• Room 0G.061 - H.S.B

    United Kingdom

Accepting PhD Students

PhD projects

Translational bioinformatics research projects within the domain of stratified medicine. Including: -development of novel methods to facilitate i) data quality control, ii) data integration, and iii) re-analysis of archived datasets; -modelling progression pathways from inflammatory disease to cancer; -developing prognostic and predictive biomarkers associated with molecular subtypes. Projects focus on statistical modelling - unsupervised and supervised learning. Suitable for those with maths/computing/life sciences backgrounds.

20112019

Research output per year

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Research Output

2019

Immune Activation by DNA Damage Predicts Response to Chemotherapy and Survival in Oesophageal Adenocarcinoma

Turkington, R., Knight, L., Blayney, J., Secrier, M., Douglas, R., Parkes, E., Sutton, E., Stevenson, L., McManus, D., Halliday, S., McCavigan, A., Logan, G., Walker, S., Steele, C., Perner, J., Bornscein, J., MacRae, S., Miremadi, A., mccarron, E., McQuaid, S. & 10 others, Arthur, K., James, J., Eatock, M., O'Neill, R., Noble, F., Underwood, T., Harkin, D., Salto-Tellez, M., Fitzgerald, R. C. & Kennedy, R., 09 Mar 2019, In : Gut. 10 p.

Research output: Contribution to journalArticle

Open Access
File
2 Citations (Scopus)
163 Downloads (Pure)
2018

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

Humphries, M., Hynes, S., Bingham, V., Cougot, D., James, J., Patel-Socha, F., Parkes, E., Blayney, J., O'Rorke, M., Irwin, G., McArt, D., Kennedy, R., Mullan, P., McQuaid, S., Salto-Tellez, M. & Buckley, N. E., 17 Dec 2018, In : Journal of Oncology. 2018, 14 p., 2937012.

Research output: Contribution to journalArticle

Open Access
File
6 Citations (Scopus)
239 Downloads (Pure)
Open Access
File
164 Downloads (Pure)

Glucose Transporter 1 Expression as a Marker of Prognosis in Oesophageal Adenocarcinoma

Blayney, J. K., Cairns, L., Li, G., McCabe, N., Stevenson, L., Peters, C. J., Reid, N. B., Spence, V. J., Chisambo, C., McManus, D., James, J., McQuaid, S., Craig, S., Arthur, K., McArt, D., Ong, C-A. J., Lao-Sirieix, P., Hamilton, P., Salto-Tellez, M., Eatock, M. & 4 others, Coleman, H. G., Fitzgerald, R. C., Kennedy, R. D. & Turkington, R. C., 06 Apr 2018, In : Oncotarget.

Research output: Contribution to journalArticle

Open Access
File
10 Citations (Scopus)
173 Downloads (Pure)

Review of Applications of High-Throughput Sequencing in Personalised Medicine: Barriers and Facilitators of Future Progress in Research and Clinical Application

Lightbody, G., Haberland, V., Browne, F., Taggart, L., Zheng, H., Parkes, E. & Blayney, J. K., 31 Jul 2018, In : Briefings in Bioinformatics.

Research output: Contribution to journalArticle

Open Access
File
6 Citations (Scopus)
437 Downloads (Pure)
2017

Association of a DNA damage response deficiency (DDRD) assay with prognosis in resected esophageal and gastric adenocarcinoma

Turkington, R., Knight, L., Douglas, R., Blayney, J., Stevenson, L., McManus, D., McCavigan, A., Walker, S., Bornschein, J., McRae, S., Noble, F., Underwood, T., O'Neill, R., McQuaid, S., Arthur, K., James, J., Eatock, M., Harkin, D., Fitzgerald, R. C. & Kennedy, R., 01 May 2017, In : Journal of Clinical Oncology : official journal of the American Society of Clinical Oncology. 35, 15_suppl, p. 4026-4026 1 p., 4026.

