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Items: 42

1.

Rapid transcriptional responses to serum exposure are associated with sensitivity and resistance to antibody-mediated complement killing in invasive Salmonella Typhimurium ST313.

Ondari EM, Klemm EJ, Msefula CL, El Ghany MA, Heath JN, Pickard DJ, Barquist L, Dougan G, Kingsley RA, MacLennan CA.

Wellcome Open Res. 2019 Apr 25;4:74. doi: 10.12688/wellcomeopenres.15059.1. eCollection 2019.

2.

Transcriptional noise and exaptation as sources for bacterial sRNAs.

Jose BR, Gardner PP, Barquist L.

Biochem Soc Trans. 2019 Apr 30;47(2):527-539. doi: 10.1042/BST20180171. Epub 2019 Mar 5. Review.

PMID:
30837318
3.

Functional analysis of Salmonella Typhi adaptation to survival in water.

Kingsley RA, Langridge G, Smith SE, Makendi C, Fookes M, Wileman TM, El Ghany MA, Keith Turner A, Dyson ZA, Sridhar S, Pickard D, Kay S, Feasey N, Wong V, Barquist L, Dougan G.

Environ Microbiol. 2018 Nov;20(11):4079-4090. doi: 10.1111/1462-2920.14458.

4.

A global genomic approach uncovers novel components for twitching motility-mediated biofilm expansion in Pseudomonas aeruginosa.

Nolan LM, Whitchurch CB, Barquist L, Katrib M, Boinett CJ, Mayho M, Goulding D, Charles IG, Filloux A, Parkhill J, Cain AK.

Microb Genom. 2018 Nov;4(11). doi: 10.1099/mgen.0.000229. Epub 2018 Nov 1.

5.

Morphological, genomic and transcriptomic responses of Klebsiella pneumoniae to the last-line antibiotic colistin.

Cain AK, Boinett CJ, Barquist L, Dordel J, Fookes M, Mayho M, Ellington MJ, Goulding D, Pickard D, Wick RR, Holt KE, Parkhill J, Thomson NR.

Sci Rep. 2018 Jun 29;8(1):9868. doi: 10.1038/s41598-018-28199-y.

6.

Global Maps of ProQ Binding In Vivo Reveal Target Recognition via RNA Structure and Stability Control at mRNA 3' Ends.

Holmqvist E, Li L, Bischler T, Barquist L, Vogel J.

Mol Cell. 2018 Jun 7;70(5):971-982.e6. doi: 10.1016/j.molcel.2018.04.017. Epub 2018 May 24.

7.

Machine learning identifies signatures of host adaptation in the bacterial pathogen Salmonella enterica.

Wheeler NE, Gardner PP, Barquist L.

PLoS Genet. 2018 May 8;14(5):e1007333. doi: 10.1371/journal.pgen.1007333. eCollection 2018 May.

8.

Role of sapA and yfgA in Susceptibility to Antibody-Mediated Complement-Dependent Killing and Virulence of Salmonella enterica Serovar Typhimurium.

Ondari EM, Heath JN, Klemm EJ, Langridge G, Barquist L, Goulding DA, Clare S, Dougan G, Kingsley RA, MacLennan CA.

Infect Immun. 2017 Aug 18;85(9). pii: e00419-17. doi: 10.1128/IAI.00419-17. Print 2017 Sep.

9.

RNA target profiles direct the discovery of virulence functions for the cold-shock proteins CspC and CspE.

Michaux C, Holmqvist E, Vasicek E, Sharan M, Barquist L, Westermann AJ, Gunn JS, Vogel J.

Proc Natl Acad Sci U S A. 2017 Jun 27;114(26):6824-6829. doi: 10.1073/pnas.1620772114. Epub 2017 Jun 13.

10.

Erratum: Distinct Salmonella Enteritidis lineages associated with enterocolitis in high-income settings and invasive disease in low-income settings.

Feasey NA, Hadfield J, Keddy KH, Dallman TJ, Jacobs J, Deng X, Wigley P, Barquist L, Langridge GC, Feltwell T, Harris SR, Mather AE, Fookes M, Aslett M, Msefula C, Kariuki S, Maclennan CA, Onsare RS, Weill FX, Le Hello S, Smith AM, McClelland M, Desai P, Parry CM, Cheesbrough J, French N, Campos J, Chabalgoity JA, Betancor L, Hopkins KL, Nair S, Humphrey TJ, Lunguya O, Cogan TA, Tapia MD, Sow SO, Tennant SM, Bornstein K, Levine MM, Lacharme-Lora L, Everett DB, Kingsley RA, Parkhill J, Heyderman RS, Dougan G, Gordon MA, Thomson NR.

