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Items: 1 to 50 of 190

1.

Loss of microbial diversity and pathogen domination of the gut microbiota in critically ill patients.

Ravi A, Halstead FD, Bamford A, Casey A, Thomson NM, van Schaik W, Snelson C, Goulden R, Foster-Nyarko E, Savva GM, Whitehouse T, Pallen MJ, Oppenheim BA.

Microb Genom. 2019 Sep;5(9). doi: 10.1099/mgen.0.000293. Epub 2019 Sep 11.

2.

Towards standardisation of naming novel prokaryotic taxa in the age of high-throughput microbiology.

Hildebrand F, Pallen MJ, Bork P.

Gut. 2019 Jun 15. pii: gutjnl-2019-319045. doi: 10.1136/gutjnl-2019-319045. [Epub ahead of print] No abstract available.

3.

Metagenomic profiling of ticks: Identification of novel rickettsial genomes and detection of tick-borne canine parvovirus.

Ravi A, Ereqat S, Al-Jawabreh A, Abdeen Z, Abu Shamma O, Hall H, Pallen MJ, Nasereddin A.

PLoS Negl Trop Dis. 2019 Jan 14;13(1):e0006805. doi: 10.1371/journal.pntd.0006805. eCollection 2019 Jan.

4.

Organization and architecture of AggR-dependent promoters from enteroaggregative Escherichia coli.

Yasir M, Icke C, Abdelwahab R, Haycocks JR, Godfrey RE, Sazinas P, Pallen MJ, Henderson IR, Busby SJW, Browning DF.

Mol Microbiol. 2019 Feb;111(2):534-551. doi: 10.1111/mmi.14172. Epub 2018 Dec 18.

5.

Giant flagellins form thick flagellar filaments in two species of marine γ-proteobacteria.

Thomson NM, Ferreira JL, Matthews-Palmer TR, Beeby M, Pallen MJ.

PLoS One. 2018 Nov 21;13(11):e0206544. doi: 10.1371/journal.pone.0206544. eCollection 2018.

6.

Bacterial Flagellins: Does Size Matter?

Thomson NM, Rossmann FM, Ferreira JL, Matthews-Palmer TR, Beeby M, Pallen MJ.

Trends Microbiol. 2018 Jul;26(7):575-581. doi: 10.1016/j.tim.2017.11.010. Epub 2017 Dec 16. Review.

PMID:
29258714
7.

Whole-genome sequencing illuminates the evolution and spread of multidrug-resistant tuberculosis in Southwest Nigeria.

Senghore M, Otu J, Witney A, Gehre F, Doughty EL, Kay GL, Butcher P, Salako K, Kehinde A, Onyejepu N, Idigbe E, Corrah T, de Jong B, Pallen MJ, Antonio M.

PLoS One. 2017 Sep 19;12(9):e0184510. doi: 10.1371/journal.pone.0184510. eCollection 2017.

8.

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.

9.

An In Vitro Chicken Gut Model Demonstrates Transfer of a Multidrug Resistance Plasmid from Salmonella to Commensal Escherichia coli.

Card RM, Cawthraw SA, Nunez-Garcia J, Ellis RJ, Kay G, Pallen MJ, Woodward MJ, Anjum MF.

MBio. 2017 Jul 18;8(4). pii: e00777-17. doi: 10.1128/mBio.00777-17.

10.

The Gut Microbiota and the Hepatologist: Will Our Bugs Prove to be the Missing Link?

Pallen MJ, Quraishi MN.

Dig Dis. 2017;35(4):377-383. doi: 10.1159/000456590. Epub 2017 May 3. Review.

PMID:
28468018
11.

Identification of the anti-mycobacterial functional properties of piperidinol derivatives.

Guy CS, Tichauer E, Kay GL, Phillips DJ, Bailey TL, Harrison J, Furze CM, Millard AD, Gibson MI, Pallen MJ, Fullam E.