Research output: Contribution to journalMeeting abstract

Conditional survival probability in patients with resected oesophageal adenocarcinoma receiving neoadjuvant chemotherapy

Turkington, R., Graham, D., Bannon, F., Noble, F., O'Neill, R., Blayney, J., Underwood, T., Kennedy, R. & Fitzgerald, R. C., 11 Oct 2017, In : Annals of oncology : official journal of the European Society for Medical Oncology / ESMO. 27, supp6, p. vi222 1 p.

Research output: Contribution to journalMeeting abstract

Open Access

Molecular Subgroup of Primary Prostate Cancer Presenting with Metastatic Biology

Walker, S. M., Knight, L. A., McCavigan, A. M., Logan, G. E., Berge, V., Sherif, A., Pandha, H., Warren, A. Y., Davidson, C., Uprichard, A., Blayney, J. K., Price, B., Jellema, G. L., Steele, C. J., Svindland, A., McDade, S. S., Eden, C. G., Foster, C., Mills, I. G., Neal, D. E. & 7 others, Mason, M. D., W Kay, E., Waugh, D. J., Harkin, D. P., Watson, R. W., Clarke, N. W. & Kennedy, R. D., 10 Apr 2017, In : European Urology.

Research output: Contribution to journalArticle

Open Access
File
10 Citations (Scopus)
212 Downloads (Pure)

PD-L1 Expression and Response to Neo-Adjuvant Chemotherapy in Esophageal Adenocarcinoma

Parkes, E., Blayney, J., mccarron, E., Douglas, R., Stevenson, L., McManus, D., McQuaid, S., Arthur, K., James, J., Salto-Tellez, M., Noble, F., Underwood, T., O'Neill, R., Fitzgerald, R. C., Kennedy, R. & Turkington, R., 01 May 2017, In : Journal of Clinical Oncology. 35, 15 supplement, p. 4023-4023 4023.

Research output: Contribution to journalMeeting abstract

The Role of High Performance, Grid and Cloud Computing in High-Throughput Sequencing

Lightbody, G., Browne, F., Zheng, H., Haberland, V. & Blayney, J., 19 Jan 2017, 2016 IEEE International Conference on Bioinformatics and Biomedicine (BIBM): Proceedings. 6 p.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Open Access
File
2 Citations (Scopus)
369 Downloads (Pure)
2016

Does the choice of hormone therapy affect medium-term outcomes following radical external beam radiotherapy for localized prostate cancer?

Lyons, C., Blayney, J., Mitchell, D. M., Harney, J. A., McAleese, J., Shum, L., Stewart, D. P., Jain, S. & O'Sullivan, J., 2016, In : Journal of Clinical Oncology. 34, 15 supplement, p. e16588-e16588 1 p., 16588.

Research output: Contribution to journalMeeting abstract

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

Dunne, P. D., Dasgupta, S., Blayney, J. K., McArt, D. G., Redmond, K. L., Weir, J-A., Bradley, C. A., Sasazuki, T., Shirasawa, S., Wang, T., Srivastava, S., Ong, C. W., Arthur, K., Salto-Tellez, M., Wilson, R. H., Johnston, P. G. & Van Schaeybroeck, S., 01 Jan 2016, In : Clinical Cancer Research. 22, 1, p. 230-242 13 p.

Research output: Contribution to journalArticle

54 Citations (Scopus)

Prior knowledge transfer across transcriptional data sets and technologies using compositional statistics yields new mislabelled ovarian cell line

Blayney, J. K., Davison, T., McCabe, N., Walker, S., Keating, K., Delaney, T., Greenan, C., Williams, A. R., McCluggage, W. G., Capes-Davis, A., Harkin, D. P., Gourley, C. & Kennedy, R. D., 28 Jun 2016, In : Nucleic Acids Research. 10 p.

