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Items: 48

1.

ACE: A Workbench Using Evolutionary Genetic Algorithms for Analyzing Association in TCGA.

Gilmore AR, Alderdice M, Savage KI, O'Reilly PG, Roddy AC, Dunne PD, Lawler M, McDade SS, Waugh DJ, McArt DG.

Cancer Res. 2019 Apr 15;79(8):2072-2075. doi: 10.1158/0008-5472.CAN-18-1976. Epub 2019 Feb 13.

PMID:
30760519
2.

Automated Tumour Recognition and Digital Pathology Scoring Unravels New Role for PD-L1 in Predicting Good Outcome in ER-/HER2+ Breast Cancer.

Humphries MP, Hynes S, Bingham V, Cougot D, James J, Patel-Socha F, Parkes EE, Blayney JK, O'Rorke MA, Irwin GW, McArt DG, Kennedy RD, Mullan PB, McQuaid S, Salto-Tellez M, Buckley NE.

J Oncol. 2018 Dec 17;2018:2937012. doi: 10.1155/2018/2937012. eCollection 2018.

3.

Impact of Variable RNA-Sequencing Depth on Gene Expression Signatures and Target Compound Robustness: Case Study Examining Brain Tumor (Glioma) Disease Progression.

Stupnikov A, O'Reilly PG, McInerney CE, Roddy AC, Dunne PD, Gilmore A, Ellis HP, Flannery T, Healy E, McIntosh SA, Savage K, Kurian KM, Emmert-Streib F, Prise KM, Salto-Tellez M, McArt DG.

JCO Precis Oncol. 2018 Sep 13;2. doi: 10.1200/PO.18.00014.

4.

Transcriptional subtyping and CD8 immunohistochemistry identifies poor prognosis stage II/III colorectal cancer patients who benefit from adjuvant chemotherapy.

Allen WL, Dunne PD, McDade S, Scanlon E, Loughrey M, Coleman H, McCann C, McLaughlin K, Nemeth Z, Syed N, Jithesh P, Arthur K, Wilson R, Coyle V, McArt D, Murray GI, Samuel L, Nuciforo P, Jimenez J, Argiles G, Dienstmann R, Tabernero J, Messerini L, Nobili S, Mini E, Sheahan K, Ryan E, Johnston PG, Van Schaeybroeck S, Lawler M, Longley DB.

JCO Precis Oncol. 2018 Jun 13;2018. doi: 10.1200/PO.17.00241.

5.

Development and Validation of a 28-gene Hypoxia-related Prognostic Signature for Localized Prostate Cancer.

Yang L, Roberts D, Takhar M, Erho N, Bibby BAS, Thiruthaneeswaran N, Bhandari V, Cheng WC, Haider S, McCorry AMB, McArt D, Jain S, Alshalalfa M, Ross A, Schaffer E, Den RB, Jeffrey Karnes R, Klein E, Hoskin PJ, Freedland SJ, Lamb AD, Neal DE, Buffa FM, Bristow RG, Boutros PC, Davicioni E, Choudhury A, West CML.

EBioMedicine. 2018 May;31:182-189. doi: 10.1016/j.ebiom.2018.04.019. Epub 2018 Apr 23.

6.

Glucose transporter 1 expression as a marker of prognosis in oesophageal adenocarcinoma.

Blayney JK, Cairns L, Li G, McCabe N, Stevenson L, Peters CJ, Reid NB, Spence VJ, Chisambo C, McManus D, James J, McQuaid S, Craig S, Arthur K, McArt D, Ong CJ, Lao-Sirieix P, Hamilton P, Salto-Tellez M, Eatock M, Coleman HG, Fitzgerald RC, Kennedy RD, Turkington RC; Oesophageal Cancer Clinical and Molecular Stratification (OCCAMS) Study Group.

Oncotarget. 2018 Apr 6;9(26):18518-18528. doi: 10.18632/oncotarget.24906. eCollection 2018 Apr 6.

7.

Depletion of DNMT1 in differentiated human cells highlights key classes of sensitive genes and an interplay with polycomb repression.

O'Neill KM, Irwin RE, Mackin SJ, Thursby SJ, Thakur A, Bertens C, Masala L, Loughery JEP, McArt DG, Walsh CP.

Epigenetics Chromatin. 2018 Mar 29;11(1):12. doi: 10.1186/s13072-018-0182-4.

8.

Bcl-xL as a poor prognostic biomarker and predictor of response to adjuvant chemotherapy specifically in BRAF-mutant stage II and III colon cancer.