Br J Pharmacol. 2017 Jul;174(14):2183-2193. doi: 10.1111/bph.13744. Epub 2017 Mar 23.

12.

The Enigmatic Esx Proteins: Looking Beyond Mycobacteria.

Unnikrishnan M, Constantinidou C, Palmer T, Pallen MJ.

Trends Microbiol. 2017 Mar;25(3):192-204. doi: 10.1016/j.tim.2016.11.004. Epub 2016 Nov 25. Review.

PMID:
27894646
13.

The emerging threat of pre-extensively drug-resistant tuberculosis in West Africa: preparing for large-scale tuberculosis research and drug resistance surveillance.

Gehre F, Otu J, Kendall L, Forson A, Kwara A, Kudzawu S, Kehinde AO, Adebiyi O, Salako K, Baldeh I, Jallow A, Jallow M, Dagnra A, Dissé K, Kadanga EA, Idigbe EO, Onubogu C, Onyejepu N, Gaye-Diallo A, Ba-Diallo A, Rabna P, Mane M, Sanogo M, Diarra B, Dezemon Z, Sanou A, Senghore M, Kwambana-Adams BA, Demba E, Faal-Jawara T, Kumar S, Tientcheu LD, Jallow A, Ceesay S, Adetifa I, Jaye A, Pallen MJ, D'Alessandro U, Kampmann B, Adegbola RA, Mboup S, Corrah T, de Jong BC, Antonio M.

BMC Med. 2016 Nov 3;14(1):160.

14.

An outbreak of pneumococcal meningitis among older children (≥5 years) and adults after the implementation of an infant vaccination programme with the 13-valent pneumococcal conjugate vaccine in Ghana.

Kwambana-Adams BA, Asiedu-Bekoe F, Sarkodie B, Afreh OK, Kuma GK, Owusu-Okyere G, Foster-Nyarko E, Ohene SA, Okot C, Worwui AK, Okoi C, Senghore M, Otu JK, Ebruke C, Bannerman R, Amponsa-Achiano K, Opare D, Kay G, Letsa T, Kaluwa O, Appiah-Denkyira E, Bampoe V, Zaman SM, Pallen MJ, D'Alessandro U, Mwenda JM, Antonio M.

BMC Infect Dis. 2016 Oct 18;16(1):575.

15.

Draft Genome Sequences of Nine Clinical Isolates of Vancomycin-Resistant Enterococci.

Higgins PG, Koehler D, Chan JZ, Cornely OA, Fätkenheuer G, Gillis M, Pallen MJ, Tien J, Seifert H, Vehreschild MJ, Millard AD.

Genome Announc. 2016 Aug 18;4(4). pii: e00803-16. doi: 10.1128/genomeA.00803-16.

16.

Transmission of Staphylococcus aureus from Humans to Green Monkeys in The Gambia as Revealed by Whole-Genome Sequencing.

Senghore M, Bayliss SC, Kwambana-Adams BA, Foster-Nyarko E, Manneh J, Dione M, Badji H, Ebruke C, Doughty EL, Thorpe HA, Jasinska AJ, Schmitt CA, Cramer JD, Turner TR, Weinstock G, Freimer NB, Pallen MJ, Feil EJ, Antonio M.

Appl Environ Microbiol. 2016 Sep 16;82(19):5910-7. doi: 10.1128/AEM.01496-16. Print 2016 Oct 1.

17.

Microbial bioinformatics 2020.

Pallen MJ.

Microb Biotechnol. 2016 Sep;9(5):681-6. doi: 10.1111/1751-7915.12389. Epub 2016 Jul 29. Review.

18.

Forensic Analysis Reveals Acute Decompensation of Chronic Heart Failure in a 3500-Year-Old Egyptian Dignitary.

Bianucci R, Loynes RD, Sutherland ML, Lallo R, Kay GL, Froesch P, Pallen MJ, Charlier P, Nerlich AG.

