUG, Hill SC, Goes de Jesus J, Aguiar RS, Iani FCM, Xavier J, Quick J, du Plessis L, Dellicour S, Thézé J, Carvalho RDO, Baele G, Wu CH, Silveira PP, Arruda MB, Pereira MA, Pereira GC, Lourenço J, Obolski U, Abade L, Vasylyeva TI, Giovanetti M, Yi D, Weiss DJ, Wint GRW, Shearer FM, Funk S, Nikolay B, Fonseca V, Adelino TER, Oliveira MAA, Silva MVF, Sacchetto L, Figueiredo PO, Rezende IM, Mello EM, Said RFC, Santos DA, Ferraz ML, Brito MG, Santana LF, Menezes MT, Brindeiro RM, Tanuri A, Dos Santos FCP, Cunha MS, Nogueira JS, Rocco IM, da Costa AC, Komninakis SCV, Azevedo V, Chieppe AO, Araujo ESM, Mendonça MCL, Dos Santos CC, Dos Santos CD, Mares-Guia AM, Nogueira RMR, Sequeira PC, Abreu RG, Garcia MHO, Abreu AL, Okumoto O, Kroon EG, de Albuquerque CFC, Lewandowski K, Pullan ST, Carroll M, de Oliveira T, Sabino EC, Souza RP, Suchard MA, Lemey P, Trindade GS, Drumond BP, Filippis AMB, Loman NJ, Cauchemez S, Alcantara LCJ, Pybus OG.

Science. 2018 Aug 31;361(6405):894-899. doi: 10.1126/science.aat7115. Epub 2018 Aug 23.

PMID:
30139911
4.

Complete Closed Genome Sequence of Nontoxigenic Invasive Corynebacterium diphtheriae bv. mitis Strain ISS 3319.

Azevedo Antunes C, Richardson EJ, Quick J, Fuentes-Utrilla P, Isom GL, Goodall EC, Möller J, Hoskisson PA, Mattos-Guaraldi AL, Cunningham AF, Loman NJ, Sangal V, Burkovski A, Henderson IR.

Genome Announc. 2018 Feb 1;6(5). pii: e01566-17. doi: 10.1128/genomeA.01566-17.

5.

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.

6.

Corrigendum: Shotgun metagenomics, from sampling to analysis.

Quince C, Walker AW, Simpson JT, Loman NJ, Segata N.

Nat Biotechnol. 2017 Dec 8;35(12):1211. doi: 10.1038/nbt1217-1211b.

PMID:
29220029
7.

Towards a genomics-informed, real-time, global pathogen surveillance system.

Gardy JL, Loman NJ.

Nat Rev Genet. 2018 Jan;19(1):9-20. doi: 10.1038/nrg.2017.88. Epub 2017 Nov 13. Review.

PMID:
29129921
8.

Shotgun metagenomics, from sampling to analysis.

Quince C, Walker AW, Simpson JT, Loman NJ, Segata N.

Nat Biotechnol. 2017 Sep 12;35(9):833-844. doi: 10.1038/nbt.3935. Review. Erratum in: Nat Biotechnol. 2017 Dec 8;35(12 ):1211.

PMID:
28898207
9.

Inhibiting mycobacterial tryptophan synthase by targeting the inter-subunit interface.

Abrahams KA, Cox JAG, Fütterer K, Rullas J, Ortega-Muro F, Loman NJ, Moynihan PJ, Pérez-Herrán E, Jiménez E, Esquivias J, Barros D, Ballell L, Alemparte C, Besra GS.

Sci Rep. 2017 Aug 25;7(1):9430. doi: 10.1038/s41598-017-09642-y.

10.

CLIMB (the Cloud Infrastructure for Microbial Bioinformatics): an online resource for the medical microbiology community.

Connor TR, Loman NJ, Thompson S, Smith A, Southgate J, Poplawski R, Bull MJ, Richardson E, Ismail M, Thompson SE, Kitchen C, Guest M, Bakke M, Sheppard SK, Pallen MJ.

Microb Genom. 2016 Sep 20;2(9):e000086. doi: 10.1099/mgen.0.000086. eCollection 2016 Sep.

11.

Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples.

