Publications

Publications

Original Research Articles

Microbiome analysis as a platform R&D tool for parasitic nematode disease management. Hogan et al.  ISME Journal, 2019 25 June

 

DNA vaccination via RALA nanoparticles in a microneedle delivery system induces a potent immune response against the endogenous prostate cancer stem cell antigen. Cole et al. Acta Biomater, 2019 9 July

 

ODX: A Fitness Tracker-Based Device for Continuous Bacterial Growth Monitoring. Yallapragada et al. Anal. Chem, 2019 3 September

 

Function2Form Bridge-Toward synthetic protein holistic performance prediction. Yallapragada et al. Proteins, 2019 7 October

 

Delivery of RALA/siFKBPL nanoparticles via electrospun bilayer nanofibres: An innovative angiogenic therapy for wound repair. Mulholland et al.  J. Control Release2019 30 October

 

Time and region-dependent manner of increased brain derived neurotrophic factor and TrkB in rat brain after binge-like methamphetamine exposure. da Silva Santos et al. Neurosci. Lett, 2019 3 November 

 

Effect of kinase inhibiting rnase attenuator (Kira) compounds on the formation of face-to-face dimers of inositol-requiring enzyme 1: Insights from computational modeling. Carlesso et al. Int. J. Mol. Sci, 2019 6 November

 

Application of a New Multiplexed Array for Rapid, Sensitive, Simultaneous and Quantitative Assessment of Spliced and Unspliced XBP1. Creedican et al. Biol. Proced. Online, 2019 15 November

 

FKBPL-based peptide, ALM201, targets angiogenesis and cancer stem cells in ovarian cancer. Annett et al. Br. J. Cancer, 2019 27 November

 

Evaluating liquid biopsies for methylomic profiling of prostate cancer. Silva et al. Epigenetics, 2020 31 January

 

Triple Combination of Ascorbate, Menadione and the Inhibition of Peroxiredoxin-1 Produces Synergistic Cytotoxic Effects in Triple-Negative Breast Cancer Cells. Bajor et al. Antioxidants. 2020 16 April 

 

Multi-Gene Prognostic Signatures and Prediction of Pathological Complete Response to Neoadjuvant Chemotherapy in ER-Positive, HER2-Negative Breast Cancer Patients. Mazo et al. Cancers (Basel), 2020 1 May

 

Novel Pt(IV) Prodrugs Displaying Antimitochondrial Effects. Tabrizi et al. Mol. Pharm, 2020 6 July 

 

Periodic propagating waves coordinate RhoGTPase network dynamics at the leading and trailing edges during cell migration. Bolado-Carrancio et al. Elife, 2020 24 July 

 

Understanding and Attitudes toward Cancer Clinical Trials among Patients with a Cancer Diagnosis: National Study through Cancer Trials Ireland. Kearns et al. Cancers. 2020 16 July

 

Characterization of FFPE-induced bacterial DNA damage and development of a repair method. Flores Bueso et al. Biology Methods and Protocols, 2020 27 July 

 

The Molecular Effects of a High Fat Diet on Endometrial Tumour Biology. Wilkinson et al. Life. 2020 10 September 

 

A functional genomic screenidentifies the deubiquitinase USP11 as a novel transcriptional regulator of ERαin breast cancer. Dwane et al. Cancer Res, 2020 1 October 

 

High Cysteinyl Leukotriene Receptor 1 Expression Correlates with Poor Survival of Uveal Melanoma Patients and Cognate Antagonist Drugs Modulate the Growth, Cancer Secretome, and Metabolism of Uveal Melanoma Cells. Slater et al. Cancers (Basel), 2020 13 Oct

 

Implementing Systems Modelling and Molecular Imaging to Predict the Efficacy of BCL-2 Inhibition in Colorectal Cancer Patient-Derived Xenograft Models. O’Farrell et al. Cancers (Basel), 2020 Oct 14

 

A novel cell permeability assay for macromolecules. Flores Bueso et al. BMC Mol. Cell Biol, 2020 30 October

 

ADAM22/LGI1 complex as a new actionable target for breast cancer brain metastasis. Charmsaz et al. BMC Medicine, 2020 19 November

 

Inhibition of Serum Response Factor Improves Response to Enzalutamide in Prostate Cancer. Watson et al. Cancers (Basel), 2020 27 November

 

A Chemo-Genomic Approach Identifies Diverse Epigenetic Therapeutic Vulnerabilities in MYCN-Amplified Neuroblastoma. Krstic et al. Front. Cell Dev. Biol,  2021 21 April

