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Items: 1 to 20 of 77

1.

Nextstrain: real-time tracking of pathogen evolution.

Hadfield J, Megill C, Bell SM, Huddleston J, Potter B, Callender C, Sagulenko P, Bedford T, Neher RA.

Bioinformatics. 2018 May 22. doi: 10.1093/bioinformatics/bty407. [Epub ahead of print]

PMID:
29790939
2.

Germline pathogenic variants in PALB2 and other cancer-predisposing genes in families with hereditary diffuse gastric cancer without CDH1 mutation: a whole-exome sequencing study.

Fewings E, Larionov A, Redman J, Goldgraben MA, Scarth J, Richardson S, Brewer C, Davidson R, Ellis I, Evans DG, Halliday D, Izatt L, Marks P, McConnell V, Verbist L, Mayes R, Clark GR, Hadfield J, Chin SF, Teixeira MR, Giger OT, Hardwick R, di Pietro M, O'Donovan M, Pharoah P, Caldas C, Fitzgerald RC, Tischkowitz M.

Lancet Gastroenterol Hepatol. 2018 Jul;3(7):489-498. doi: 10.1016/S2468-1253(18)30079-7. Epub 2018 Apr 27.

3.

Population-based analysis of ocular Chlamydia trachomatis in trachoma-endemic West African communities identifies genomic markers of disease severity.

Last AR, Pickering H, Roberts CH, Coll F, Phelan J, Burr SE, Cassama E, Nabicassa M, Seth-Smith HMB, Hadfield J, Cutcliffe LT, Clarke IN, Mabey DCW, Bailey RL, Clark TG, Thomson NR, Holland MJ.

Genome Med. 2018 Feb 26;10(1):15. doi: 10.1186/s13073-018-0521-x.

4.

A profusion of confusion in NGS methods naming.

Hadfield J, Retief J.

Nat Methods. 2018 Jan 3;15(1):7-8. doi: 10.1038/nmeth.4558. No abstract available.

PMID:
29298293
5.

Mycoplasma genitalium: whole genome sequence analysis, recombination and population structure.

Fookes MC, Hadfield J, Harris S, Parmar S, Unemo M, Jensen JS, Thomson NR.

BMC Genomics. 2017 Dec 28;18(1):993. doi: 10.1186/s12864-017-4399-6.

6.

Differentiation dynamics of mammary epithelial cells revealed by single-cell RNA sequencing.

Bach K, Pensa S, Grzelak M, Hadfield J, Adams DJ, Marioni JC, Khaled WT.

Nat Commun. 2017 Dec 11;8(1):2128. doi: 10.1038/s41467-017-02001-5.

7.

Determining best outcomes from community-acquired pneumonia and how to achieve them.

Hadfield J, Bennett L.

Respirology. 2018 Feb;23(2):138-147. doi: 10.1111/resp.13218. Epub 2017 Nov 17. Review.

8.

The Hidden Genomics of Chlamydia trachomatis.

Hadfield J, Bénard A, Domman D, Thomson N.

Curr Top Microbiol Immunol. 2018;412:107-131. doi: 10.1007/82_2017_39.

PMID:
29071471
9.

Phandango: an interactive viewer for bacterial population genomics.

Hadfield J, Croucher NJ, Goater RJ, Abudahab K, Aanensen DM, Harris SR.

Bioinformatics. 2017 Sep 25. doi: 10.1093/bioinformatics/btx610. [Epub ahead of print]

10.

Comprehensive global genome dynamics of Chlamydia trachomatis show ancient diversification followed by contemporary mixing and recent lineage expansion.

Hadfield J, Harris SR, Seth-Smith HMB, Parmar S, Andersson P, Giffard PM, Schachter J, Moncada J, Ellison L, Vaulet MLG, Fermepin MR, Radebe F, Mendoza S, Ouburg S, Morré SA, Sachse K, Puolakkainen M, Korhonen SJ, Sonnex C, Wiggins R, Jalal H, Brunelli T, Casprini P, Pitt R, Ison C, Savicheva A, Shipitsyna E, Hadad R, Kari L, Burton MJ, Mabey D, Solomon AW, Lewis D, Marsh P, Unemo M, Clarke IN, Parkhill J, Thomson NR.

