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Items: 34

1.

The phylogeography and incidence of multi-drug resistant typhoid fever in sub-Saharan Africa.

Park SE, Pham DT, Boinett C, Wong VK, Pak GD, Panzner U, Espinoza LMC, von Kalckreuth V, Im J, Schütt-Gerowitt H, Crump JA, Breiman RF, Adu-Sarkodie Y, Owusu-Dabo E, Rakotozandrindrainy R, Soura AB, Aseffa A, Gasmelseed N, Keddy KH, May J, Sow AG, Aaby P, Biggs HM, Hertz JT, Montgomery JM, Cosmas L, Olack B, Fields B, Sarpong N, Razafindrabe TJL, Raminosoa TM, Kabore LP, Sampo E, Teferi M, Yeshitela B, El Tayeb MA, Sooka A, Meyer CG, Krumkamp R, Dekker DM, Jaeger A, Poppert S, Tall A, Niang A, Bjerregaard-Andersen M, Løfberg SV, Seo HJ, Jeon HJ, Deerin JF, Park J, Konings F, Ali M, Clemens JD, Hughes P, Sendagala JN, Vudriko T, Downing R, Ikumapayi UN, Mackenzie GA, Obaro S, Argimon S, Aanensen DM, Page A, Keane JA, Duchene S, Dyson Z, Holt KE, Dougan G, Marks F, Baker S.

Nat Commun. 2018 Nov 30;9(1):5094. doi: 10.1038/s41467-018-07370-z.

2.

Corrigendum: SeroBA: rapid high-throughput serotyping of Streptococcus pneumoniae from whole genome sequence data.

Epping L, van Tonder AJ, Gladstone RA, Bentley SD, Page AJ, Keane JA; The Global Pneumococcal Sequencing Consortium.

Microb Genom. 2018 Aug;4(8). doi: 10.1099/mgen.0.000204. No abstract available.

3.

Rapid multi-locus sequence typing direct from uncorrected long reads using Krocus.

Page AJ, Keane JA.

PeerJ. 2018 Jul 31;6:e5233. doi: 10.7717/peerj.5233. eCollection 2018.

4.

SeroBA: rapid high-throughput serotyping of Streptococcus pneumoniae from whole genome sequence data.

Epping L, van Tonder AJ, Gladstone RA, The Global Pneumococcal Sequencing Consortium, Bentley SD, Page AJ, Keane JA.

Microb Genom. 2018 Jul;4(7). doi: 10.1099/mgen.0.000186. Epub 2018 Jun 15. Erratum in: Microb Genom. 2018 Aug;4(8):.

5.

PlasmidTron: assembling the cause of phenotypes and genotypes from NGS data.

Page AJ, Wailan A, Shao Y, Judge K, Dougan G, Klemm EJ, Thomson NR, Keane JA.

Microb Genom. 2018 Mar;4(3). doi: 10.1099/mgen.0.000164. Epub 2018 Mar 12.

6.

Automatic mining of symptom severity from psychiatric evaluation notes.

Karystianis G, Nevado AJ, Kim CH, Dehghan A, Keane JA, Nenadic G.

Int J Methods Psychiatr Res. 2018 Mar;27(1). doi: 10.1002/mpr.1602. Epub 2017 Dec 22.

7.

ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads.

Hunt M, Mather AE, Sánchez-Busó L, Page AJ, Parkhill J, Keane JA, Harris SR.

Microb Genom. 2017 Sep 4;3(10):e000131. doi: 10.1099/mgen.0.000131. eCollection 2017 Oct.

8.

Phylogenetic Analysis of Klebsiella pneumoniae from Hospitalized Children, Pakistan.

Ejaz H, Wang N, Wilksch JJ, Page AJ, Cao H, Gujaran S, Keane JA, Lithgow T, Ul-Haq I, Dougan G, Strugnell RA, Heinz E.

Emerg Infect Dis. 2017 Nov;23(11):1872-1875. doi: 10.3201/eid2311.170833.

9.

Comparison of classical multi-locus sequence typing software for next-generation sequencing data.

Page AJ, Alikhan NF, Carleton HA, Seemann T, Keane JA, Katz LS.

Microb Genom. 2017 Jul 4;3(8):e000124. doi: 10.1099/mgen.0.000124. eCollection 2017 Aug. Review.

10.

Learning to identify Protected Health Information by integrating knowledge- and data-driven algorithms: A case study on psychiatric evaluation notes.

Dehghan A, Kovacevic A, Karystianis G, Keane JA, Nenadic G.

J Biomed Inform. 2017 Nov;75S:S28-S33. doi: 10.1016/j.jbi.2017.06.005. Epub 2017 Jun 7.

