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Items: 21

1.

Evaluating stably expressed genes in single cells.

Lin Y, Ghazanfar S, Strbenac D, Wang A, Patrick E, Lin DM, Speed T, Yang JYH, Yang P.

Gigascience. 2019 Sep 1;8(9). pii: giz106. doi: 10.1093/gigascience/giz106.

2.

Melanoma Explorer: a web application to allow easy reanalysis of publicly available and clinically annotated melanoma omics data sets.

Strbenac D, Wang K, Wang X, Dong J, Mann GJ, Mueller S, Yang JYH.

Melanoma Res. 2019 Jun;29(3):342-344. doi: 10.1097/CMR.0000000000000533.

PMID:
31026248
3.

DCARS: differential correlation across ranked samples.

Ghazanfar S, Strbenac D, Ormerod JT, Yang JYH, Patrick E.

Bioinformatics. 2019 Mar 1;35(5):823-829. doi: 10.1093/bioinformatics/bty698.

PMID:
30102408
4.

Quantitative Performance Evaluator for Proteomics (QPEP): Web-based Application for Reproducible Evaluation of Proteomics Preprocessing Methods.

Strbenac D, Zhong L, Raftery MJ, Wang P, Wilson SR, Armstrong NJ, Yang JYH.

J Proteome Res. 2017 Jul 7;16(7):2359-2369. doi: 10.1021/acs.jproteome.6b00882. Epub 2017 Jun 5.

PMID:
28580786
5.

Nodal and BMP expression during the transition to pentamery in the sea urchin Heliocidaris erythrogramma: insights into patterning the enigmatic echinoderm body plan.

Koop D, Cisternas P, Morris VB, Strbenac D, Yang JY, Wray GA, Byrne M.

BMC Dev Biol. 2017 Feb 13;17(1):4. doi: 10.1186/s12861-017-0145-1.

6.

Differential distribution improves gene selection stability and has competitive classification performance for patient survival.

Strbenac D, Mann GJ, Yang JY, Ormerod JT.

Nucleic Acids Res. 2016 Jul 27;44(13):e119. doi: 10.1093/nar/gkw444. Epub 2016 May 17.

7.

PD-L1 Negative Status is Associated with Lower Mutation Burden, Differential Expression of Immune-Related Genes, and Worse Survival in Stage III Melanoma.

Madore J, Strbenac D, Vilain R, Menzies AM, Yang JY, Thompson JF, Long GV, Mann GJ, Scolyer RA, Wilmott JS.

Clin Cancer Res. 2016 Aug 1;22(15):3915-23. doi: 10.1158/1078-0432.CCR-15-1714. Epub 2016 Mar 9.

8.

Targeting activating mutations of EZH2 leads to potent cell growth inhibition in human melanoma by derepression of tumor suppressor genes.

Tiffen JC, Gunatilake D, Gallagher SJ, Gowrishankar K, Heinemann A, Cullinane C, Dutton-Regester K, Pupo GM, Strbenac D, Yang JY, Madore J, Mann GJ, Hayward NK, McArthur GA, Filipp FV, Hersey P.

Oncotarget. 2015 Sep 29;6(29):27023-36. doi: 10.18632/oncotarget.4809.

9.

Combining BET and HDAC inhibitors synergistically induces apoptosis of melanoma and suppresses AKT and YAP signaling.

Heinemann A, Cullinane C, De Paoli-Iseppi R, Wilmott JS, Gunatilake D, Madore J, Strbenac D, Yang JY, Gowrishankar K, Tiffen JC, Prinjha RK, Smithers N, McArthur GA, Hersey P, Gallagher SJ.

Oncotarget. 2015 Aug 28;6(25):21507-21.

10.

Transcriptomic analysis of Nodal- and BMP-associated genes during juvenile development of the sea urchin Heliocidaris erythrogramma.

Byrne M, Koop D, Cisternas P, Strbenac D, Yang JY, Wray GA.

Mar Genomics. 2015 Dec;24 Pt 1:41-5. doi: 10.1016/j.margen.2015.05.019. Epub 2015 Jun 9.

PMID:
26066611
11.

ClassifyR: an R package for performance assessment of classification with applications to transcriptomics.

Strbenac D, Mann GJ, Ormerod JT, Yang JY.