Nat Genet. 2017 Mar 30;49(4):651. doi: 10.1038/ng0417-651c. No abstract available.

PMID:
28358127
11.

The primary transcriptome of Neisseria meningitidis and its interaction with the RNA chaperone Hfq.

Heidrich N, Bauriedl S, Barquist L, Li L, Schoen C, Vogel J.

Nucleic Acids Res. 2017 Jun 2;45(10):6147-6167. doi: 10.1093/nar/gkx168.

12.

Resolving host-pathogen interactions by dual RNA-seq.

Westermann AJ, Barquist L, Vogel J.

PLoS Pathog. 2017 Feb 16;13(2):e1006033. doi: 10.1371/journal.ppat.1006033. eCollection 2017 Feb. Review.

13.

Molecular phenotyping of infection-associated small non-coding RNAs.

Barquist L, Westermann AJ, Vogel J.

Philos Trans R Soc Lond B Biol Sci. 2016 Nov 5;371(1707). pii: 20160081. doi: 10.1098/rstb.2016.0081. Review.

14.

Distinct Salmonella Enteritidis lineages associated with enterocolitis in high-income settings and invasive disease in low-income settings.

Feasey NA, Hadfield J, Keddy KH, Dallman TJ, Jacobs J, Deng X, Wigley P, Barquist L, Langridge GC, Feltwell T, Harris SR, Mather AE, Fookes M, Aslett M, Msefula C, Kariuki S, Maclennan CA, Onsare RS, Weill FX, Le Hello S, Smith AM, McClelland M, Desai P, Parry CM, Cheesbrough J, French N, Campos J, Chabalgoity JA, Betancor L, Hopkins KL, Nair S, Humphrey TJ, Lunguya O, Cogan TA, Tapia MD, Sow SO, Tennant SM, Bornstein K, Levine MM, Lacharme-Lora L, Everett DB, Kingsley RA, Parkhill J, Heyderman RS, Dougan G, Gordon MA, Thomson NR.

Nat Genet. 2016 Oct;48(10):1211-1217. doi: 10.1038/ng.3644. Epub 2016 Aug 22. Erratum in: Nat Genet. 2017 Mar 30;49(4):651.

15.

A profile-based method for identifying functional divergence of orthologous genes in bacterial genomes.

Wheeler NE, Barquist L, Kingsley RA, Gardner PP.

Bioinformatics. 2016 Dec 1;32(23):3566-3574. doi: 10.1093/bioinformatics/btw518. Epub 2016 Aug 8.

16.

The in vitro and in vivo effects of constitutive light expression on a bioluminescent strain of the mouse enteropathogen Citrobacter rodentium.

Read HM, Mills G, Johnson S, Tsai P, Dalton J, Barquist L, Print CG, Patrick WM, Wiles S.

PeerJ. 2016 Jun 22;4:e2130. doi: 10.7717/peerj.2130. eCollection 2016.

17.

Studying RNA Homology and Conservation with Infernal: From Single Sequences to RNA Families.

Barquist L, Burge SW, Gardner PP.

Curr Protoc Bioinformatics. 2016 Jun 20;54:12.13.1-12.13.25. doi: 10.1002/cpbi.4.

18.

Global RNA recognition patterns of post-transcriptional regulators Hfq and CsrA revealed by UV crosslinking in vivo.

Holmqvist E, Wright PR, Li L, Bischler T, Barquist L, Reinhardt R, Backofen R, Vogel J.

EMBO J. 2016 May 2;35(9):991-1011. doi: 10.15252/embj.201593360. Epub 2016 Apr 4.

19.

The TraDIS toolkit: sequencing and analysis for dense transposon mutant libraries.

Barquist L, Mayho M, Cummins C, Cain AK, Boinett CJ, Page AJ, Langridge GC, Quail MA, Keane JA, Parkhill J.

Bioinformatics. 2016 Apr 1;32(7):1109-11. doi: 10.1093/bioinformatics/btw022. Epub 2016 Jan 21.

20.

Dual RNA-seq unveils noncoding RNA functions in host-pathogen interactions.

Westermann AJ, Förstner KU, Amman F, Barquist L, Chao Y, Schulte LN, Müller L, Reinhardt R, Stadler PF, Vogel J.

Nature. 2016 Jan 28;529(7587):496-501. doi: 10.1038/nature16547. Epub 2016 Jan 20.

PMID:
26789254
21.

Accelerating Discovery and Functional Analysis of Small RNAs with New Technologies.

Barquist L, Vogel J.

Annu Rev Genet. 2015;49:367-94. doi: 10.1146/annurev-genet-112414-054804. Epub 2015 Oct 14. Review.

