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Items: 41

1.

A Framework for Engineering Stress Resilient Plants Using Genetic Feedback Control and Regulatory Network Rewiring.

Foo M, Gherman I, Zhang P, Bates DG, Denby KJ.

ACS Synth Biol. 2018 Jun 15;7(6):1553-1564. doi: 10.1021/acssynbio.8b00037. Epub 2018 May 23.

PMID:
29746091
2.

Predictors of Intravenous Immunoglobulin Nonresponse and Racial Disparities in Kawasaki Disease.

Clark DE, Denby KJ, Kaufman LM, Fill MA, Piya B, Krishnaswami S, Fonnesbeck C, Halasa N.

Pediatr Infect Dis J. 2018 Dec;37(12):1227-1234. doi: 10.1097/INF.0000000000002019.

PMID:
29570178
3.

Bringing numerous methods for expression and promoter analysis to a public cloud computing service.

Polanski K, Gao B, Mason SA, Brown P, Ott S, Denby KJ, Wild DL.

Bioinformatics. 2018 Mar 1;34(5):884-886. doi: 10.1093/bioinformatics/btx692.

4.

Streptococcus intermedius: An Unusual Case of Purulent Pericarditis.

Denby KJ, Byrne RD, Gómez-Duarte OG.

Case Rep Infect Dis. 2017;2017:5864694. doi: 10.1155/2017/5864694. Epub 2017 Aug 28.

5.

Management of Kawasaki disease in adults.

Denby KJ, Clark DE, Markham LW.

Heart. 2017 Nov;103(22):1760-1769. doi: 10.1136/heartjnl-2017-311774. Epub 2017 Jul 27. Review.

PMID:
28751537
6.

The mechanism of a formaldehyde-sensing transcriptional regulator.

Denby KJ, Iwig J, Bisson C, Westwood J, Rolfe MD, Sedelnikova SE, Higgins K, Maroney MJ, Baker PJ, Chivers PT, Green J.

Sci Rep. 2016 Dec 9;6:38879. doi: 10.1038/srep38879.

7.

Insect Gallers and Their Plant Hosts: From Omics Data to Systems Biology.

Oates CN, Denby KJ, Myburg AA, Slippers B, Naidoo S.

Int J Mol Sci. 2016 Nov 18;17(11). pii: E1891. Review.

8.

Time-Series Transcriptomics Reveals That AGAMOUS-LIKE22 Affects Primary Metabolism and Developmental Processes in Drought-Stressed Arabidopsis.

Bechtold U, Penfold CA, Jenkins DJ, Legaie R, Moore JD, Lawson T, Matthews JS, Vialet-Chabrand SR, Baxter L, Subramaniam S, Hickman R, Florance H, Sambles C, Salmon DL, Feil R, Bowden L, Hill C, Baker NR, Lunn JE, Finkenstädt B, Mead A, Buchanan-Wollaston V, Beynon J, Rand DA, Wild DL, Denby KJ, Ott S, Smirnoff N, Mullineaux PM.

Plant Cell. 2016 Feb;28(2):345-66. doi: 10.1105/tpc.15.00910. Epub 2016 Feb 3.

9.

Jasmonate signalling drives time-of-day differences in susceptibility of Arabidopsis to the fungal pathogen Botrytis cinerea.

Ingle RA, Stoker C, Stone W, Adams N, Smith R, Grant M, Carré I, Roden LC, Denby KJ.

Plant J. 2015 Dec;84(5):937-48. doi: 10.1111/tpj.13050. Epub 2015 Nov 21.

10.

Whole genome resequencing of Botrytis cinerea isolates identifies high levels of standing diversity.

Atwell S, Corwin JA, Soltis NE, Subedy A, Denby KJ, Kliebenstein DJ.

Front Microbiol. 2015 Sep 24;6:996. doi: 10.3389/fmicb.2015.00996. eCollection 2015.

11.

Modelling signaling networks underlying plant defence.

Windram O, Denby KJ.

Curr Opin Plant Biol. 2015 Oct;27:165-71. doi: 10.1016/j.pbi.2015.07.007. Epub 2015 Aug 21. Review.

12.

Reassess the t Test: Interact with All Your Data via ANOVA.

Brady SM, Burow M, Busch W, Carlborg Ö, Denby KJ, Glazebrook J, Hamilton ES, Harmer SL, Haswell ES, Maloof JN, Springer NM, Kliebenstein DJ.

Plant Cell. 2015 Aug;27(8):2088-94. doi: 10.1105/tpc.15.00238. Epub 2015 Jul 28.

13.

Adaptation of anaerobic cultures of Escherichia coli K-12 in response to environmental trimethylamine-N-oxide.