J Forensic Sci. 2016 Sep;61(5):1378-81. doi: 10.1111/1556-4029.13138. Epub 2016 Jun 30.

PMID:
27362779
19.

Draft Genome Sequences of Six Novel Bacterial Isolates from Chicken Ceca.

Duggett NA, Kay GL, Sergeant MJ, Bedford M, Constantinidou CI, Penn CW, Millard AD, Pallen MJ.

Genome Announc. 2016 May 26;4(3). pii: e00448-16. doi: 10.1128/genomeA.00448-16.

20.

The gut-adherent microbiota of PSC-IBD is distinct to that of IBD.

Quraishi MN, Sergeant M, Kay G, Iqbal T, Chan J, Constantinidou C, Trivedi P, Ferguson J, Adams DH, Pallen M, Hirschfield GM.

Gut. 2017 Feb;66(2):386-388. doi: 10.1136/gutjnl-2016-311915. Epub 2016 Apr 19. No abstract available.

PMID:
27196590
21.

Draft Genome Sequences of 11 Clinical Isolates of Acinetobacter baumannii.

Higgins PG, Chan JZ, Seifert H, Pallen MJ, Millard AD.

Genome Announc. 2016 Apr 14;4(2). pii: e00269-16. doi: 10.1128/genomeA.00269-16.

22.

Role of Clinicogenomics in Infectious Disease Diagnostics and Public Health Microbiology.

Westblade LF, van Belkum A, Grundhoff A, Weinstock GM, Pamer EG, Pallen MJ, Dunne WM Jr.

J Clin Microbiol. 2016 Jul;54(7):1686-1693. doi: 10.1128/JCM.02664-15. Epub 2016 Feb 24.

23.

Draft Genome Sequence of the Pandoraea apista LMG 16407 Type Strain.

Millard AD, Westblade LF, LiPuma JJ, Vavikolanu K, Read TD, Pallen MJ, Burd EM, Constantinidou CI.

Genome Announc. 2015 Nov 12;3(6). pii: e01300-15. doi: 10.1128/genomeA.01300-15.

24.

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
25.

The pla gene, encoding plasminogen activator, is not specific to Yersinia pestis.

Hänsch S, Cilli E, Catalano G, Gruppioni G, Bianucci R, Stenseth NC, Bramanti B, Pallen MJ.

BMC Res Notes. 2015 Oct 5;8:535. doi: 10.1186/s13104-015-1525-x.

26.

Differences in the Faecal Microbiome in Schistosoma haematobium Infected Children vs. Uninfected Children.

Kay GL, Millard A, Sergeant MJ, Midzi N, Gwisai R, Mduluza T, Ivens A, Nausch N, Mutapi F, Pallen M.

PLoS Negl Trop Dis. 2015 Jun 26;9(6):e0003861. doi: 10.1371/journal.pntd.0003861. eCollection 2015. Erratum in: PLoS Negl Trop Dis. 2015 Jul;9(7):e0003969.

27.

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.

28.

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.

29.

Archaeology. Sedimentary DNA from a submerged site reveals wheat in the British Isles 8000 years ago.

Smith O, Momber G, Bates R, Garwood P, Fitch S, Pallen M, Gaffney V, Allaby RG.

Science. 2015 Feb 27;347(6225):998-1001. doi: 10.1126/science.1261278.

30.

Complete genome sequence of Pig-tailed macaque rhadinovirus 2 and its evolutionary relationship with rhesus macaque rhadinovirus and human herpesvirus 8/Kaposi's sarcoma-associated herpesvirus.

Bruce AG, Thouless ME, Haines AS, Pallen MJ, Grundhoff A, Rose TM.

J Virol. 2015 Apr;89(7):3888-909. doi: 10.1128/JVI.03597-14. Epub 2015 Jan 21.

31.