Quick J, Grubaugh ND, Pullan ST, Claro IM, Smith AD, Gangavarapu K, Oliveira G, Robles-Sikisaka R, Rogers TF, Beutler NA, Burton DR, Lewis-Ximenez LL, de Jesus JG, Giovanetti M, Hill SC, Black A, Bedford T, Carroll MW, Nunes M, Alcantara LC Jr, Sabino EC, Baylis SA, Faria NR, Loose M, Simpson JT, Pybus OG, Andersen KG, Loman NJ.

Nat Protoc. 2017 Jun;12(6):1261-1276. doi: 10.1038/nprot.2017.066. Epub 2017 May 24.

12.

Establishment and cryptic transmission of Zika virus in Brazil and the Americas.

Faria NR, Quick J, Claro IM, Thézé J, de Jesus JG, Giovanetti M, Kraemer MUG, Hill SC, Black A, da Costa AC, Franco LC, Silva SP, Wu CH, Raghwani J, Cauchemez S, du Plessis L, Verotti MP, de Oliveira WK, Carmo EH, Coelho GE, Santelli ACFS, Vinhal LC, Henriques CM, Simpson JT, Loose M, Andersen KG, Grubaugh ND, Somasekar S, Chiu CY, Muñoz-Medina JE, Gonzalez-Bonilla CR, Arias CF, Lewis-Ximenez LL, Baylis SA, Chieppe AO, Aguiar SF, Fernandes CA, Lemos PS, Nascimento BLS, Monteiro HAO, Siqueira IC, de Queiroz MG, de Souza TR, Bezerra JF, Lemos MR, Pereira GF, Loudal D, Moura LC, Dhalia R, França RF, Magalhães T, Marques ET Jr, Jaenisch T, Wallau GL, de Lima MC, Nascimento V, de Cerqueira EM, de Lima MM, Mascarenhas DL, Neto JPM, Levin AS, Tozetto-Mendoza TR, Fonseca SN, Mendes-Correa MC, Milagres FP, Segurado A, Holmes EC, Rambaut A, Bedford T, Nunes MRT, Sabino EC, Alcantara LCJ, Loman NJ, Pybus OG.

Nature. 2017 Jun 15;546(7658):406-410. doi: 10.1038/nature22401. Epub 2017 May 24.

13.

Genomic epidemiology reveals multiple introductions of Zika virus into the United States.

Grubaugh ND, Ladner JT, Kraemer MUG, Dudas G, Tan AL, Gangavarapu K, Wiley MR, White S, Thézé J, Magnani DM, Prieto K, Reyes D, Bingham AM, Paul LM, Robles-Sikisaka R, Oliveira G, Pronty D, Barcellona CM, Metsky HC, Baniecki ML, Barnes KG, Chak B, Freije CA, Gladden-Young A, Gnirke A, Luo C, MacInnis B, Matranga CB, Park DJ, Qu J, Schaffner SF, Tomkins-Tinch C, West KL, Winnicki SM, Wohl S, Yozwiak NL, Quick J, Fauver JR, Khan K, Brent SE, Reiner RC Jr, Lichtenberger PN, Ricciardi MJ, Bailey VK, Watkins DI, Cone MR, Kopp EW 4th, Hogan KN, Cannons AC, Jean R, Monaghan AJ, Garry RF, Loman NJ, Faria NR, Porcelli MC, Vasquez C, Nagle ER, Cummings DAT, Stanek D, Rambaut A, Sanchez-Lockhart M, Sabeti PC, Gillis LD, Michael SF, Bedford T, Pybus OG, Isern S, Palacios G, Andersen KG.

Nature. 2017 Jun 15;546(7658):401-405. doi: 10.1038/nature22400. Epub 2017 May 24.

14.

Virus genomes reveal factors that spread and sustained the Ebola epidemic.

