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Items: 27

1.

Inferring Gene Regulatory Networks from Multiple Datasets.

Penfold CA, Gherman I, Sybirna A, Wild DL.

Methods Mol Biol. 2019;1883:251-282. doi: 10.1007/978-1-4939-8882-2_11. Review.

PMID:
30547404
2.

Antibodies to Costimulatory Receptor 4-1BB Enhance Anti-tumor Immunity via T Regulatory Cell Depletion and Promotion of CD8 T Cell Effector Function.

Buchan SL, Dou L, Remer M, Booth SG, Dunn SN, Lai C, Semmrich M, Teige I, Mårtensson L, Penfold CA, Chan HTC, Willoughby JE, Mockridge CI, Dahal LN, Cleary KLS, James S, Rogel A, Kannisto P, Jernetz M, Williams EL, Healy E, Verbeek JS, Johnson PWM, Frendéus B, Cragg MS, Glennie MJ, Gray JC, Al-Shamkhani A, Beers SA.

Immunity. 2018 Nov 20;49(5):958-970.e7. doi: 10.1016/j.immuni.2018.09.014. Epub 2018 Nov 13.

PMID:
30446386
3.

Branch-recombinant Gaussian processes for analysis of perturbations in biological time series.

Penfold CA, Sybirna A, Reid JE, Huang Y, Wernisch L, Ghahramani Z, Grant M, Surani MA.

Bioinformatics. 2018 Sep 1;34(17):i1005-i1013. doi: 10.1093/bioinformatics/bty603.

4.

Comparative transcriptome analysis in Arabidopsis ein2/ore3 and ahk3/ore12 mutants during dark-induced leaf senescence.

Kim J, Park SJ, Lee IH, Chu H, Penfold CA, Kim JH, Buchanan-Wollaston V, Nam HG, Woo HR, Lim PO.

J Exp Bot. 2018 May 25;69(12):3023-3036. doi: 10.1093/jxb/ery137.

5.

Complex Interplay between Epitope Specificity and Isotype Dictates the Biological Activity of Anti-human CD40 Antibodies.

Yu X, Chan HTC, Orr CM, Dadas O, Booth SG, Dahal LN, Penfold CA, O'Brien L, Mockridge CI, French RR, Duriez P, Douglas LR, Pearson AR, Cragg MS, Tews I, Glennie MJ, White AL.

Cancer Cell. 2018 Apr 9;33(4):664-675.e4. doi: 10.1016/j.ccell.2018.02.009. Epub 2018 Mar 22.

6.

PD-1 Blockade and CD27 Stimulation Activate Distinct Transcriptional Programs That Synergize for CD8+ T-Cell-Driven Antitumor Immunity.

Buchan SL, Fallatah M, Thirdborough SM, Taraban VY, Rogel A, Thomas LJ, Penfold CA, He LZ, Curran MA, Keler T, Al-Shamkhani A.

Clin Cancer Res. 2018 May 15;24(10):2383-2394. doi: 10.1158/1078-0432.CCR-17-3057. Epub 2018 Mar 7.

7.

Augmentation of CD134 (OX40)-dependent NK anti-tumour activity is dependent on antibody cross-linking.

Turaj AH, Cox KL, Penfold CA, French RR, Mockridge CI, Willoughby JE, Tutt AL, Griffiths J, Johnson PWM, Glennie MJ, Levy R, Cragg MS, Lim SH.

Sci Rep. 2018 Feb 2;8(1):2278. doi: 10.1038/s41598-018-20656-y.

8.

Stella modulates transcriptional and endogenous retrovirus programs during maternal-to-zygotic transition.

Huang Y, Kim JK, Do DV, Lee C, Penfold CA, Zylicz JJ, Marioni JC, Hackett JA, Surani MA.

Elife. 2017 Mar 21;6. pii: e22345. doi: 10.7554/eLife.22345.

9.

Inferring the perturbation time from biological time course data.

Yang J, Penfold CA, Grant MR, Rattray M.

Bioinformatics. 2016 Oct 1;32(19):2956-64. doi: 10.1093/bioinformatics/btw329. Epub 2016 Jun 10.

10.

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.

11.

Transcriptional Dynamics Driving MAMP-Triggered Immunity and Pathogen Effector-Mediated Immunosuppression in Arabidopsis Leaves Following Infection with Pseudomonas syringae pv tomato DC3000.

Lewis LA, Polanski K, de Torres-Zabala M, Jayaraman S, Bowden L, Moore J, Penfold CA, Jenkins DJ, Hill C, Baxter L, Kulasekaran S, Truman W, Littlejohn G, Prusinska J, Mead A, Steinbrenner J, Hickman R, Rand D, Wild DL, Ott S, Buchanan-Wollaston V, Smirnoff N, Beynon J, Denby K, Grant M.

Plant Cell. 2015 Nov;27(11):3038-64. doi: 10.1105/tpc.15.00471. Epub 2015 Nov 13.

12.

Development and Characterization of Monoclonal Antibodies Specific for Mouse and Human Fcγ Receptors.