PMID:
26473381
22.

Correction: Signatures of Adaptation in Human Invasive Salmonella Typhimurium ST313 Populations from Sub-Saharan Africa.

Okoro CK, Barquist L, Connor TR, Harris SR, Clare S, Stevens MP, Arends MJ, Hale C, Kane L, Pickard DJ, Hill J, Harcourt K, Parkhill J, Dougan G, Kingsley RA.

PLoS Negl Trop Dis. 2015 Jun 15;9(6):e0003848. doi: 10.1371/journal.pntd.0003848. eCollection 2015 Jun. No abstract available.

23.

Signatures of adaptation in human invasive Salmonella Typhimurium ST313 populations from sub-Saharan Africa.

Okoro CK, Barquist L, Connor TR, Harris SR, Clare S, Stevens MP, Arends MJ, Hale C, Kane L, Pickard DJ, Hill J, Harcourt K, Parkhill J, Dougan G, Kingsley RA.

PLoS Negl Trop Dis. 2015 Mar 24;9(3):e0003611. doi: 10.1371/journal.pntd.0003611. eCollection 2015 Mar. Erratum in: PLoS Negl Trop Dis. 2015 Jun;9(6):e0003848. PLoS Negl Trop Dis. 2015 Aug;9(8):e0003970.

24.

High-throughput analysis of gene essentiality and sporulation in Clostridium difficile.

Dembek M, Barquist L, Boinett CJ, Cain AK, Mayho M, Lawley TD, Fairweather NF, Fagan RP.

MBio. 2015 Feb 24;6(2):e02383. doi: 10.1128/mBio.02383-14.

25.

Patterns of genome evolution that have accompanied host adaptation in Salmonella.

Langridge GC, Fookes M, Connor TR, Feltwell T, Feasey N, Parsons BN, Seth-Smith HM, Barquist L, Stedman A, Humphrey T, Wigley P, Peters SE, Maskell DJ, Corander J, Chabalgoity JA, Barrow P, Parkhill J, Dougan G, Thomson NR.

Proc Natl Acad Sci U S A. 2015 Jan 20;112(3):863-8. doi: 10.1073/pnas.1416707112. Epub 2014 Dec 22.

26.

Robust identification of noncoding RNA from transcriptomes requires phylogenetically-informed sampling.

Lindgreen S, Umu SU, Lai AS, Eldai H, Liu W, McGimpsey S, Wheeler NE, Biggs PJ, Thomson NR, Barquist L, Poole AM, Gardner PP.

PLoS Comput Biol. 2014 Oct 30;10(10):e1003907. doi: 10.1371/journal.pcbi.1003907. eCollection 2014 Oct.

27.

Parallel independent evolution of pathogenicity within the genus Yersinia.

Reuter S, Connor TR, Barquist L, Walker D, Feltwell T, Harris SR, Fookes M, Hall ME, Petty NK, Fuchs TM, Corander J, Dufour M, Ringwood T, Savin C, Bouchier C, Martin L, Miettinen M, Shubin M, Riehm JM, Laukkanen-Ninios R, Sihvonen LM, Siitonen A, Skurnik M, Falcão JP, Fukushima H, Scholz HC, Prentice MB, Wren BW, Parkhill J, Carniel E, Achtman M, McNally A, Thomson NR.

Proc Natl Acad Sci U S A. 2014 May 6;111(18):6768-73. doi: 10.1073/pnas.1317161111. Epub 2014 Apr 21.

28.

An introduction to RNA databases.

Hoeppner MP, Barquist LE, Gardner PP.

Methods Mol Biol. 2014;1097:107-23. doi: 10.1007/978-1-62703-709-9_6. Review.

PMID:
24639157
29.

Functional genomics reveals that Clostridium difficile Spo0A coordinates sporulation, virulence and metabolism.

Pettit LJ, Browne HP, Yu L, Smits WK, Fagan RP, Barquist L, Martin MJ, Goulding D, Duncan SH, Flint HJ, Dougan G, Choudhary JS, Lawley TD.

BMC Genomics. 2014 Feb 25;15:160. doi: 10.1186/1471-2164-15-160.

30.

Characterization of the yehUT two-component regulatory system of Salmonella enterica Serovar Typhi and Typhimurium.

Wong VK, Pickard DJ, Barquist L, Sivaraman K, Page AJ, Hart PJ, Arends MJ, Holt KE, Kane L, Mottram LF, Ellison L, Bautista R, McGee CJ, Kay SJ, Wileman TM, Kenney LJ, MacLennan CA, Kingsley RA, Dougan G.