Denby KJ, Rolfe MD, Crick E, Sanguinetti G, Poole RK, Green J.

Environ Microbiol. 2015 Jul;17(7):2477-91. doi: 10.1111/1462-2920.12726. Epub 2015 Feb 3.

14.

Increased resistance to biotrophic pathogens in the Arabidopsis constitutive induced resistance 1 mutant is EDS1 and PAD4-dependent and modulated by environmental temperature.

Carstens M, McCrindle TK, Adams N, Diener A, Guzha DT, Murray SL, Parker JE, Denby KJ, Ingle RA.

PLoS One. 2014 Oct 10;9(10):e109853. doi: 10.1371/journal.pone.0109853. eCollection 2014.

15.

Carbon monoxide-releasing molecule-3 (CORM-3; Ru(CO)3Cl(glycinate)) as a tool to study the concerted effects of carbon monoxide and nitric oxide on bacterial flavohemoglobin Hmp: applications and pitfalls.

Tinajero-Trejo M, Denby KJ, Sedelnikova SE, Hassoubah SA, Mann BE, Poole RK.

J Biol Chem. 2014 Oct 24;289(43):29471-82. doi: 10.1074/jbc.M114.573444. Epub 2014 Sep 5.

16.

Network modeling to understand plant immunity.

Windram O, Penfold CA, Denby KJ.

Annu Rev Phytopathol. 2014;52:93-111. doi: 10.1146/annurev-phyto-102313-050103. Epub 2014 May 4. Review.

PMID:
24821185
17.

Wigwams: identifying gene modules co-regulated across multiple biological conditions.

Polanski K, Rhodes J, Hill C, Zhang P, Jenkins DJ, Kiddle SJ, Jironkin A, Beynon J, Buchanan-Wollaston V, Ott S, Denby KJ.

Bioinformatics. 2014 Apr 1;30(7):962-70. doi: 10.1093/bioinformatics/btt728. Epub 2013 Dec 18.

18.

Widening the differential for brain masses in human immunodeficiency virus-positive patients: syphilitic cerebral gummata.

Land AM, Nelson GA, Bell SG, Denby KJ, Estrada CA, Willett LL.

Am J Med Sci. 2013 Sep;346(3):253-5. doi: 10.1097/MAJ.0b013e31828c9f22.

PMID:
23588265
19.

A local regulatory network around three NAC transcription factors in stress responses and senescence in Arabidopsis leaves.

Hickman R, Hill C, Penfold CA, Breeze E, Bowden L, Moore JD, Zhang P, Jackson A, Cooke E, Bewicke-Copley F, Mead A, Beynon J, Wild DL, Denby KJ, Ott S, Buchanan-Wollaston V.

Plant J. 2013 Jul;75(1):26-39. doi: 10.1111/tpj.12194. Epub 2013 May 11.

20.

Gene-for-gene tolerance to bacterial wilt in Arabidopsis.

Van der Linden L, Bredenkamp J, Naidoo S, Fouché-Weich J, Denby KJ, Genin S, Marco Y, Berger DK.

Mol Plant Microbe Interact. 2013 Apr;26(4):398-406. doi: 10.1094/MPMI-07-12-0188-R.

21.

Arabidopsis defense against Botrytis cinerea: chronology and regulation deciphered by high-resolution temporal transcriptomic analysis.

Windram O, Madhou P, McHattie S, Hill C, Hickman R, Cooke E, Jenkins DJ, Penfold CA, Baxter L, Breeze E, Kiddle SJ, Rhodes J, Atwell S, Kliebenstein DJ, Kim YS, Stegle O, Borgwardt K, Zhang C, Tabrett A, Legaie R, Moore J, Finkenstadt B, Wild DL, Mead A, Rand D, Beynon J, Ott S, Buchanan-Wollaston V, Denby KJ.

Plant Cell. 2012 Sep;24(9):3530-57. doi: 10.1105/tpc.112.102046. Epub 2012 Sep 28.

22.

MEDIATOR25 acts as an integrative hub for the regulation of jasmonate-responsive gene expression in Arabidopsis.

Çevik V, Kidd BN, Zhang P, Hill C, Kiddle S, Denby KJ, Holub EB, Cahill DM, Manners JM, Schenk PM, Beynon J, Kazan K.

Plant Physiol. 2012 Sep;160(1):541-55. doi: 10.1104/pp.112.202697. Epub 2012 Jul 22.

23.

Nonparametric Bayesian inference for perturbed and orthologous gene regulatory networks.

Penfold CA, Buchanan-Wollaston V, Denby KJ, Wild DL.

Bioinformatics. 2012 Jun 15;28(12):i233-41. doi: 10.1093/bioinformatics/bts222.

24.