Research output: Contribution to journalArticle

Open Access
File
4 Citations (Scopus)
221 Downloads (Pure)
2015

Biomarker Discovery, High Performance and Cloud Computing: A Comprehensive Review

Blayney, J., Haberland, V., Lightbody, G. & Browne, F., 17 Dec 2015, Bioinformatics and Biomedicine (BIBM), 2015 IEEE International Conference. p. 1514-1519 6 p.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

3 Citations (Scopus)

ID: 263 Loss of IL-6/Stat3 signalling drives metastatic prostate cancer in mice and men

Pencik, J., Schlederer, M., Gruber, W., Unger, C., Walker, S., Chalaris, A., Marie, I., Hassler, M. R., Javaheri, T., Aksov, O., Blayney, J., Mazal, P., Grebien, F., Egger, G., Poli, V., Eferl, R., Kennedy, R., Fend, F., Scharpf, M., Braun, M. & 14 others, Perner, S., Levy, D. E., Malcolm, T., Turner, SD., Haitel, A., Susani, M., Moazzami, A., Rose-John, S., Aberger, F., Merkel, O., Morrigi, R., Culig, Z., Dolznig, H. & Kenner, L., Nov 2015, In : Cytokine. 76, 1, p. 112 1 p.

Research output: Contribution to journalMeeting abstract

PICan: An integromics framework for dynamic cancer biomarker discovery

McArt, D. G., Blayney, J. K., Boyle, D. P., Irwin, G. W., Moran, M., Hutchinson, R. A., Bankhead, P., Kieran, D., Wang, Y., Dunne, P. D., Kennedy, R. D., Mullan, P. B., Harkin, D. P., Catherwood, M. A., James, J. A., Salto-Tellez, M. & Hamilton, P. W., 01 Jun 2015, In : Molecular oncology. 9, 6, p. 1234-1240 7 p.

Research output: Contribution to journalArticle

13 Citations (Scopus)

STAT3 regulated ARF expression suppresses prostate cancer metastasis

Pencik, J., Schlederer, M., Gruber, W., Unger, C., Walker, S. M., Chalaris, A., Marié, I. J., Hassler, M. R., Javaheri, T., Aksoy, O., Blayney, J. K., Prutsch, N., Skucha, A., Herac, M., Krämer, O. H., Mazal, P., Grebien, F., Egger, G., Poli, V., Mikulits, W. & 21 others, Eferl, R., Esterbauer, H., Kennedy, R., Fend, F., Scharpf, M., Braun, M., Perner, S., Levy, D. E., Malcolm, T., Turner, S. D., Haitel, A., Susani, M., Moazzami, A., Rose-John, S., Aberger, F., Merkel, O., Moriggl, R., Culig, Z., Dolznig, H., Kenner, L. & Kennedy, R., 22 Jul 2015, In : Nature Communications. 6, 15 p., 7736.

Research output: Contribution to journalArticle

Open Access
File
69 Citations (Scopus)
168 Downloads (Pure)
2014

ADAM17-Dependent c-MET-STAT3 Signaling Mediates Resistance to MEK Inhibitors in KRAS Mutant Colorectal Cancer

Van Schaeybroeck, S., Kalimutho, M., Dunne, P. D., Carson, R., Allen, W., Jithesh, P. V., Redmond, K. L., Sasazuki, T., Shirasawa, S., Blayney, J., Michieli, P., Fenning, C., Lenz, H-J., Lawler, M., Longley, D. B. & Johnston, P. G., 26 Jun 2014, In : Cell Reports. 7, 6, p. 1940-1955 16 p.

Research output: Contribution to journalArticle

Open Access
File
52 Citations (Scopus)
318 Downloads (Pure)

A preoperative clinical staging and metabolic imaging model to predict prognosis in early-stage esophageal adenocarcinoma

Turkington, R. C., Blayney, J. K., Jalil, A., Goody, R. B., Papafili, A., Henderson, C., McManus, D., Johnston, P., Kennedy, R. & Eatock, M. M., 20 Jan 2014, In : Journal of Clinical Oncology. 32, 3 (Suppl), 1 p.

Research output: Contribution to journalMeeting abstract

AXL Is a Key Regulator of Inherent and Chemotherapy-Induced Invasion and Predicts a Poor Clinical Outcome in Early-Stage Colon Cancer

Dunne, P. D., McArt, D. G., Blayney, J. K., Kalimutho, M., Greer, S., Wang, T., Srivastava, S., Ong, C. W., Arthur, K., Loughrey, M., Redmond, K., Longley, D. B., Salto-Tellez, M., Johnston, P. G. & Van Schaeybroeck, S., 01 Jan 2014, In : Clinical Cancer Research. 20, 1, p. 164-175 12 p.