Dunne PD, Coleman HG, Bankhead P, Alderdice M, Gray RT, McQuaid S, Bingham V, Loughrey MB, James JA, McCorry AMB, Gilmore A, Holohan C, Klingbiel D, Tejpar S, Johnston PG, McArt DG, Di Nicolantonio F, Longley DB, Lawler M.

Oncotarget. 2018 Feb 13;9(17):13834-13847. doi: 10.18632/oncotarget.24481. eCollection 2018 Mar 2.

9.

Prospective patient stratification into robust cancer-cell intrinsic subtypes from colorectal cancer biopsies.

Alderdice M, Richman SD, Gollins S, Stewart JP, Hurt C, Adams R, McCorry AM, Roddy AC, Vimalachandran D, Isella C, Medico E, Maughan T, McArt DG, Lawler M, Dunne PD.

J Pathol. 2018 May;245(1):19-28. doi: 10.1002/path.5051. Epub 2018 Mar 25.

10.

Integrated tumor identification and automated scoring minimizes pathologist involvement and provides new insights to key biomarkers in breast cancer.

Bankhead P, Fernández JA, McArt DG, Boyle DP, Li G, Loughrey MB, Irwin GW, Harkin DP, James JA, McQuaid S, Salto-Tellez M, Hamilton PW.

Lab Invest. 2018 Jan;98(1):15-26. doi: 10.1038/labinvest.2017.131. Epub 2017 Dec 18.

11.

QuPath: Open source software for digital pathology image analysis.

Bankhead P, Loughrey MB, Fernández JA, Dombrowski Y, McArt DG, Dunne PD, McQuaid S, Gray RT, Murray LJ, Coleman HG, James JA, Salto-Tellez M, Hamilton PW.

Sci Rep. 2017 Dec 4;7(1):16878. doi: 10.1038/s41598-017-17204-5.

12.

Validation of a Metastatic Assay using biopsies to improve risk stratification in patients with prostate cancer treated with radical radiation therapy.

Jain S, Lyons CA, Walker SM, McQuaid S, Hynes SO, Mitchell DM, Pang B, Logan GE, McCavigan AM, O'Rourke D, McArt DG, McDade SS, Mills IG, Prise KM, Knight LA, Steele CJ, Medlow PW, Berge V, Katz B, Loblaw DA, Harkin DP, James JA, O'Sullivan JM, Kennedy RD, Waugh DJ.

Ann Oncol. 2018 Jan 1;29(1):215-222. doi: 10.1093/annonc/mdx637.

13.

IHC-based subcellular quantification provides new insights into prognostic relevance of FLIP and procaspase-8 in non-small-cell lung cancer.

Hutchinson RA, Coleman HG, Gately K, Young V, Nicholson S, Cummins R, Kay E, Hynes SO, Dunne PD, Senevirathne S, Hamilton PW, McArt DG, Longley DB.

Cell Death Discov. 2017 Aug 14;3:17050. doi: 10.1038/cddiscovery.2017.50. eCollection 2017.

14.

Natural killer-like signature observed post therapy in locally advanced rectal cancer is a determinant of pathological response and improved survival.

Alderdice M, Dunne PD, Cole AJ, O'Reilly PG, McArt DG, Bingham V, Fuchs MA, McQuaid S, Loughrey MB, Murray GI, Samuel LM, Lawler M, Wilson RH, Salto-Tellez M, Coyle VM.

Mod Pathol. 2017 Sep;30(9):1287-1298. doi: 10.1038/modpathol.2017.47. Epub 2017 Jun 16.

15.

Cancer-cell intrinsic gene expression signatures overcome intratumoural heterogeneity bias in colorectal cancer patient classification.

Dunne PD, Alderdice M, O'Reilly PG, Roddy AC, McCorry AMB, Richman S, Maughan T, McDade SS, Johnston PG, Longley DB, Kay E, McArt DG, Lawler M.

Nat Commun. 2017 May 31;8:15657. doi: 10.1038/ncomms15657.

16.

KRAS mutant colorectal cancer gene signatures identified angiotensin II receptor blockers as potential therapies.

Wen Q, Dunne PD, O'Reilly PG, Li G, Bjourson AJ, McArt DG, Hamilton PW, Zhang SD.

Oncotarget. 2017 Jan 10;8(2):3206-3225. doi: 10.18632/oncotarget.13884.

17.

Transcriptional upregulation of c-MET is associated with invasion and tumor budding in colorectal cancer.

Bradley CA, Dunne PD, Bingham V, McQuaid S, Khawaja H, Craig S, James J, Moore WL, McArt DG, Lawler M, Dasgupta S, Johnston PG, Van Schaeybroeck S.

