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Items: 26

1.

Metagenomic sequencing at the epicenter of the Nigeria 2018 Lassa fever outbreak.

Kafetzopoulou LE, Pullan ST, Lemey P, Suchard MA, Ehichioya DU, Pahlmann M, Thielebein A, Hinzmann J, Oestereich L, Wozniak DM, Efthymiadis K, Schachten D, Koenig F, Matjeschk J, Lorenzen S, Lumley S, Ighodalo Y, Adomeh DI, Olokor T, Omomoh E, Omiunu R, Agbukor J, Ebo B, Aiyepada J, Ebhodaghe P, Osiemi B, Ehikhametalor S, Akhilomen P, Airende M, Esumeh R, Muoebonam E, Giwa R, Ekanem A, Igenegbale G, Odigie G, Okonofua G, Enigbe R, Oyakhilome J, Yerumoh EO, Odia I, Aire C, Okonofua M, Atafo R, Tobin E, Asogun D, Akpede N, Okokhere PO, Rafiu MO, Iraoyah KO, Iruolagbe CO, Akhideno P, Erameh C, Akpede G, Isibor E, Naidoo D, Hewson R, Hiscox JA, Vipond R, Carroll MW, Ihekweazu C, Formenty P, Okogbenin S, Ogbaini-Emovon E, Günther S, Duraffour S.

Science. 2019 Jan 4;363(6422):74-77. doi: 10.1126/science.aau9343.

PMID:
30606844
2.

Assessment of metagenomic Nanopore and Illumina sequencing for recovering whole genome sequences of chikungunya and dengue viruses directly from clinical samples.

Kafetzopoulou LE, Efthymiadis K, Lewandowski K, Crook A, Carter D, Osborne J, Aarons E, Hewson R, Hiscox JA, Carroll MW, Vipond R, Pullan ST.

Euro Surveill. 2018 Dec;23(50). doi: 10.2807/1560-7917.ES.2018.23.50.1800228.

3.

Closed Genome Sequence Obtained Using Hybrid Nanopore/Illumina Assembly of a Bacillus anthracis Isolate from an Animal-Skin-Drum-Associated Anthrax Case in the United Kingdom.

Pullan ST, Miles RW, Lewandowski K, Vipond R.

Microbiol Resour Announc. 2018 Oct 4;7(13). pii: e00802-18. doi: 10.1128/MRA.00802-18. eCollection 2018 Oct.

4.

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
5.

Isolation of Oropouche Virus from Febrile Patient, Ecuador.

Wise EL, Pullan ST, Márquez S, Paz V, Mosquera JD, Zapata S, Jackson SK, Fejer G, Trueba G, Logue CH.

Emerg Infect Dis. 2018 May;24(5):935-937. doi: 10.3201/eid2405.171569.

6.

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.

7.

First Complete Genome Sequences of Zika Virus Isolated from Febrile Patient Sera in Ecuador.

Márquez S, Carrera J, Pullan ST, Lewandowski K, Paz V, Loman N, Quick J, Bonsall D, Powell R, Thézé J, Pybus OG, Klenerman P, Eisenberg J, Coloma J, Carroll MW, Trueba G, Logue CH.

Genome Announc. 2017 Feb 23;5(8). pii: e01673-16. doi: 10.1128/genomeA.01673-16.

8.

Expression of Aspergillus niger CAZymes is determined by compositional changes in wheat straw generated by hydrothermal or ionic liquid pretreatments.

Daly P, van Munster JM, Blythe MJ, Ibbett R, Kokolski M, Gaddipati S, Lindquist E, Singan VR, Barry KW, Lipzen A, Ngan CY, Petzold CJ, Chan LJG, Pullan ST, Delmas S, Waldron PR, Grigoriev IV, Tucker GA, Simmons BA, Archer DB.

Biotechnol Biofuels. 2017 Feb 7;10:35. doi: 10.1186/s13068-017-0700-9. eCollection 2017.

9.

The Effect of Nucleic Acid Extraction Platforms and Sample Storage on the Integrity of Viral RNA for Use in Whole Genome Sequencing.

Lewandowski K, Bell A, Miles R, Carne S, Wooldridge D, Manso C, Hennessy N, Bailey D, Pullan ST, Gharbia S, Vipond R.

J Mol Diagn. 2017 Mar;19(2):303-312. doi: 10.1016/j.jmoldx.2016.10.005. Epub 2016 Dec 30.

PMID:
28041870
10.

Complete Genome Sequence of Zika Virus Isolated from Semen.

Atkinson B, Graham V, Miles RW, Lewandowski K, Dowall SD, Pullan ST, Hewson R.

Genome Announc. 2016 Oct 13;4(5). pii: e01116-16. doi: 10.1128/genomeA.01116-16.

11.

Complete Genome Sequence of Seoul Virus Strain Tchoupitoulas.

Miles RW, Lewandowski K, Atkinson B, Pullan ST, Lloyd G, Bailey D.

Genome Announc. 2016 Jun 9;4(3). pii: e00480-16. doi: 10.1128/genomeA.00480-16.

12.

The effect of growth rate on pyrazinamide activity in Mycobacterium tuberculosis - insights for early bactericidal activity?

Pullan ST, Allnutt JC, Devine R, Hatch KA, Jeeves RE, Hendon-Dunn CL, Marsh PD, Bacon J.

BMC Infect Dis. 2016 May 17;16:205. doi: 10.1186/s12879-016-1533-z.

13.

Whole-genome sequencing investigation of animal-skin-drum-associated UK anthrax cases reveals evidence of mixed populations and relatedness to a US case.