Dudas G, Carvalho LM, Bedford T, Tatem AJ, Baele G, Faria NR, Park DJ, Ladner JT, Arias A, Asogun D, Bielejec F, Caddy SL, Cotten M, D'Ambrozio J, Dellicour S, Di Caro A, Diclaro JW, Duraffour S, Elmore MJ, Fakoli LS, Faye O, Gilbert ML, Gevao SM, Gire S, Gladden-Young A, Gnirke A, Goba A, Grant DS, Haagmans BL, Hiscox JA, Jah U, Kugelman JR, Liu D, Lu J, Malboeuf CM, Mate S, Matthews DA, Matranga CB, Meredith LW, Qu J, Quick J, Pas SD, Phan MVT, Pollakis G, Reusken CB, Sanchez-Lockhart M, Schaffner SF, Schieffelin JS, Sealfon RS, Simon-Loriere E, Smits SL, Stoecker K, Thorne L, Tobin EA, Vandi MA, Watson SJ, West K, Whitmer S, Wiley MR, Winnicki SM, Wohl S, Wölfel R, Yozwiak NL, Andersen KG, Blyden SO, Bolay F, Carroll MW, Dahn B, Diallo B, Formenty P, Fraser C, Gao GF, Garry RF, Goodfellow I, Günther S, Happi CT, Holmes EC, Kargbo B, Keïta S, Kellam P, Koopmans MPG, Kuhn JH, Loman NJ, Magassouba N, Naidoo D, Nichol ST, Nyenswah T, Palacios G, Pybus OG, Sabeti PC, Sall A, Ströher U, Wurie I, Suchard MA, Lemey P, Rambaut A.

Nature. 2017 Apr 20;544(7650):309-315. doi: 10.1038/nature22040. Epub 2017 Apr 12.

15.

Ebola Virus Persistence in Breast Milk After No Reported Illness: A Likely Source of Virus Transmission From Mother to Child.

Sissoko D, Keïta M, Diallo B, Aliabadi N, Fitter DL, Dahl BA, Akoi Bore J, Raymond Koundouno F, Singethan K, Meisel S, Enkirch T, Mazzarelli A, Amburgey V, Faye O, Alpha Sall A, Magassouba N, Carroll MW, Anglaret X, Malvy D, Formenty P, Bruce Aylward R, Keïta S, Harouna Djingarey M, Loman NJ, Günther S, Duraffour S.

Clin Infect Dis. 2017 Feb 15;64(4):513-516. doi: 10.1093/cid/ciw793.

16.
17.

Unusual Ebola Virus Chain of Transmission, Conakry, Guinea, 2014-2015.

Keita M, Duraffour S, Loman NJ, Rambaut A, Diallo B, Magassouba N, Carroll MW, Quick J, Sall AA, Glynn JR, Formenty P, Subissi L, Faye O.

Emerg Infect Dis. 2016 Dec;22(12):2149-2152. doi: 10.3201/eid2212.160847.

18.

Resurgence of Ebola Virus Disease in Guinea Linked to a Survivor With Virus Persistence in Seminal Fluid for More Than 500 Days.

Diallo B, Sissoko D, Loman NJ, Bah HA, Bah H, Worrell MC, Conde LS, Sacko R, Mesfin S, Loua A, Kalonda JK, Erondu NA, Dahl BA, Handrick S, Goodfellow I, Meredith LW, Cotten M, Jah U, Guetiya Wadoum RE, Rollin P, Magassouba N, Malvy D, Anglaret X, Carroll MW, Aylward RB, Djingarey MH, Diarra A, Formenty P, Keïta S, Günther S, Rambaut A, Duraffour S.

Clin Infect Dis. 2016 Nov 15;63(10):1353-1356. Epub 2016 Sep 1.

19.

Mobile real-time surveillance of Zika virus in Brazil.

Faria NR, Sabino EC, Nunes MR, Alcantara LC, Loman NJ, Pybus OG.

Genome Med. 2016 Sep 29;8(1):97.

20.

Identification of KasA as the cellular target of an anti-tubercular scaffold.

Abrahams KA, Chung CW, Ghidelli-Disse S, Rullas J, Rebollo-López MJ, Gurcha SS, Cox JA, Mendoza A, Jiménez-Navarro E, Martínez-Martínez MS, Neu M, Shillings A, Homes P, Argyrou A, Casanueva R, Loman NJ, Moynihan PJ, Lelièvre J, Selenski C, Axtman M, Kremer L, Bantscheff M, Angulo-Barturen I, Izquierdo MC, Cammack NC, Drewes G, Ballell L, Barros D, Besra GS, Bates RH.

Nat Commun. 2016 Sep 1;7:12581. doi: 10.1038/ncomms12581.

21.

Real-time, portable genome sequencing for Ebola surveillance.