Oncotarget. 2016 Nov 29;7(48):78932-78945. doi: 10.18632/oncotarget.12933.

18.

samExploreR: exploring reproducibility and robustness of RNA-seq results based on SAM files.

Stupnikov A, Tripathi S, de Matos Simoes R, McArt D, Salto-Tellez M, Glazko G, Dehmer M, Emmert-Streib F.

Bioinformatics. 2016 Nov 1;32(21):3345-3347. Epub 2016 Jul 10.

PMID:
27402900
19.

Building a 'Repository of Science': The importance of integrating biobanks within molecular pathology programmes.

Lewis C, McQuaid S, Hamilton PW, Salto-Tellez M, McArt D, James JA.

Eur J Cancer. 2016 Nov;67:191-199. doi: 10.1016/j.ejca.2016.08.009. Epub 2016 Sep 24. Review.

PMID:
27677055
20.

Embracing an integromic approach to tissue biomarker research in cancer: Perspectives and lessons learned.

Li G, Bankhead P, Dunne PD, O'Reilly PG, James JA, Salto-Tellez M, Hamilton PW, McArt DG.

Brief Bioinform. 2017 Jul 1;18(4):634-646. doi: 10.1093/bib/bbw044.

21.

Immune-Derived PD-L1 Gene Expression Defines a Subgroup of Stage II/III Colorectal Cancer Patients with Favorable Prognosis Who May Be Harmed by Adjuvant Chemotherapy.

Dunne PD, McArt DG, O'Reilly PG, Coleman HG, Allen WL, Loughrey M, Van Schaeybroeck S, McDade S, Salto-Tellez M, Longley DB, Lawler M, Johnston PG.

Cancer Immunol Res. 2016 Jul;4(7):582-91. doi: 10.1158/2326-6066.CIR-15-0302. Epub 2016 May 13.

22.

Stratified analysis reveals chemokine-like factor (CKLF) as a potential prognostic marker in the MSI-immune consensus molecular subtype CMS1 of colorectal cancer.

Dunne PD, O'Reilly PG, Coleman HG, Gray RT, Longley DB, Johnston PG, Salto-Tellez M, Lawler M, McArt DG.

Oncotarget. 2016 Jun 14;7(24):36632-36644. doi: 10.18632/oncotarget.9126.

23.

Challenging the Cancer Molecular Stratification Dogma: Intratumoral Heterogeneity Undermines Consensus Molecular Subtypes and Potential Diagnostic Value in Colorectal Cancer.

Dunne PD, McArt DG, Bradley CA, O'Reilly PG, Barrett HL, Cummins R, O'Grady T, Arthur K, Loughrey MB, Allen WL, McDade SS, Waugh DJ, Hamilton PW, Longley DB, Kay EW, Johnston PG, Lawler M, Salto-Tellez M, Van Schaeybroeck S.

Clin Cancer Res. 2016 Aug 15;22(16):4095-104. doi: 10.1158/1078-0432.CCR-16-0032. Epub 2016 May 5.

24.

QUADrATiC: scalable gene expression connectivity mapping for repurposing FDA-approved therapeutics.

O'Reilly PG, Wen Q, Bankhead P, Dunne PD, McArt DG, McPherson S, Hamilton PW, Mills KI, Zhang SD.

BMC Bioinformatics. 2016 May 4;17(1):198. doi: 10.1186/s12859-016-1062-1.

25.

Quantification of HER2 heterogeneity in breast cancer-implications for identification of sub-dominant clones for personalised treatment.

Buckley NE, Forde C, McArt DG, Boyle DP, Mullan PB, James JA, Maxwell P, McQuaid S, Salto-Tellez M.

Sci Rep. 2016 Mar 21;6:23383. doi: 10.1038/srep23383.

26.

Delivering a research-enabled multistakeholder partnership for enhanced patient care at a population level: The Northern Ireland Comprehensive Cancer Program.

Lawler M, Gavin A, Salto-Tellez M, Kennedy RD, Van Schaeybroeck S, Wilson RH, Harkin DP, Grayson M, Boyd RE, Hamilton PW, McArt DG, James J, Robson T, Ladner RD, Prise KM, O'Sullivan JM, Harrison T, Murray L, Johnston PG, Waugh DJ.

Cancer. 2016 Mar 1;122(5):664-73. doi: 10.1002/cncr.29814. Epub 2015 Dec 22. No abstract available.

27.

Molecular classification of non-invasive breast lesions for personalised therapy and chemoprevention.