Tutt AL, James S, Laversin SA, Tipton TR, Ashton-Key M, French RR, Hussain K, Vaughan AT, Dou L, Earley A, Dahal LN, Lu C, Dunscombe M, Chan HT, Penfold CA, Kim JH, Potter EA, Mockridge CI, Roghanian A, Oldham RJ, Cox KL, Lim SH, Teige I, Frendéus B, Glennie MJ, Beers SA, Cragg MS.

J Immunol. 2015 Dec 1;195(11):5503-16. doi: 10.4049/jimmunol.1402988. Epub 2015 Oct 28.

13.

Inferring orthologous gene regulatory networks using interspecies data fusion.

Penfold CA, Millar JB, Wild DL.

Bioinformatics. 2015 Jun 15;31(12):i97-105. doi: 10.1093/bioinformatics/btv267.

14.

CSI: a nonparametric Bayesian approach to network inference from multiple perturbed time series gene expression data.

Penfold CA, Shifaz A, Brown PE, Nicholson A, Wild DL.

Stat Appl Genet Mol Biol. 2015 Jun;14(3):307-10. doi: 10.1515/sagmb-2014-0082.

PMID:
26030796
15.

Conformation of the human immunoglobulin G2 hinge imparts superagonistic properties to immunostimulatory anticancer antibodies.

White AL, Chan HT, French RR, Willoughby J, Mockridge CI, Roghanian A, Penfold CA, Booth SG, Dodhy A, Polak ME, Potter EA, Ardern-Jones MR, Verbeek JS, Johnson PW, Al-Shamkhani A, Cragg MS, Beers SA, Glennie MJ.

Cancer Cell. 2015 Jan 12;27(1):138-48. doi: 10.1016/j.ccell.2014.11.001. Epub 2014 Dec 11.

16.

Correcting for link loss in causal network inference caused by regulator interference.

Wang Y, Penfold CA, Hodgson DA, Gifford ML, Burroughs NJ.

Bioinformatics. 2014 Oct;30(19):2779-86. doi: 10.1093/bioinformatics/btu388. Epub 2014 Jun 19.

17.

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
18.

Modelling transcriptional networks in leaf senescence.

Penfold CA, Buchanan-Wollaston V.

J Exp Bot. 2014 Jul;65(14):3859-73. doi: 10.1093/jxb/eru054. Epub 2014 Mar 5. Review.

PMID:
24600015
19.

Immunotherapy targeting inhibitory Fcγ receptor IIB (CD32b) in the mouse is limited by monoclonal antibody consumption and receptor internalization.

Williams EL, Tutt AL, Beers SA, French RR, Chan CH, Cox KL, Roghanian A, Penfold CA, Butts CL, Boross P, Verbeek JS, Cragg MS, Glennie MJ.

J Immunol. 2013 Oct 15;191(8):4130-40. doi: 10.4049/jimmunol.1301430. Epub 2013 Sep 11.

20.

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.

21.

How to infer gene networks from expression profiles, revisited.

Penfold CA, Wild DL.

Interface Focus. 2011 Dec 6;1(6):857-70. doi: 10.1098/rsfs.2011.0053. Epub 2011 Aug 10.

22.

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.

23.

Development and characterisation of monoclonal antibodies specific for the murine inhibitory FcγRIIB (CD32B).

Williams EL, Tutt AL, French RR, Chan HT, Lau B, Penfold CA, Mockridge CI, Roghanian A, Cox KL, Verbeek JS, Glennie MJ, Cragg MS.

Eur J Immunol. 2012 Aug;42(8):2109-20. doi: 10.1002/eji.201142302. Epub 2012 Jul 4.

24.

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.

25.

Modeling meiotic chromosomes indicates a size dependent contribution of telomere clustering and chromosome rigidity to homologue juxtaposition.

Penfold CA, Brown PE, Lawrence ND, Goldman AS.

PLoS Comput Biol. 2012;8(5):e1002496. doi: 10.1371/journal.pcbi.1002496. Epub 2012 May 3.

26.

High-resolution temporal profiling of transcripts during Arabidopsis leaf senescence reveals a distinct chronology of processes and regulation.

Breeze E, Harrison E, McHattie S, Hughes L, Hickman R, Hill C, Kiddle S, Kim YS, Penfold CA, Jenkins D, Zhang C, Morris K, Jenner C, Jackson S, Thomas B, Tabrett A, Legaie R, Moore JD, Wild DL, Ott S, Rand D, Beynon J, Denby K, Mead A, Buchanan-Wollaston V.

Plant Cell. 2011 Mar;23(3):873-94. doi: 10.1105/tpc.111.083345. Epub 2011 Mar 29.

27.

Monoclonal antibody therapy of B cell lymphoma: signaling activity on tumor cells appears more important than recruitment of effectors.

Tutt AL, French RR, Illidge TM, Honeychurch J, McBride HM, Penfold CA, Fearon DT, Parkhouse RM, Klaus GG, Glennie MJ.

J Immunol. 1998 Sep 15;161(6):3176-85.

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