11.

Robust high-throughput prokaryote de novo assembly and improvement pipeline for Illumina data.

Page AJ, De Silva N, Hunt M, Quail MA, Parkhill J, Harris SR, Otto TD, Keane JA.

Microb Genom. 2016 Aug 25;2(8):e000083. doi: 10.1099/mgen.0.000083. eCollection 2016 Aug.

12.

SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments.

Page AJ, Taylor B, Delaney AJ, Soares J, Seemann T, Keane JA, Harris SR.

Microb Genom. 2016 Apr 29;2(4):e000056. doi: 10.1099/mgen.0.000056. eCollection 2016 Apr.

13.

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.

14.

Circlator: automated circularization of genome assemblies using long sequencing reads.

Hunt M, Silva ND, Otto TD, Parkhill J, Keane JA, Harris SR.

Genome Biol. 2015 Dec 29;16:294. doi: 10.1186/s13059-015-0849-0.

15.

Quantification of structural changes in the corpus callosumin children with profound hypoxic-ischaemic brain injury.

Stivaros SM, Radon MR, Mileva R, Connolly DJ, Cowell PE, Hoggard N, Wright NB, Tang V, Gledson A, Batty R, Keane JA, Griffiths PD.

Pediatr Radiol. 2016 Jan;46(1):73-81. doi: 10.1007/s00247-015-3444-3. Epub 2015 Sep 24.

16.

Combining knowledge- and data-driven methods for de-identification of clinical narratives.

Dehghan A, Kovacevic A, Karystianis G, Keane JA, Nenadic G.

J Biomed Inform. 2015 Dec;58 Suppl:S53-9. doi: 10.1016/j.jbi.2015.06.029. Epub 2015 Jul 22.

17.

Roary: rapid large-scale prokaryote pan genome analysis.

Page AJ, Cummins CA, Hunt M, Wong VK, Reuter S, Holden MT, Fookes M, Falush D, Keane JA, Parkhill J.

Bioinformatics. 2015 Nov 15;31(22):3691-3. doi: 10.1093/bioinformatics/btv421. Epub 2015 Jul 20.

18.

Using local lexicalized rules to identify heart disease risk factors in clinical notes.

Karystianis G, Dehghan A, Kovacevic A, Keane JA, Nenadic G.

J Biomed Inform. 2015 Dec;58 Suppl:S183-8. doi: 10.1016/j.jbi.2015.06.013. Epub 2015 Jun 29.

19.

Phylogeographical analysis of the dominant multidrug-resistant H58 clade of Salmonella Typhi identifies inter- and intracontinental transmission events.

Wong VK, Baker S, Pickard DJ, Parkhill J, Page AJ, Feasey NA, Kingsley RA, Thomson NR, Keane JA, Weill FX, Edwards DJ, Hawkey J, Harris SR, Mather AE, Cain AK, Hadfield J, Hart PJ, Thieu NT, Klemm EJ, Glinos DA, Breiman RF, Watson CH, Kariuki S, Gordon MA, Heyderman RS, Okoro C, Jacobs J, Lunguya O, Edmunds WJ, Msefula C, Chabalgoity JA, Kama M, Jenkins K, Dutta S, Marks F, Campos J, Thompson C, Obaro S, MacLennan CA, Dolecek C, Keddy KH, Smith AM, Parry CM, Karkey A, Mulholland EK, Campbell JI, Dongol S, Basnyat B, Dufour M, Bandaranayake D, Naseri TT, Singh SP, Hatta M, Newton P, Onsare RS, Isaia L, Dance D, Davong V, Thwaites G, Wijedoru L, Crump JA, De Pinna E, Nair S, Nilles EJ, Thanh DP, Turner P, Soeng S, Valcanis M, Powling J, Dimovski K, Hogg G, Farrar J, Holt KE, Dougan G.

Nat Genet. 2015 Jun;47(6):632-9. doi: 10.1038/ng.3281. Epub 2015 May 11.

20.

Conditional-ready mouse embryonic stem cell derived macrophages enable the study of essential genes in macrophage function.

Yeung AT, Hale C, Xia J, Tate PH, Goulding D, Keane JA, Mukhopadhyay S, Forrester L, Billker O, Skarnes WC, Hancock RE, Dougan G.

Sci Rep. 2015 Mar 10;5:8908. doi: 10.1038/srep08908.

21.

IVA: accurate de novo assembly of RNA virus genomes.

Hunt M, Gall A, Ong SH, Brener J, Ferns B, Goulder P, Nastouli E, Keane JA, Kellam P, Otto TD.

Bioinformatics. 2015 Jul 15;31(14):2374-6. doi: 10.1093/bioinformatics/btv120. Epub 2015 Feb 28.

