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Items: 1 to 50 of 215

1.

RNA sequencing: the teenage years.

Stark R, Grzelak M, Hadfield J.

Nat Rev Genet. 2019 Jul 24. doi: 10.1038/s41576-019-0150-2. [Epub ahead of print] Review.

PMID:
31341269
2.

The effects of denitrification parameterization and potential benefits of spatially targeted regulation for the reduction of N-discharges from agriculture.

Sarris TS, Scott DM, Close ME, Humphries B, Moore C, Burbery LF, Rajanayaka C, Barkle G, Hadfield J.

J Environ Manage. 2019 Oct 1;247:299-312. doi: 10.1016/j.jenvman.2019.06.074. Epub 2019 Jun 25.

PMID:
31252229
3.

A baseline assessment of emerging organic contaminants in New Zealand groundwater.

Moreau M, Hadfield J, Hughey J, Sanders F, Lapworth DJ, White D, Civil W.

Sci Total Environ. 2019 Oct 10;686:425-439. doi: 10.1016/j.scitotenv.2019.05.210. Epub 2019 May 18.

4.

Evolutionary epidemiology predicts the emergence of glyphosate resistance in a major agricultural weed.

Comont D, Hicks H, Crook L, Hull R, Cocciantelli E, Hadfield J, Childs D, Freckleton R, Neve P.

New Phytol. 2019 Aug;223(3):1584-1594. doi: 10.1111/nph.15800. Epub 2019 Apr 11.

PMID:
30883786
5.

The evolution of phenotypic plasticity when environments fluctuate in time and space.

King JG, Hadfield JD.

Evol Lett. 2019 Jan 31;3(1):15-27. doi: 10.1002/evl3.100. eCollection 2019 Feb.

6.

Clinical and laboratory-induced colistin-resistance mechanisms in Acinetobacter baumannii.

Boinett CJ, Cain AK, Hawkey J, Do Hoang NT, Khanh NNT, Thanh DP, Dordel J, Campbell JI, Lan NPH, Mayho M, Langridge GC, Hadfield J, Chau NVV, Thwaites GE, Parkhill J, Thomson NR, Holt KE, Baker S.

Microb Genom. 2019 Feb;5(2). doi: 10.1099/mgen.0.000246. Epub 2019 Feb 5.

7.

No evidence for sibling or parent-offspring coadaptation in a wild population of blue tits, despite high power.

Thomson CE, Hadfield JD.

Evolution. 2019 Jan;73(1):28-41. doi: 10.1111/evo.13642. Epub 2018 Nov 27.

8.

Changes in temperature alter the potential outcomes of virus host shifts.

Roberts KE, Hadfield JD, Sharma MD, Longdon B.

PLoS Pathog. 2018 Oct 19;14(10):e1007185. doi: 10.1371/journal.ppat.1007185. eCollection 2018 Oct.

9.

Breed-specific differences in the immune response to lipopolysaccharide in ewes.

Hadfield JM, Bowdridge EC, Holásková I, Elsasser TH, Dailey RA.

J Anim Sci. 2018 Sep 29;96(10):4220-4228. doi: 10.1093/jas/sky288.

PMID:
30107562
10.

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 Dec 1;34(23):4121-4123. doi: 10.1093/bioinformatics/bty407.

11.

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.

12.

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.

13.

RNA-Interference Pathways Display High Rates of Adaptive Protein Evolution in Multiple Invertebrates.

Palmer WH, Hadfield JD, Obbard DJ.

Genetics. 2018 Apr;208(4):1585-1599. doi: 10.1534/genetics.117.300567. Epub 2018 Feb 1.

14.

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
15.

Redefine statistical significance.