Genome Res. 2017 Jul;27(7):1220-1229. doi: 10.1101/gr.212647.116. Epub 2017 Jun 6.

11.

Disseminated Mycobacterium malmoense and Salmonella Infections Associated with a Novel Variant in NFKBIA.

Staples E, Morillo-Gutierrez B, Davies J, Petersheim D, Massaad M, Slatter M, Dimou D, Doffinger R, Hackett S, Kumararatne D, Hadfield J, Eldridge MD, Geha RS, Abinun M, Thaventhiran JED.

J Clin Immunol. 2017 Jul;37(5):415-418. doi: 10.1007/s10875-017-0390-x. Epub 2017 Apr 17. No abstract available.

12.

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
13.

The role of Kenya in the trans-African spread of maize streak virus strain A.

Pande D, Madzokere E, Hartnady P, Kraberger S, Hadfield J, Rosario K, Jäschke A, Monjane AL, Owor BE, Dida MM, Shepherd DN, Martin DP, Varsani A, Harkins GW.

Virus Res. 2017 Mar 15;232:69-76. doi: 10.1016/j.virusres.2017.02.005. Epub 2017 Feb 9.

PMID:
28192163
14.

A Biobank of Breast Cancer Explants with Preserved Intra-tumor Heterogeneity to Screen Anticancer Compounds.

Bruna A, Rueda OM, Greenwood W, Batra AS, Callari M, Batra RN, Pogrebniak K, Sandoval J, Cassidy JW, Tufegdzic-Vidakovic A, Sammut SJ, Jones L, Provenzano E, Baird R, Eirew P, Hadfield J, Eldridge M, McLaren-Douglas A, Barthorpe A, Lightfoot H, O'Connor MJ, Gray J, Cortes J, Baselga J, Marangoni E, Welm AL, Aparicio S, Serra V, Garnett MJ, Caldas C.

Cell. 2016 Sep 22;167(1):260-274.e22. doi: 10.1016/j.cell.2016.08.041. Epub 2016 Sep 15.

15.

Emergence of host-adapted Salmonella Enteritidis through rapid evolution in an immunocompromised host.

Klemm EJ, Gkrania-Klotsas E, Hadfield J, Forbester JL, Harris SR, Hale C, Heath JN, Wileman T, Clare S, Kane L, Goulding D, Otto TD, Kay S, Doffinger R, Cooke FJ, Carmichael A, Lever AM, Parkhill J, MacLennan CA, Kumararatne D, Dougan G, Kingsley RA.

Nat Microbiol. 2016 Jan 25;1:15023. doi: 10.1038/nmicrobiol.2015.23.

PMID:
27572160
16.

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.

17.

A bit of a mouthful.

Hadfield J, David S.

Nat Rev Microbiol. 2016 Aug 11;14(9):548. doi: 10.1038/nrmicro.2016.124.

PMID:
27510861
18.

Emergence of host-adapted Salmonella Enteritidis through rapid evolution in an immunocompromised host.

Klemm EJ, Gkrania-Klotsas E, Hadfield J, Forbester JL, Harris SR, Hale C, Heath JN, Wileman T, Clare S, Kane L, Goulding D, Otto TD, Kay S, Doffinger R, Cooke FJ, Carmichael A, Lever AM, Parkhill J, MacLennan CA, Kumararatne D, Dougan G, Kingsley RA.

Nat Microbiol. 2016 Mar;1(3). pii: 15023. doi: 10.1038/nmicrobiol.2015.23. Epub 2016 Jan 25.

19.

Bioanalyzer chips can be used interchangeably for many analyses of DNA or RNA.

Davies J, Denyer T, Hadfield J.

Biotechniques. 2016 Apr 1;60(4):197-9. doi: 10.2144/000114403. eCollection 2016 Apr.

20.

Chlamydia trachomatis from Australian Aboriginal people with trachoma are polyphyletic composed of multiple distinctive lineages.

Andersson P, Harris SR, Seth Smith HM, Hadfield J, O'Neill C, Cutcliffe LT, Douglas FP, Asche LV, Mathews JD, Hutton SI, Sarovich DS, Tong SY, Clarke IN, Thomson NR, Giffard PM.

Nat Commun. 2016 Feb 25;7:10688. doi: 10.1038/ncomms10688.

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