Constitutive expression of a grapevine polygalacturonase-inhibiting protein affects gene expression and cell wall properties in uninfected tobacco.

Alexandersson E, Becker JV, Jacobson D, Nguema-Ona E, Steyn C, Denby KJ, Vivier MA.

BMC Res Notes. 2011 Nov 13;4:493. doi: 10.1186/1756-0500-4-493.

25.

Spatial and temporal transcriptomic analysis of the Arabidopsis thaliana-Botrytis cinerea interaction.

Mulema JM, Denby KJ.

Mol Biol Rep. 2012 Apr;39(4):4039-49. doi: 10.1007/s11033-011-1185-4. Epub 2011 Jul 23.

PMID:
21785916
26.

Inferring the time-invariant topology of a nonlinear sparse gene regulatory network using fully Bayesian spline autoregression.

Morrissey ER, Juárez MA, Denby KJ, Burroughs NJ.

Biostatistics. 2011 Oct;12(4):682-94. doi: 10.1093/biostatistics/kxr009. Epub 2011 May 5.

PMID:
21551122
27.

On reverse engineering of gene interaction networks using time course data with repeated measurements.

Morrissey ER, Juárez MA, Denby KJ, Burroughs NJ.

Bioinformatics. 2010 Sep 15;26(18):2305-12. doi: 10.1093/bioinformatics/btq421. Epub 2010 Jul 16.

PMID:
20639410
28.

A robust Bayesian two-sample test for detecting intervals of differential gene expression in microarray time series.

Stegle O, Denby KJ, Cooke EJ, Wild DL, Ghahramani Z, Borgwardt KM.

J Comput Biol. 2010 Mar;17(3):355-67. doi: 10.1089/cmb.2009.0175.

29.

Temporal clustering by affinity propagation reveals transcriptional modules in Arabidopsis thaliana.

Kiddle SJ, Windram OP, McHattie S, Mead A, Beynon J, Buchanan-Wollaston V, Denby KJ, Mukherjee S.

Bioinformatics. 2010 Feb 1;26(3):355-62. doi: 10.1093/bioinformatics/btp673. Epub 2009 Dec 8.

PMID:
19996165
30.

R/BHC: fast Bayesian hierarchical clustering for microarray data.

Savage RS, Heller K, Xu Y, Ghahramani Z, Truman WM, Grant M, Denby KJ, Wild DL.

BMC Bioinformatics. 2009 Aug 6;10:242. doi: 10.1186/1471-2105-10-242.

31.

OXI1 protein kinase is required for plant immunity against Pseudomonas syringae in Arabidopsis.

Petersen LN, Ingle RA, Knight MR, Denby KJ.

J Exp Bot. 2009;60(13):3727-35. doi: 10.1093/jxb/erp219. Epub 2009 Jul 2.

32.

Granger causality vs. dynamic Bayesian network inference: a comparative study.

Zou C, Denby KJ, Feng J.

BMC Bioinformatics. 2009 Apr 24;10:122. doi: 10.1186/1471-2105-10-122. Erratum in: BMC Bioinformatics. 2009;10:401. Denby, Katherine J [added].

33.
34.

PAMP recognition and the plant-pathogen arms race.

Ingle RA, Carstens M, Denby KJ.

Bioessays. 2006 Sep;28(9):880-9. Review.

PMID:
16937346
35.

The signature of seeds in resurrection plants: a molecular and physiological comparison of desiccation tolerance in seeds and vegetative tissues.

Illing N, Denby KJ, Collett H, Shen A, Farrant JM.

Integr Comp Biol. 2005 Nov;45(5):771-87. doi: 10.1093/icb/45.5.771.

PMID:
21676829
36.
37.
38.

A constitutive PR-1::luciferase expression screen identifies Arabidopsis mutants with differential disease resistance to both biotrophic and necrotrophic pathogens.

Murray SL, Adams N, Kliebenstein DJ, Loake GJ, Denby KJ.

Mol Plant Pathol. 2005 Jan 1;6(1):31-41. doi: 10.1111/j.1364-3703.2004.00261.x.

PMID:
20565636
39.

Identification of Botrytis cinerea susceptibility loci in Arabidopsis thaliana.

Denby KJ, Kumar P, Kliebenstein DJ.

Plant J. 2004 May;38(3):473-86.

40.

Diverse regulatory mechanisms of amino acid biosynthesis in plants.

Denby KJ, Last RL.

Genet Eng (N Y). 1999;21:173-89. Review. No abstract available.

PMID:
10822497
41.

Carbon Catabolite Repression Regulates Glyoxylate Cycle Gene Expression in Cucumber.

Graham IA, Denby KJ, Leaver CJ.

Plant Cell. 1994 May;6(5):761-772.

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