Pullan ST, Pearson TR, Latham J, Mason J, Atkinson B, Silman NJ, Marston CK, Sahl JW, Birdsell D, Hoffmaster AR, Keim P, Vipond R.

Microb Genom. 2015 Nov 7;1(5):e000039. doi: 10.1099/mgen.0.000039. eCollection 2015 Nov.

14.

RNA-sequencing reveals the complexities of the transcriptional response to lignocellulosic biofuel substrates in Aspergillus niger.

Pullan ST, Daly P, Delmas S, Ibbett R, Kokolski M, Neiteler A, van Munster JM, Wilson R, Blythe MJ, Gaddipati S, Tucker GA, Archer DB.

Fungal Biol Biotechnol. 2014 Nov 17;1(1):1-14. doi: 10.1186/s40694-014-0003-x.

15.

Mycobacterium tuberculosis Is Resistant to Isoniazid at a Slow Growth Rate by Single Nucleotide Polymorphisms in katG Codon Ser315.

Jeeves RE, Marriott AA, Pullan ST, Hatch KA, Allnutt JC, Freire-Martin I, Hendon-Dunn CL, Watson R, Witney AA, Tyler RH, Arnold C, Marsh PD, McHugh TD, Bacon J.

PLoS One. 2015 Sep 18;10(9):e0138253. doi: 10.1371/journal.pone.0138253. eCollection 2015.

16.

RNA-sequencing reveals the complexities of the transcriptional response to lignocellulosic biofuel substrates in Aspergillus niger.

Pullan ST, Daly P, Delmas S, Ibbett R, Kokolski M, Neiteler A, van Munster JM, Wilson R, Blythe MJ, Gaddipati S, Tucker GA, Archer DB.

Fungal Biol Biotechnol. 2014 Nov 17;1:3. doi: 10.1186/s40694-014-0003-x. eCollection 2014.

17.

The role of carbon starvation in the induction of enzymes that degrade plant-derived carbohydrates in Aspergillus niger.

van Munster JM, Daly P, Delmas S, Pullan ST, Blythe MJ, Malla S, Kokolski M, Noltorp ECM, Wennberg K, Fetherston R, Beniston R, Yu X, Dupree P, Archer DB.

Fungal Genet Biol. 2014 Nov;72:34-47. doi: 10.1016/j.fgb.2014.04.006. Epub 2014 Apr 29.

18.

Development of an unmarked gene deletion system for the filamentous fungi Aspergillus niger and Talaromyces versatilis.

Delmas S, Llanos A, Parrou JL, Kokolski M, Pullan ST, Shunburne L, Archer DB.

Appl Environ Microbiol. 2014 Jun;80(11):3484-7. doi: 10.1128/AEM.00625-14. Epub 2014 Mar 28.

19.

Genome-wide transcriptional response of Trichoderma reesei to lignocellulose using RNA sequencing and comparison with Aspergillus niger.

Ries L, Pullan ST, Delmas S, Malla S, Blythe MJ, Archer DB.

BMC Genomics. 2013 Aug 9;14:541. doi: 10.1186/1471-2164-14-541.

20.

Trancriptional landscape of Aspergillus niger at breaking of conidial dormancy revealed by RNA-sequencing.

Novodvorska M, Hayer K, Pullan ST, Wilson R, Blythe MJ, Stam H, Stratford M, Archer DB.

BMC Genomics. 2013 Apr 11;14:246. doi: 10.1186/1471-2164-14-246.

21.

Uncovering the genome-wide transcriptional responses of the filamentous fungus Aspergillus niger to lignocellulose using RNA sequencing.

Delmas S, Pullan ST, Gaddipati S, Kokolski M, Malla S, Blythe MJ, Ibbett R, Campbell M, Liddell S, Aboobaker A, Tucker GA, Archer DB.

PLoS Genet. 2012;8(8):e1002875. doi: 10.1371/journal.pgen.1002875. Epub 2012 Aug 9.

22.

Genome-wide analysis of the role of GlnR in Streptomyces venezuelae provides new insights into global nitrogen regulation in actinomycetes.

Pullan ST, Chandra G, Bibb MJ, Merrick M.

BMC Genomics. 2011 Apr 4;12:175. doi: 10.1186/1471-2164-12-175.

23.

Microbial responses to nitric oxide and nitrosative stress: growth, "omic," and physiological methods.

Pullan ST, Monk CE, Lee L, Poole RK.

Methods Enzymol. 2008;437:499-519. doi: 10.1016/S0076-6879(07)37025-0. Review.

PMID:
18433644
24.

Nitric oxide in chemostat-cultured Escherichia coli is sensed by Fnr and other global regulators: unaltered methionine biosynthesis indicates lack of S nitrosation.

Pullan ST, Gidley MD, Jones RA, Barrett J, Stevanin TM, Read RC, Green J, Poole RK.

J Bacteriol. 2007 Mar;189(5):1845-55. Epub 2006 Dec 22.

25.

Transcriptional responses of Escherichia coli to S-nitrosoglutathione under defined chemostat conditions reveal major changes in methionine biosynthesis.

Flatley J, Barrett J, Pullan ST, Hughes MN, Green J, Poole RK.

J Biol Chem. 2005 Mar 18;280(11):10065-72. Epub 2005 Jan 12.

26.

A novel metallo-beta-lactamase, Mbl1b, produced by the environmental bacterium Caulobacter crescentus.

Simm AM, Higgins CS, Pullan ST, Avison MB, Niumsup P, Erdozain O, Bennett PM, Walsh TR.

FEBS Lett. 2001 Dec 14;509(3):350-4.

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