Genomic epidemiology of a protracted hospital outbreak caused by multidrug-resistant Acinetobacter baumannii in Birmingham, England.

Halachev MR, Chan JZ, Constantinidou CI, Cumley N, Bradley C, Smith-Banks M, Oppenheim B, Pallen MJ.

Genome Med. 2014 Nov 20;6(11):70. doi: 10.1186/s13073-014-0070-x. eCollection 2014.

32.

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.

33.

Culture-independent detection and characterisation of Mycobacterium tuberculosis and M. africanum in sputum samples using shotgun metagenomics on a benchtop sequencer.

Doughty EL, Sergeant MJ, Adetifa I, Antonio M, Pallen MJ.

PeerJ. 2014 Sep 23;2:e585. doi: 10.7717/peerj.585. eCollection 2014.

34.

Recovery of a medieval Brucella melitensis genome using shotgun metagenomics.

Kay GL, Sergeant MJ, Giuffra V, Bandiera P, Milanese M, Bramanti B, Bianucci R, Pallen MJ.

MBio. 2014 Jul 15;5(4):e01337-14. doi: 10.1128/mBio.01337-14.

35.

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.

36.

Extensive microbial and functional diversity within the chicken cecal microbiome.

Sergeant MJ, Constantinidou C, Cogan TA, Bedford MR, Penn CW, Pallen MJ.

PLoS One. 2014 Mar 21;9(3):e91941. doi: 10.1371/journal.pone.0091941. eCollection 2014.

37.

Diagnostic metagenomics: potential applications to bacterial, viral and parasitic infections.

Pallen MJ.

Parasitology. 2014 Dec;141(14):1856-62. doi: 10.1017/S0031182014000134. Epub 2014 Feb 27. Review.

38.

Microarray analysis of the Ler regulon in enteropathogenic and enterohaemorrhagic Escherichia coli strains.

Bingle LE, Constantinidou C, Shaw RK, Islam MS, Patel M, Snyder LA, Lee DJ, Penn CW, Busby SJ, Pallen MJ.

PLoS One. 2014 Jan 14;9(1):e80160. doi: 10.1371/journal.pone.0080160. eCollection 2014.

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.

Bridging the gap between the technological singularity and mainstream medicine: highlighting a course on technology and the future of medicine.

Solez K, Bernier A, Crichton J, Graves H, Kuttikat P, Lockwood R, Marovitz WF, Monroe D, Pallen M, Pandya S, Pearce D, Saleh A, Sandhu N, Sergi C, Tuszynski J, Waugh E, White J, Woodside M, Wyndham R, Zaiane O, Zakus D.

Glob J Health Sci. 2013 Sep 9;5(6):112-25. doi: 10.5539/gjhs.v5n6p112.

41.

Metagenomic analysis of tuberculosis in a mummy.

Chan JZ, Sergeant MJ, Lee OY, Minnikin DE, Besra GS, Pap I, Spigelman M, Donoghue HD, Pallen MJ.

N Engl J Med. 2013 Jul 18;369(3):289-90. doi: 10.1056/NEJMc1302295. No abstract available.

PMID:
23863071
42.

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.

43.

Genomics and outbreak investigation: from sequence to consequence.

Robinson ER, Walker TM, Pallen MJ.

Genome Med. 2013 Apr 29;5(4):36. doi: 10.1186/gm440. eCollection 2013. Review.

44.

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.

45.

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
46.

Reply to Updating benchtop sequencing performance comparison.

Pallen MJ.

Nat Biotechnol. 2013 Apr;31(4):296. doi: 10.1038/nbt.2531. No abstract available.

PMID:
23563422
47.

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.

48.

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.

49.

Genome sequencing in clinical microbiology.

Chan JZ, Pallen MJ, Oppenheim B, Constantinidou C.

Nat Biotechnol. 2012 Nov;30(11):1068-71. doi: 10.1038/nbt.2410. No abstract available.

PMID:
23138305
50.

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.

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