PLoS One. 2013 Dec 30;8(12):e84567. doi: 10.1371/journal.pone.0084567. eCollection 2013.

31.

RNA-seq reveals the RNA binding proteins, Hfq and RsmA, play various roles in virulence, antibiotic production and genomic flux in Serratia sp. ATCC 39006.

Wilf NM, Reid AJ, Ramsay JP, Williamson NR, Croucher NJ, Gatto L, Hester SS, Goulding D, Barquist L, Lilley KS, Kingsley RA, Dougan G, Salmond GP.

BMC Genomics. 2013 Nov 22;14:822. doi: 10.1186/1471-2164-14-822.

32.

Dominant role of nucleotide substitution in the diversification of serotype 3 pneumococci over decades and during a single infection.

Croucher NJ, Mitchell AM, Gould KA, Inverarity D, Barquist L, Feltwell T, Fookes MC, Harris SR, Dordel J, Salter SJ, Browall S, Zemlickova H, Parkhill J, Normark S, Henriques-Normark B, Hinds J, Mitchell TJ, Bentley SD.

PLoS Genet. 2013;9(10):e1003868. doi: 10.1371/journal.pgen.1003868. Epub 2013 Oct 10.

33.

Genome and transcriptome adaptation accompanying emergence of the definitive type 2 host-restricted Salmonella enterica serovar Typhimurium pathovar.

Kingsley RA, Kay S, Connor T, Barquist L, Sait L, Holt KE, Sivaraman K, Wileman T, Goulding D, Clare S, Hale C, Seshasayee A, Harris S, Thomson NR, Gardner P, Rabsch W, Wigley P, Humphrey T, Parkhill J, Dougan G.

MBio. 2013 Aug 27;4(5):e00565-13. doi: 10.1128/mBio.00565-13.

34.

The agr locus regulates virulence and colonization genes in Clostridium difficile 027.

Martin MJ, Clare S, Goulding D, Faulds-Pain A, Barquist L, Browne HP, Pettit L, Dougan G, Lawley TD, Wren BW.

J Bacteriol. 2013 Aug;195(16):3672-81. doi: 10.1128/JB.00473-13. Epub 2013 Jun 14.

35.

Approaches to querying bacterial genomes with transposon-insertion sequencing.

Barquist L, Boinett CJ, Cain AK.

RNA Biol. 2013 Jul;10(7):1161-9. doi: 10.4161/rna.24765. Epub 2013 Apr 23. Review.

36.

A comparison of dense transposon insertion libraries in the Salmonella serovars Typhi and Typhimurium.

Barquist L, Langridge GC, Turner DJ, Phan MD, Turner AK, Bateman A, Parkhill J, Wain J, Gardner PP.

Nucleic Acids Res. 2013 Apr;41(8):4549-64. doi: 10.1093/nar/gkt148. Epub 2013 Mar 6.

37.

Rfam 11.0: 10 years of RNA families.

Burge SW, Daub J, Eberhardt R, Tate J, Barquist L, Nawrocki EP, Eddy SR, Gardner PP, Bateman A.

Nucleic Acids Res. 2013 Jan;41(Database issue):D226-32. doi: 10.1093/nar/gks1005. Epub 2012 Nov 3.

38.

A high-resolution view of genome-wide pneumococcal transformation.

Croucher NJ, Harris SR, Barquist L, Parkhill J, Bentley SD.

PLoS Pathog. 2012;8(6):e1002745. doi: 10.1371/journal.ppat.1002745. Epub 2012 Jun 14.

39.

HandAlign: Bayesian multiple sequence alignment, phylogeny and ancestral reconstruction.

Westesson O, Barquist L, Holmes I.

Bioinformatics. 2012 Apr 15;28(8):1170-1. doi: 10.1093/bioinformatics/bts058. Epub 2012 Jan 28.

40.

RNIE: genome-wide prediction of bacterial intrinsic terminators.

Gardner PP, Barquist L, Bateman A, Nawrocki EP, Weinberg Z.

Nucleic Acids Res. 2011 Aug;39(14):5845-52. doi: 10.1093/nar/gkr168. Epub 2011 Apr 7.

41.

Evolutionary modeling and prediction of non-coding RNAs in Drosophila.

Bradley RK, Uzilov AV, Skinner ME, Bendaña YR, Barquist L, Holmes I.

PLoS One. 2009 Aug 11;4(8):e6478. doi: 10.1371/journal.pone.0006478.

42.

xREI: a phylo-grammar visualization webserver.

Barquist L, Holmes I.

Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W65-9. doi: 10.1093/nar/gkn283. Epub 2008 Jun 3.

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