Research output: Contribution to journalArticle

63 Citations (Scopus)

EpHA2 is an essential driver of invasion and a novel target in KRAS mutant colorectal cancer

Dunne, P., McArt, D., Blayney, J., Dasgupta, S., Salto-Tellez, M., Johnston, P. & Van Schaeybroeck, S., 2014, EpHA2 is an essential driver of invasion and a novel target in KRAS mutant colorectal cancer . Proceedings: AACR Annual Meeting 2014; April 5-9, San Diego, Vol. Abstract 2079.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

EphA2 is an essential driver of invasion downstream of the KRAS signalling cascade in colorectal cancer.

Dunne, P., McArt, D., Blayney, J., Dasgupta, S., Salto-Tellez, M., Johnston, P. & Van Schaeybroeck, S., Nov 2014, EphA2 is an essential driver of invasion downstream of the KRAS signalling cascade in colorectal cancer.. National Cancer Research Institute

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Open Access
File
46 Citations (Scopus)
273 Downloads (Pure)

The Role of the c-MET/HGF Signalling Axis as a Critical Regulator of Invasion and Migration in Colorectal Cancer

Bradley, C., Dunne, P., Redmond, K., McArt, D., Arthur, K., McQuaid, S., Blayney, J., Salto-Tellez, M., Johnston, P. & Van Schaeybroeck, S., Nov 2014, The Role of the c-MET/HGF Signalling Axis as a Critical Regulator of Invasion and Migration in Colorectal Cancer. National Cancer Research Institute

Research output: Chapter in Book/Report/Conference proceedingConference contribution

2013
Open Access
File
21 Citations (Scopus)
405 Downloads (Pure)

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

McArt, D. G., Dunne, P. D., Blayney, J. K., Salto-Tellez, M., Van Schaeybroeck, S., Hamilton, P. W. & Zhang, S. D., Jun 2013, In : PLoS ONE. 8, 6, p. 1-15 15 p., e66902.

Research output: Contribution to journalArticle

Open Access
File
13 Citations (Scopus)
272 Downloads (Pure)
2012

TMAX – a Database System Integrating Tissue Biomarker & Genomic Data

Wang, Y., Kieran, D., Blayney, J., McArt, D., Savage, K., Fennell, D., James, J., Salto-Tellez, M. & Hamilton, P., 2012.

Research output: Contribution to conferencePaper

2011

Gene Expression Meta-Analysis Identifies VDAC1 as a Predictor of Poor Outcome in Early Stage Non-Small Cell Lung Cancer

Grills, C., Jithesh, P., Blayney, J., Zhang, S-D. & Fennell, D., Jan 2011, In : PLoS ONE. 6, 1, p. e14635 1 p., e14635.

Research output: Contribution to journalArticle

40 Citations (Scopus)

PARP inhibition induces BAX/BAK-independent synthetic lethality of BRCA1-deficient non-small cell lung cancer

Paul, I., Savage, K., Blayney, J., Lamers-Schmidt, E., Gately, K., Kerr, K., Sheaff, M., Arthur, K., Richard, D. J., Hamilton, P., James, J., O'Byrne, K. J., Harkin, P., Quinn, J. E. & Fennell, D., Aug 2011, In : Journal of Pathology. 224, 4, p. 564-574 11 p.

Research output: Contribution to journalArticle

25 Citations (Scopus)

Profiling of the BRCA1 transcriptome through microarray and ChIP-chip analysis

Gorski, J. J., Savage, K. I., Mulligan, J. M., McDade, S. S., Blayney, J. K., Ge, Z. & Harkin, P., 01 Dec 2011, In : Nucleic Acids Research. 39, 22, p. 9536-9548 13 p.

Research output: Contribution to journalArticle

38 Citations (Scopus)