22.

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins.

Croucher NJ, Page AJ, Connor TR, Delaney AJ, Keane JA, Bentley SD, Parkhill J, Harris SR.

Nucleic Acids Res. 2015 Feb 18;43(3):e15. doi: 10.1093/nar/gku1196. Epub 2014 Nov 20.

23.

Epithelial IL-22RA1-mediated fucosylation promotes intestinal colonization resistance to an opportunistic pathogen.

Pham TA, Clare S, Goulding D, Arasteh JM, Stares MD, Browne HP, Keane JA, Page AJ, Kumasaka N, Kane L, Mottram L, Harcourt K, Hale C, Arends MJ, Gaffney DJ; Sanger Mouse Genetics Project, Dougan G, Lawley TD.

Cell Host Microbe. 2014 Oct 8;16(4):504-16. doi: 10.1016/j.chom.2014.08.017. Epub 2014 Sep 25.

24.

Text mining of cancer-related information: review of current status and future directions.

Spasić I, Livsey J, Keane JA, Nenadić G.

Int J Med Inform. 2014 Sep;83(9):605-23. doi: 10.1016/j.ijmedinf.2014.06.009. Epub 2014 Jun 24. Review.

25.

Combining rules and machine learning for extraction of temporal expressions and events from clinical narratives.

Kovacevic A, Dehghan A, Filannino M, Keane JA, Nenadic G.

J Am Med Inform Assoc. 2013 Sep-Oct;20(5):859-66. doi: 10.1136/amiajnl-2013-001625. Epub 2013 Apr 20.

26.

The genomes of four tapeworm species reveal adaptations to parasitism.

Tsai IJ, Zarowiecki M, Holroyd N, Garciarrubio A, Sánchez-Flores A, Brooks KL, Tracey A, Bobes RJ, Fragoso G, Sciutto E, Aslett M, Beasley H, Bennett HM, Cai X, Camicia F, Clark R, Cucher M, De Silva N, Day TA, Deplazes P, Estrada K, Fernández C, Holland PWH, Hou J, Hu S, Huckvale T, Hung SS, Kamenetzky L, Keane JA, Kiss F, Koziol U, Lambert O, Liu K, Luo X, Luo Y, Macchiaroli N, Nichol S, Paps J, Parkinson J, Pouchkina-Stantcheva N, Riddiford N, Rosenzvit M, Salinas G, Wasmuth JD, Zamanian M, Zheng Y; Taenia solium Genome Consortium, Cai J, Soberón X, Olson PD, Laclette JP, Brehm K, Berriman M.

Nature. 2013 Apr 4;496(7443):57-63. doi: 10.1038/nature12031. Epub 2013 Mar 13.

27.

Topic categorisation of statements in suicide notes with integrated rules and machine learning.

Kovačević A, Dehghan A, Keane JA, Nenadic G.

Biomed Inform Insights. 2012;5(Suppl. 1):115-24. doi: 10.4137/BII.S8978. Epub 2012 Jan 30.

28.

Medication information extraction with linguistic pattern matching and semantic rules.

Spasic I, Sarafraz F, Keane JA, Nenadic G.

J Am Med Inform Assoc. 2010 Sep-Oct;17(5):532-5. doi: 10.1136/jamia.2010.003657.

29.

A text mining approach to the prediction of disease status from clinical discharge summaries.

Yang H, Spasic I, Keane JA, Nenadic G.

J Am Med Inform Assoc. 2009 Jul-Aug;16(4):596-600. doi: 10.1197/jamia.M3096. Epub 2009 Apr 23.

30.

Identification of transcription factor contexts in literature using machine learning approaches.

Yang H, Nenadic G, Keane JA.

BMC Bioinformatics. 2008 Apr 11;9 Suppl 3:S11. doi: 10.1186/1471-2105-9-S3-S11.

31.

A cascaded approach to normalising gene mentions in biomedical literature.

Yang H, Nenadic G, Keane JA.

Bioinformation. 2007 Dec 30;2(5):197-206.

32.

Using T3, an improved decision tree classifier, for mining stroke-related medical data.

Tjortjis C, Saraee M, Theodoulidis B, Keane JA.

Methods Inf Med. 2007;46(5):523-9.

PMID:
17938773
33.

Perihepatitis associated with pelvic infection: the Fitz-Hugh-Curtis syndrome.

Keane JA, McKimm RJ, David CM.

N Z Med J. 1982 Oct 27;95(718):725-8.

PMID:
6959027
34.

Disturbances of pigmentation with chloroquine.

DALL JL, KEANE JA.

Br Med J. 1959 May 30;1(5134):1387-9. No abstract available.

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