Quick J, Loman NJ, Duraffour S, Simpson JT, Severi E, Cowley L, Bore JA, Koundouno R, Dudas G, Mikhail A, Ouédraogo N, Afrough B, Bah A, Baum JH, Becker-Ziaja B, Boettcher JP, Cabeza-Cabrerizo M, Camino-Sanchez A, Carter LL, Doerrbecker J, Enkirch T, Dorival IGG, Hetzelt N, Hinzmann J, Holm T, Kafetzopoulou LE, Koropogui M, Kosgey A, Kuisma E, Logue CH, Mazzarelli A, Meisel S, Mertens M, Michel J, Ngabo D, Nitzsche K, Pallash E, Patrono LV, Portmann J, Repits JG, Rickett NY, Sachse A, Singethan K, Vitoriano I, Yemanaberhan RL, Zekeng EG, Trina R, Bello A, Sall AA, Faye O, Faye O, Magassouba N, Williams CV, Amburgey V, Winona L, Davis E, Gerlach J, Washington F, Monteil V, Jourdain M, Bererd M, Camara A, Somlare H, Camara A, Gerard M, Bado G, Baillet B, Delaune D, Nebie KY, Diarra A, Savane Y, Pallawo RB, Gutierrez GJ, Milhano N, Roger I, Williams CJ, Yattara F, Lewandowski K, Taylor J, Rachwal P, Turner D, Pollakis G, Hiscox JA, Matthews DA, O'Shea MK, Johnston AM, Wilson D, Hutley E, Smit E, Di Caro A, Woelfel R, Stoecker K, Fleischmann E, Gabriel M, Weller SA, Koivogui L, Diallo B, Keita S, Rambaut A, Formenty P, Gunther S, Carroll MW.

Nature. 2016 Feb 11;530(7589):228-232. doi: 10.1038/nature16996. Epub 2016 Feb 3.

22.

Twenty years of bacterial genome sequencing.

Loman NJ, Pallen MJ.

Nat Rev Microbiol. 2015 Dec;13(12):787-94. doi: 10.1038/nrmicro3565. Epub 2015 Nov 9. Review.

PMID:
26548914
23.

A complete bacterial genome assembled de novo using only nanopore sequencing data.

Loman NJ, Quick J, Simpson JT.

Nat Methods. 2015 Aug;12(8):733-5. doi: 10.1038/nmeth.3444. Epub 2015 Jun 15.

PMID:
26076426
24.

Rapid draft sequencing and real-time nanopore sequencing in a hospital outbreak of Salmonella.

Quick J, Ashton P, Calus S, Chatt C, Gossain S, Hawker J, Nair S, Neal K, Nye K, Peters T, De Pinna E, Robinson E, Struthers K, Webber M, Catto A, Dallman TJ, Hawkey P, Loman NJ.

Genome Biol. 2015 May 30;16:114. doi: 10.1186/s13059-015-0677-2.

25.

Parallel evolutionary pathways to antibiotic resistance selected by biocide exposure.

Webber MA, Whitehead RN, Mount M, Loman NJ, Pallen MJ, Piddock LJ.

J Antimicrob Chemother. 2015 Aug;70(8):2241-8. doi: 10.1093/jac/dkv109. Epub 2015 May 7.

26.

Eighteenth-century genomes show that mixed infections were common at time of peak tuberculosis in Europe.

Kay GL, Sergeant MJ, Zhou Z, Chan JZ, Millard A, Quick J, Szikossy I, Pap I, Spigelman M, Loman NJ, Achtman M, Donoghue HD, Pallen MJ.

Nat Commun. 2015 Apr 7;6:6717. doi: 10.1038/ncomms7717.

27.

Successful test launch for nanopore sequencing.

Loman NJ, Watson M.

Nat Methods. 2015 Apr;12(4):303-4. doi: 10.1038/nmeth.3327. No abstract available.

PMID:
25825834
28.

Mycobacterial dihydrofolate reductase inhibitors identified using chemogenomic methods and in vitro validation.

Mugumbate G, Abrahams KA, Cox JA, Papadatos G, van Westen G, Lelièvre J, Calus ST, Loman NJ, Ballell L, Barros D, Overington JP, Besra GS.

PLoS One. 2015 Mar 23;10(3):e0121492. doi: 10.1371/journal.pone.0121492. eCollection 2015.

29.

Erratum: A reference bacterial genome dataset generated on the MinION(TM) portable single-molecule nanopore sequencer.