Bioinformatics. 2015 Jun 1;31(11):1851-3. doi: 10.1093/bioinformatics/btv066. Epub 2015 Feb 1.

PMID:
25644269
12.

Wnt inhibitory factor 1 (WIF1) is a marker of osteoblastic differentiation stage and is not silenced by DNA methylation in osteosarcoma.

Baker EK, Taylor S, Gupte A, Chalk AM, Bhattacharya S, Green AC, Martin TJ, Strbenac D, Robinson MD, Purton LE, Walkley CR.

Bone. 2015 Apr;73:223-32. doi: 10.1016/j.bone.2014.12.063. Epub 2015 Jan 5.

PMID:
25571841
13.

Detection and classification of peaks in 5' cap RNA sequencing data.

Strbenac D, Armstrong NJ, Yang JY.

BMC Genomics. 2013;14 Suppl 5:S9. doi: 10.1186/1471-2164-14-S5-S9. Epub 2013 Oct 16.

14.

Regional activation of the cancer genome by long-range epigenetic remodeling.

Bert SA, Robinson MD, Strbenac D, Statham AL, Song JZ, Hulf T, Sutherland RL, Coolen MW, Stirzaker C, Clark SJ.

Cancer Cell. 2013 Jan 14;23(1):9-22. doi: 10.1016/j.ccr.2012.11.006. Epub 2012 Dec 13.

15.

Copy-number-aware differential analysis of quantitative DNA sequencing data.

Robinson MD, Strbenac D, Stirzaker C, Statham AL, Song J, Speed TP, Clark SJ.

Genome Res. 2012 Dec;22(12):2489-96. doi: 10.1101/gr.139055.112. Epub 2012 Aug 9.

16.

Savant Genome Browser 2: visualization and analysis for population-scale genomics.

Fiume M, Smith EJ, Brook A, Strbenac D, Turner B, Mezlini AM, Robinson MD, Wodak SJ, Brudno M.

Nucleic Acids Res. 2012 Jul;40(Web Server issue):W615-21. doi: 10.1093/nar/gks427. Epub 2012 May 25.

17.

Acetylation of H2A.Z is a key epigenetic modification associated with gene deregulation and epigenetic remodeling in cancer.

Vald├ęs-Mora F, Song JZ, Statham AL, Strbenac D, Robinson MD, Nair SS, Patterson KI, Tremethick DJ, Stirzaker C, Clark SJ.

Genome Res. 2012 Feb;22(2):307-21. doi: 10.1101/gr.118919.110. Epub 2011 Jul 25.

18.

Discovery pipeline for epigenetically deregulated miRNAs in cancer: integration of primary miRNA transcription.

Hulf T, Sibbritt T, Wiklund ED, Bert S, Strbenac D, Statham AL, Robinson MD, Clark SJ.

BMC Genomics. 2011 Jan 21;12:54. doi: 10.1186/1471-2164-12-54.

19.

Evaluation of affinity-based genome-wide DNA methylation data: effects of CpG density, amplification bias, and copy number variation.

Robinson MD, Stirzaker C, Statham AL, Coolen MW, Song JZ, Nair SS, Strbenac D, Speed TP, Clark SJ.

Genome Res. 2010 Dec;20(12):1719-29. doi: 10.1101/gr.110601.110. Epub 2010 Nov 2. Erratum in: Genome Res. 2011 Jan;21(1):146.

20.

Comparison of methyl-DNA immunoprecipitation (MeDIP) and methyl-CpG binding domain (MBD) protein capture for genome-wide DNA methylation analysis reveal CpG sequence coverage bias.

Nair SS, Coolen MW, Stirzaker C, Song JZ, Statham AL, Strbenac D, Robinson MD, Clark SJ.

Epigenetics. 2011 Jan;6(1):34-44. doi: 10.4161/epi.6.1.13313. Epub 2011 Jan 1.

PMID:
20818161
21.

Repitools: an R package for the analysis of enrichment-based epigenomic data.

Statham AL, Strbenac D, Coolen MW, Stirzaker C, Clark SJ, Robinson MD.

Bioinformatics. 2010 Jul 1;26(13):1662-3. doi: 10.1093/bioinformatics/btq247. Epub 2010 May 10.

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