Benjamin DJ, Berger JO, Johannesson M, Nosek BA, Wagenmakers EJ, Berk R, Bollen KA, Brembs B, Brown L, Camerer C, Cesarini D, Chambers CD, Clyde M, Cook TD, De Boeck P, Dienes Z, Dreber A, Easwaran K, Efferson C, Fehr E, Fidler F, Field AP, Forster M, George EI, Gonzalez R, Goodman S, Green E, Green DP, Greenwald AG, Hadfield JD, Hedges LV, Held L, Hua Ho T, Hoijtink H, Hruschka DJ, Imai K, Imbens G, Ioannidis JPA, Jeon M, Jones JH, Kirchler M, Laibson D, List J, Little R, Lupia A, Machery E, Maxwell SE, McCarthy M, Moore DA, Morgan SL, Munafó M, Nakagawa S, Nyhan B, Parker TH, Pericchi L, Perugini M, Rouder J, Rousseau J, Savalei V, Schönbrodt FD, Sellke T, Sinclair B, Tingley D, Van Zandt T, Vazire S, Watts DJ, Winship C, Wolpert RL, Xie Y, Young C, Zinman J, Johnson VE.

Nat Hum Behav. 2018 Jan;2(1):6-10. doi: 10.1038/s41562-017-0189-z. No abstract available.

PMID:
30980045
16.

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.

17.

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.

18.

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.

19.

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. Review.

PMID:
29071471
20.

Haematological indices and haematinic levels after mini gastric bypass: a matched comparison with Roux-en-Y gastric bypass.

Madhok BM, Mahawar KK, Hadfield JN, Courtney M, Stubbing-Moore A, Koshy S, Small PK.

Clin Obes. 2018 Feb;8(1):43-49. doi: 10.1111/cob.12227. Epub 2017 Oct 23.

PMID:
29063708
21.

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]

22.

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.

23.

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.

24.

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
25.

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
26.

Estimating the ability of plants to plastically track temperature-mediated shifts in the spring phenological optimum.

Tansey CJ, Hadfield JD, Phillimore AB.

Glob Chang Biol. 2017 Aug;23(8):3321-3334. doi: 10.1111/gcb.13624. Epub 2017 Feb 10.

PMID:
28185374
27.

Tubulin-binding dibenz[c,e]oxepines: Part 2. Structural variation and biological evaluation as tumour vasculature disrupting agents.

Rossington SB, Hadfield JA, Shnyder SD, Wallace TW, Williams KJ.

Bioorg Med Chem. 2017 Mar 1;25(5):1630-1642. doi: 10.1016/j.bmc.2017.01.027. Epub 2017 Jan 19.

PMID:
28143677
28.

Selection on parental performance opposes selection for larger body mass in a wild population of blue tits.

Thomson CE, Bayer F, Crouch N, Farrell S, Heap E, Mittell E, Zurita-Cassinello M, Hadfield JD.

Evolution. 2017 Mar;71(3):716-732. doi: 10.1111/evo.13169. Epub 2017 Feb 10.

PMID:
28106259
29.

Fraud Not a Primary Cause of Irreproducible Results: A Reply to Clark et al.

Parker TH, Forstmeier W, Koricheva J, Fidler F, Hadfield JD, Chee YE, Kelly CD, Gurevitch J, Nakagawa S.

Trends Ecol Evol. 2016 Dec;31(12):900. doi: 10.1016/j.tree.2016.09.004. Epub 2016 Sep 29. No abstract available.

PMID:
27693086
30.

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.

31.

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
32.

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.

33.

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
34.

Transparency in Ecology and Evolution: Real Problems, Real Solutions.

Parker TH, Forstmeier W, Koricheva J, Fidler F, Hadfield JD, Chee YE, Kelly CD, Gurevitch J, Nakagawa S.

Trends Ecol Evol. 2016 Sep;31(9):711-719. doi: 10.1016/j.tree.2016.07.002. Epub 2016 Jul 25.

PMID:
27461041
35.

The spatial scale of local adaptation in a stochastic environment.

Hadfield JD.

Ecol Lett. 2016 Jul;19(7):780-8. doi: 10.1111/ele.12614. Epub 2016 May 18.

PMID:
27188689
36.

Passerines may be sufficiently plastic to track temperature-mediated shifts in optimum lay date.

Phillimore AB, Leech DI, Pearce-Higgins JW, Hadfield JD.

Glob Chang Biol. 2016 Oct;22(10):3259-72. doi: 10.1111/gcb.13302. Epub 2016 May 13.