 

A systematic analysis of signaling reactivation and drug resistance. Kholodenko et al. Cell Rep, 2021 21 April

 

Pepblock Builder VR – An Open-Source Tool for Gaming-Based Bio-Edutainment in Interactive Protein Design. Yallapragada et al. Front Bioeng Biotechnol, 2021 14 May 

 

Prognostic value of the 6-gene OncoMasTR test in hormone receptor-positive HER2-negative early-stage breast cancer: Comparative analysis with standard clinicopathological factorsEur J Cancer, 2021 2 June 

 

Feature Fusion of Raman Chemical Imaging and Digital Histopathology using Machine Learning for Prostate Cancer Detection. Doherty et al. Analyst, 2021 28 Jun

 

KBoost: a new method to infer gene regulatory networks from gene expression data. Iglesias-Martinez et al. Sci Rep, 2021 29 July

 

The stressosome, a caspase‐8‐activating signalling complex assembled in response to cell stress in an ATG5‐mediated manner. Mnich et al. J Cell Mol Med, 2021 7 Aug

 

PRR11 unveiled as a top candidate biomarker within the RBM3 ‐regulated transcriptome in pancreatic cancer. Hau et al. J Pathol Clin Res, 2021 11 Aug 

 

Transcriptional profiling of early differentiation of primary human mesenchymal stem cells into chondrocytes. Schwarzl et al. bioRxiv, 2021 13 August 

 

Longitudinal analysis of individual cfDNA methylome patterns in metastatic prostate cancer. Silva et al. Clin Epigenetics, 2021 28 Aug 

 

Effect of the Rehabilitation Program, ReStOre, on Serum Biomarkers in a Randomized Control Trial of Esophagogastric Cancer Survivors. Kennedy et al. Front Oncol, 2021 15 Sep

 

Biopsy bacterial signature can predict patient tissue malignancy. Hogan et al. Sci Rep, 2021, 21 September

 

The Role of BiP and the IRE1α-XBP1 Axis in Rhabdomyosarcoma Pathology. Aghaei et al. Cancers (Basel), 2021 30 Sep

 

Association of circulating short chain fatty acid levels with colorectal adenomas and colorectal cancer. Genua et al. Clin. Nutr. ESPEN, 2021 5 October 

 

Mapping molecular subtype specific alterations in breast cancer brain metastases identifies clinically relevant vulnerabilities. Cosgrove et al. Nat Commun, 2022 Jan 26

 

Pre-clinical and clinical studies on the role of RBM3 in muscle-invasive bladder cancer: longitudinal expression, transcriptome-level effects and modulation of chemosensitivity. Wahlin et al. BMC Cancer, 2022 2 Feb

 

Investigating a clinically actionable BRAF mutation for monitoring low-grade serous ovarian cancer: A case report. Silva et al. Case Rep Womens Health, 2022 Feb 6

 

A clinically compatible drug-screening platform based on organotypic cultures identifies vulnerabilities to prevent and treat brain metastasis. Zhu et al. EMBO Mol Med, 2022 Mar 7

 

Dexamethasone promotes breast cancer stem cells in obese and not lean mice. Annett et al. Pharmacol Res Perspect, 2022 14 March

 

Stratification of radiosensitive brain metastases based on an actionable S100A9/RAGE resistance mechanism. Monteiro et al. Nat Med, 2022 Apr 11

 

Regulated IRE1α-dependent decay (RIDD)-mediated reprograming of lipid metabolism in cancer. Almanza et al. Nat Commun, 2022 May 6

 

Analytical Validation of a Novel 6-Gene Signature for Prediction of Distant Recurrence in Estrogen Receptor-Positive, HER2-Negative, Early-Stage Breast Cancer. Loughman et al. Clin Chem, 2022 Jun 1

 

Temporal and spatial changes in bone mineral content and mechanical properties during breast-cancer bone metastases. Verbruggen et al. Bone Rep, 2022 Jun 12

 

Analysis of Alternative mRNA Splicing in Vemurafenib-Resistant Melanoma Cells. Bokharaie et al. Biomolecules, 2022 Jul 17

 

Inhibition of IRE1α RNase activity sensitizes patient-derived acute myeloid leukaemia cells to proteasome inhibitors. Creedican et al. J Cell Mol Med, 2022 Aug

 