Quick J, Quinlan AR, Loman NJ.

Gigascience. 2015 Feb 13;4:6. doi: 10.1186/s13742-015-0043-z. eCollection 2015.

30.

Real-time digital pathogen surveillance - the time is now.

Gardy J, Loman NJ, Rambaut A.

Genome Biol. 2015 Jul 30;16(1):155. doi: 10.1186/s13059-015-0726-x.

31.

Biochemical and structural characterization of mycobacterial aspartyl-tRNA synthetase AspS, a promising TB drug target.

Gurcha SS, Usha V, Cox JA, Fütterer K, Abrahams KA, Bhatt A, Alderwick LJ, Reynolds RC, Loman NJ, Nataraj V, Alemparte C, Barros D, Lloyd AJ, Ballell L, Hobrath JV, Besra GS.

PLoS One. 2014 Nov 19;9(11):e113568. doi: 10.1371/journal.pone.0113568. eCollection 2014.

32.

Reagent and laboratory contamination can critically impact sequence-based microbiome analyses.

Salter SJ, Cox MJ, Turek EM, Calus ST, Cookson WO, Moffatt MF, Turner P, Parkhill J, Loman NJ, Walker AW.

BMC Biol. 2014 Nov 12;12:87. doi: 10.1186/s12915-014-0087-z.

33.

A reference bacterial genome dataset generated on the MinION™ portable single-molecule nanopore sequencer.

Quick J, Quinlan AR, Loman NJ.

Gigascience. 2014 Oct 20;3:22. doi: 10.1186/2047-217X-3-22. eCollection 2014. Erratum in: Gigascience. 2015;4:6.

34.

Seeking the source of Pseudomonas aeruginosa infections in a recently opened hospital: an observational study using whole-genome sequencing.

Quick J, Cumley N, Wearn CM, Niebel M, Constantinidou C, Thomas CM, Pallen MJ, Moiemen NS, Bamford A, Oppenheim B, Loman NJ.

BMJ Open. 2014 Nov 4;4(11):e006278. doi: 10.1136/bmjopen-2014-006278.

35.

Binning metagenomic contigs by coverage and composition.

Alneberg J, Bjarnason BS, de Bruijn I, Schirmer M, Quick J, Ijaz UZ, Lahti L, Loman NJ, Andersson AF, Quince C.

Nat Methods. 2014 Nov;11(11):1144-6. doi: 10.1038/nmeth.3103. Epub 2014 Sep 14.

PMID:
25218180
36.

Poretools: a toolkit for analyzing nanopore sequence data.

Loman NJ, Quinlan AR.

Bioinformatics. 2014 Dec 1;30(23):3399-401. doi: 10.1093/bioinformatics/btu555. Epub 2014 Aug 20.

37.

Characterization of mutations in the PAS domain of the EvgS sensor kinase selected by laboratory evolution for acid resistance in Escherichia coli.

Johnson MD, Bell J, Clarke K, Chandler R, Pathak P, Xia Y, Marshall RL, Weinstock GM, Loman NJ, Winn PJ, Lund PA.

Mol Microbiol. 2014 Sep;93(5):911-27. doi: 10.1111/mmi.12704. Epub 2014 Jul 24.

38.

Draft Genome Sequence of Elizabethkingia meningoseptica Isolated from a Traumatic Wound.

Quick J, Constantinidou C, Pallen MJ, Oppenheim B, Loman NJ.

Genome Announc. 2014 May 8;2(3). pii: e00355-14. doi: 10.1128/genomeA.00355-14.

39.

Epidemiological investigation of Pseudomonas aeruginosa isolates from a six-year-long hospital outbreak using high-throughput whole genome sequencing.

Snyder LA, Loman NJ, Faraj LA, Levi K, Weinstock G, Boswell TC, Pallen MJ, Ala'Aldeen DA.

Euro Surveill. 2013 Oct 17;18(42). pii: 20611.

40.

Extreme genetic fragility of the HIV-1 capsid.

Rihn SJ, Wilson SJ, Loman NJ, Alim M, Bakker SE, Bhella D, Gifford RJ, Rixon FJ, Bieniasz PD.

PLoS Pathog. 2013;9(6):e1003461. doi: 10.1371/journal.ppat.1003461. Epub 2013 Jun 20.