PMID:
27173755
37.

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.

38.

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.

39.

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

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

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

40.

Rates of organ donation in a UK tertiary cardiac arrest centre following out-of-hospital cardiac arrest.

Cheetham OV, Thomas MJ, Hadfield J, O'Higgins F, Mitchell C, Rooney KD.

Resuscitation. 2016 Apr;101:41-3. doi: 10.1016/j.resuscitation.2016.01.003. Epub 2016 Jan 23.

PMID:
26812522
41.

It's diversity all the way down.

David S, Hadfield J.

Nat Rev Microbiol. 2015 Dec;13(12):740. doi: 10.1038/nrmicro3587. Epub 2015 Nov 9.

PMID:
26548911
42.

Corrigendum: Progesterone receptor modulates ERα action in breast cancer.

Mohammed H, Russell IA, Stark R, Rueda OM, Hickey TE, Tarulli GA, Serandour AA, Birrell SN, Bruna A, Saadi A, Menon S, Hadfield J, Pugh M, Raj GV, Brown GD, D'Santos C, Robinson JL, Silva G, Launchbury R, Perou CM, Stingl J, Caldas C, Tilley WD, Carroll JS.

Nature. 2015 Oct 1;526(7571):144. doi: 10.1038/nature14959. Epub 2015 Aug 5. No abstract available.

PMID:
26245370
43.

Progesterone receptor modulates ERα action in breast cancer.

Mohammed H, Russell IA, Stark R, Rueda OM, Hickey TE, Tarulli GA, Serandour AA, Birrell SN, Bruna A, Saadi A, Menon S, Hadfield J, Pugh M, Raj GV, Brown GD, D'Santos C, Robinson JL, Silva G, Launchbury R, Perou CM, Stingl J, Caldas C, Tilley WD, Carroll JS.

Nature. 2015 Jul 16;523(7560):313-7. doi: 10.1038/nature14583. Epub 2015 Jul 8. Erratum in: Nature. 2015 Oct 1;526(7571):144. Serandour, Aurelien A A[Corrected to Serandour, Aurelien A].

44.

Three-dimensional imaging and uptake of the anticancer drug combretastatin in cell spheroids and photoisomerization in gels with multiphoton excitation.

Scherer KM, Bisby RH, Botchway SW, Hadfield JA, Haycock JW, Parker AW.

J Biomed Opt. 2015 Jul;20(7):78003. doi: 10.1117/1.JBO.20.7.078003.

45.

Heritability of heterozygosity offers a new way of understanding why dominant gene action contributes to additive genetic variance.

Nietlisbach P, Hadfield JD.

Evolution. 2015 Jul;69(7):1948-52. doi: 10.1111/evo.12704. Epub 2015 Jul 14.

PMID:
26100570
46.

Are molecular markers useful predictors of adaptive potential?

Mittell EA, Nakagawa S, Hadfield JD.

Ecol Lett. 2015 Aug;18(8):772-8. doi: 10.1111/ele.12454. Epub 2015 May 18.

PMID:
25989024
47.

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.

48.

The influence of nonrandom extra-pair paternity on heritability estimates derived from wild pedigrees.

Firth JA, Hadfield JD, Santure AW, Slate J, Sheldon BC.

Evolution. 2015 May;69(5):1336-44. doi: 10.1111/evo.12649. Epub 2015 Apr 27.

49.

The causes and consequences of changes in virulence following pathogen host shifts.

Longdon B, Hadfield JD, Day JP, Smith SC, McGonigle JE, Cogni R, Cao C, Jiggins FM.

PLoS Pathog. 2015 Mar 16;11(3):e1004728. doi: 10.1371/journal.ppat.1004728. eCollection 2015 Mar.

50.

Anticancer phototherapy using activation of E-combretastatins by two-photon-induced isomerization.

Scherer KM, Bisby RH, Botchway SW, Hadfield JA, Parker AW.

J Biomed Opt. 2015 May;20(5):051004. doi: 10.1117/1.JBO.20.5.051004.

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