Buckley N, Boyle D, McArt D, Irwin G, Harkin DP, Lioe T, McQuaid S, James JA, Maxwell P, Hamilton P, Mullan PB, Salto-Tellez M.

Oncotarget. 2015 Dec 22;6(41):43244-54. doi: 10.18632/oncotarget.6525.

28.

Automated tumor analysis for molecular profiling in lung cancer.

Hamilton PW, Wang Y, Boyd C, James JA, Loughrey MB, Hougton JP, Boyle DP, Kelly P, Maxwell P, McCleary D, Diamond J, McArt DG, Tunstall J, Bankhead P, Salto-Tellez M.

Oncotarget. 2015 Sep 29;6(29):27938-52. doi: 10.18632/oncotarget.4391.

29.

Comprehensive molecular pathology analysis of small bowel adenocarcinoma reveals novel targets with potential for clinical utility.

Alvi MA, McArt DG, Kelly P, Fuchs MA, Alderdice M, McCabe CM, Bingham V, McGready C, Tripathi S, Emmert-Streib F, Loughrey MB, McQuaid S, Maxwell P, Hamilton PW, Turkington R, James JA, Wilson RH, Salto-Tellez M.

Oncotarget. 2015 Aug 28;6(25):20863-74.

30.

EphA2 Expression Is a Key Driver of Migration and Invasion and a Poor Prognostic Marker in Colorectal Cancer.

Dunne PD, Dasgupta S, Blayney JK, McArt DG, Redmond KL, Weir JA, Bradley CA, Sasazuki T, Shirasawa S, Wang T, Srivastava S, Ong CW, Arthur K, Salto-Tellez M, Wilson RH, Johnston PG, Van Schaeybroeck S.

Clin Cancer Res. 2016 Jan 1;22(1):230-242. doi: 10.1158/1078-0432.CCR-15-0603. Epub 2015 Aug 17.

31.

p16 as a prognostic indicator in ovarian/tubal high-grade serous carcinoma.

Beirne JP, McArt DG, James JA, Salto-Tellez M, Maxwell P, McCluggage WG.

Histopathology. 2016 Mar;68(4):615-8. doi: 10.1111/his.12777. Epub 2015 Sep 13. No abstract available.

PMID:
26173002
32.

Epidermal growth factor receptor immunohistochemistry: new opportunities in metastatic colorectal cancer.

Hutchinson RA, Adams RA, McArt DG, Salto-Tellez M, Jasani B, Hamilton PW.

J Transl Med. 2015 Jul 7;13:217. doi: 10.1186/s12967-015-0531-z. Review.

33.

The prognostic value of the stem-like group in colorectal cancer using a panel of immunohistochemistry markers.

Ong CW, Chong PY, McArt DG, Chan JY, Tan HT, Kumar AP, Chung MC, Clément MV, Soong R, Van Schaeybroeck S, Waugh DJ, Johnston PG, Dunne PD, Salto-Tellez M.

Oncotarget. 2015 May 20;6(14):12763-73.

34.

PICan: An integromics framework for dynamic cancer biomarker discovery.

McArt DG, Blayney JK, Boyle DP, Irwin GW, Moran M, Hutchinson RA, Bankhead P, Kieran D, Wang Y, Dunne PD, Kennedy RD, Mullan PB, Harkin DP, Catherwood MA, James JA, Salto-Tellez M, Hamilton PW.

Mol Oncol. 2015 Jun;9(6):1234-40. doi: 10.1016/j.molonc.2015.02.002. Epub 2015 Mar 4.

35.

Analysis of wntless (WLS) expression in gastric, ovarian, and breast cancers reveals a strong association with HER2 overexpression.

Stewart J, James J, McCluggage GW, McQuaid S, Arthur K, Boyle D, Mullan P, McArt D, Yan B, Irwin G, Harkin DP, Zhengdeng L, Ong CW, Yu J, Virshup DM, Salto-Tellez M.

Mod Pathol. 2015 Mar;28(3):428-36. doi: 10.1038/modpathol.2014.114. Epub 2014 Sep 26.

36.

Digital pathology and image analysis in tissue biomarker research.

Hamilton PW, Bankhead P, Wang Y, Hutchinson R, Kieran D, McArt DG, James J, Salto-Tellez M.

Methods. 2014 Nov;70(1):59-73. doi: 10.1016/j.ymeth.2014.06.015. Epub 2014 Jul 15. Review.

PMID:
25034370
37.

TBX2 represses CST6 resulting in uncontrolled legumain activity to sustain breast cancer proliferation: a novel cancer-selective target pathway with therapeutic opportunities.