41.

Clonal expansion within pneumococcal serotype 6C after use of seven-valent vaccine.

Loman NJ, Gladstone RA, Constantinidou C, Tocheva AS, Jefferies JM, Faust SN, O'Connor L, Chan J, Pallen MJ, Clarke SC.

PLoS One. 2013 May 28;8(5):e64731. doi: 10.1371/journal.pone.0064731. Print 2013.

42.

Tetrahydropyrazolo[1,5-a]pyrimidine-3-carboxamide and N-benzyl-6',7'-dihydrospiro[piperidine-4,4'-thieno[3,2-c]pyran] analogues with bactericidal efficacy against Mycobacterium tuberculosis targeting MmpL3.

Remuiñán MJ, Pérez-Herrán E, Rullás J, Alemparte C, Martínez-Hoyos M, Dow DJ, Afari J, Mehta N, Esquivias J, Jiménez E, Ortega-Muro F, Fraile-Gabaldón MT, Spivey VL, Loman NJ, Pallen MJ, Constantinidou C, Minick DJ, Cacho M, Rebollo-López MJ, González C, Sousa V, Angulo-Barturen I, Mendoza-Losana A, Barros D, Besra GS, Ballell L, Cammack N.

PLoS One. 2013 Apr 17;8(4):e60933. doi: 10.1371/journal.pone.0060933. Print 2013.

43.

A culture-independent sequence-based metagenomics approach to the investigation of an outbreak of Shiga-toxigenic Escherichia coli O104:H4.

Loman NJ, Constantinidou C, Christner M, Rohde H, Chan JZ, Quick J, Weir JC, Quince C, Smith GP, Betley JR, Aepfelbacher M, Pallen MJ.

JAMA. 2013 Apr 10;309(14):1502-10. doi: 10.1001/jama.2013.3231.

PMID:
23571589
44.

Identification of novel imidazo[1,2-a]pyridine inhibitors targeting M. tuberculosis QcrB.

Abrahams KA, Cox JA, Spivey VL, Loman NJ, Pallen MJ, Constantinidou C, Fernández R, Alemparte C, Remuiñán MJ, Barros D, Ballell L, Besra GS.

PLoS One. 2012;7(12):e52951. doi: 10.1371/journal.pone.0052951. Epub 2012 Dec 31.

45.

Defining bacterial species in the genomic era: insights from the genus Acinetobacter.

Chan JZ, Halachev MR, Loman NJ, Constantinidou C, Pallen MJ.

BMC Microbiol. 2012 Dec 23;12:302. doi: 10.1186/1471-2180-12-302.

46.

Genome analysis of a highly virulent serotype 1 strain of Streptococcus pneumoniae from West Africa.

Williams TM, Loman NJ, Ebruke C, Musher DM, Adegbola RA, Pallen MJ, Weinstock GM, Antonio M.

PLoS One. 2012;7(10):e26742. doi: 10.1371/journal.pone.0026742. Epub 2012 Oct 17.

47.

High-throughput bacterial genome sequencing: an embarrassment of choice, a world of opportunity.

Loman NJ, Constantinidou C, Chan JZ, Halachev M, Sergeant M, Penn CW, Robinson ER, Pallen MJ.

Nat Rev Microbiol. 2012 Sep;10(9):599-606. doi: 10.1038/nrmicro2850. Epub 2012 Aug 6. Review.

PMID:
22864262
48.

Performance comparison of benchtop high-throughput sequencing platforms.

Loman NJ, Misra RV, Dallman TJ, Constantinidou C, Gharbia SE, Wain J, Pallen MJ.

Nat Biotechnol. 2012 May;30(5):434-9. doi: 10.1038/nbt.2198. Erratum in: Nat Biotechnol. 2012 Jun;30(6):562.

PMID:
22522955
49.

Calculating orthologs in bacteria and Archaea: a divide and conquer approach.

Halachev MR, Loman NJ, Pallen MJ.

PLoS One. 2011;6(12):e28388. doi: 10.1371/journal.pone.0028388. Epub 2011 Dec 12.

50.

Are diagnostic and public health bacteriology ready to become branches of genomic medicine?

Pallen MJ, Loman NJ.

Genome Med. 2011 Aug 23;3(8):53. doi: 10.1186/gm269.

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