D'Costa ZC, Higgins C, Ong CW, Irwin GW, Boyle D, McArt DG, McCloskey K, Buckley NE, Crawford NT, Thiagarajan L, Murray JT, Kennedy RD, Mulligan KA, Harkin DP, Waugh DJ, Scott CJ, Salto-Tellez M, Williams R, Mullan PB.

Oncotarget. 2014 Mar 30;5(6):1609-20.

38.

The prognostic significance of the aberrant extremes of p53 immunophenotypes in breast cancer.

Boyle DP, McArt DG, Irwin G, Wilhelm-Benartzi CS, Lioe TF, Sebastian E, McQuaid S, Hamilton PW, James JA, Mullan PB, Catherwood MA, Harkin DP, Salto-Tellez M.

Histopathology. 2014 Sep;65(3):340-52. doi: 10.1111/his.12398. Epub 2014 Apr 16.

PMID:
24612173
39.

Prognostic and therapeutic relevance of FLIP and procaspase-8 overexpression in non-small cell lung cancer.

Riley JS, Hutchinson R, McArt DG, Crawford N, Holohan C, Paul I, Van Schaeybroeck S, Salto-Tellez M, Johnston PG, Fennell DA, Gately K, O'Byrne K, Cummins R, Kay E, Hamilton P, Stasik I, Longley DB.

Cell Death Dis. 2013 Dec 5;4:e951. doi: 10.1038/cddis.2013.481.

40.

AXL is a key regulator of inherent and chemotherapy-induced invasion and predicts a poor clinical outcome in early-stage colon cancer.

Dunne PD, McArt DG, Blayney JK, Kalimutho M, Greer S, Wang T, Srivastava S, Ong CW, Arthur K, Loughrey M, Redmond K, Longley DB, Salto-Tellez M, Johnston PG, Van Schaeybroeck S.

Clin Cancer Res. 2014 Jan 1;20(1):164-75. doi: 10.1158/1078-0432.CCR-13-1354. Epub 2013 Oct 29.

41.

cudaMap: a GPU accelerated program for gene expression connectivity mapping.

McArt DG, Bankhead P, Dunne PD, Salto-Tellez M, Hamilton P, Zhang SD.

BMC Bioinformatics. 2013 Oct 11;14:305. doi: 10.1186/1471-2105-14-305.

42.

Validation of next generation sequencing technologies in comparison to current diagnostic gold standards for BRAF, EGFR and KRAS mutational analysis.

McCourt CM, McArt DG, Mills K, Catherwood MA, Maxwell P, Waugh DJ, Hamilton P, O'Sullivan JM, Salto-Tellez M.

PLoS One. 2013 Jul 26;8(7):e69604. doi: 10.1371/journal.pone.0069604. Print 2013.

43.

Connectivity Mapping for Candidate Therapeutics Identification Using Next Generation Sequencing RNA-Seq Data.

McArt DG, Dunne PD, Blayney JK, Salto-Tellez M, Van Schaeybroeck S, Hamilton PW, Zhang SD.

PLoS One. 2013 Jun 26;8(6):e66902. doi: 10.1371/journal.pone.0066902. Print 2013.

44.

Probation as a setting for building well-being through integrated service provision: evaluating an Offender Health Trainer service.

Dooris M, McArt D, Hurley MA, Baybutt M.

Perspect Public Health. 2013 Jul;133(4):199-206. doi: 10.1177/1757913913486036. Epub 2013 May 13.

PMID:
23670905
45.

Identification of candidate small-molecule therapeutics to cancer by gene-signature perturbation in connectivity mapping.

McArt DG, Zhang SD.

PLoS One. 2011 Jan 31;6(1):e16382. doi: 10.1371/journal.pone.0016382.

46.

Comet sensitivity in assessing DNA damage and repair in different cell cycle stages.

McArt DG, McKerr G, Saetzler K, Howard CV, Downes CS, Wasson GR.

Mutagenesis. 2010 May;25(3):299-303. doi: 10.1093/mutage/geq006. Epub 2010 Feb 16.

PMID:
20159793
47.

Modelling the comet assay.

McArt DG, McKerr G, Howard CV, Saetzler K, Wasson GR.

Biochem Soc Trans. 2009 Aug;37(Pt 4):914-7. doi: 10.1042/BST0370914. Review.

PMID:
19614618
48.

Systematic random sampling of the comet assay.

McArt DG, Wasson GR, McKerr G, Saetzler K, Reed M, Howard CV.

Mutagenesis. 2009 Jul;24(4):373-8. doi: 10.1093/mutage/gep020. Epub 2009 May 28.

PMID:
19477933

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