A Systems Biology Approach to Investigate Kinase Signal Transduction Networks That Are Involved in Triple Negative Breast Cancer Resistance to Cisplatin. Mukherjee et al. J Pers Med, 2022 Aug 3

 

Enhancing arginase 2 expression using target site blockers as a strategy to modulate macrophage phenotype. De Santi et al. Mol Ther Nucleic Acids, 2022 Aug 4

 

Proteasomal down-regulation of the proapoptotic MST2 pathway contributes to BRAF inhibitor resistance in melanoma. Romano et al. Life Sci Alliance, 2022 Aug 29

 

Control of cell state transitions. Rukhlenko et al. Int. J. Mol. Sci, 2022 Sep 14

 

Mapping the Immune Landscape in Metastatic Melanoma Reveals Localized Cell–Cell Interactions That Predict Immunotherapy Response. Antoranz et al. Cancer Res, 2022 Sep 16

 

CRABP2 - A novel biomarker for high-risk endometrial cancer.  Egan et al. Gynecol Oncol, 2022 Sep 24 

 

Yeast β-Glucan Improves Insulin Sensitivity and Hepatic Lipid Metabolism in Mice Humanized with Obese Type 2 Diabetic Gut Microbiota. Mitchelson et al. Mol Nutr Food Res, 2022 Oct 1

 

Endoplasmic Reticulum Stress-Regulated Chaperones as a Serum Biomarker Panel for Parkinson's Disease. Mnich et al. Mol Neurobiol, 2022 Dec 7

 

1,4-dihydroxy quininib modulates the secretome of uveal melanoma tumour explants and a marker of oxidative phosphorylation in a metastatic xenograft model. Slater et al. Front Med, 2023 Jan 9

 

Cell State Transitions and Phenotypic Heterogeneity in Luminal Breast Cancer Implicating MicroRNAs as Potential Regulators. Richard et al. Int J Mol Sci, 2023 Feb 9

 

 Memory of stochastic single-cell apoptotic signaling promotes chemoresistance in neuroblastoma. Hastings et al. Sci Adv, 2023 Mar 3


 
Interactome dynamics of RAF1-BRAF kinase monomers and dimers. Iglesias-Martinez et al. Sci Data, 2023 Apr 12

 

Development, Validation, and Clinical Utility of a Six-gene Signature to Predict Aggressive Prostate Cancer. Krzyzanowska et al. Eur Urol Focus, 2023 Apr 25
   

 
 
 
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Review Articles

Clinical Decision Support Systems in Breast Cancer: A Systematic Review. Mazo et al. Cancers (Basel), 2020 6 February

 

Targeting MAPK Signaling in Cancer: Mechanisms of Drug Resistance and Sensitivity. Lee et al. Int. J. Mol. Sci, 2020 7 February

 

Tumour Cell Secretome in Chemoresistance and Tumour Recurrence. Madden E et al. Trends Cancer, 2020 25 March

 

Advances in tissue-based imaging: impact on oncology research and clinical practice. Rahman et al. Expert Rev. Mol. Diagn, 2020 08 June  

 

Obesity, COVID-19 and innate immunometabolism. Gleeson et al. Br J Nutr, 2020 7 September

 

Regulating metabolic inflammation by nutritional modulation. Charles-Messance et al. J. Allergy Clin. Immunol, 2020 21 August

 

Systems biology approaches to macromolecules: the role of dynamic protein assemblies in information processing. Rukhlenko et al. Curr. Opin. Struct. Biol., 2020 24 October

 

Obesity and Cancer Metastasis: Molecular and Translational Perspectives. Annett et al. Cancers (Basel), 2020 16 December

 

Signaling Dynamics Regulating Crosstalks between T-Cell Activation and Immune Checkpoints. Kreileder et al. Trends Cell Biol, 2020 30 December

 

Regulation of lipid metabolism by the unfolded protein response. Moncan et al. J Cell Mol Med, 2021 04 January 

 

An Emerging Role for the Unfolded Protein Response in Pancreatic Cancer. Robinson et al. Cancers (Basel), 2021 12 January

 

The Ins and Outs of RAS Effector Complexes. Kiel et al. Biomolecules, 2021 7 Feb

 

Boron Clusters as Breast Cancer Therapeutics. Murphy et al. J. Inorg. Biochem, 2021 4 March

 

Emerging RAS-directed therapies for cancer. Conroy et al. Cancer Drug Resist, 2021 8 April

 

Hidden Targets in RAF Signalling Pathways to Block Oncogenic RAS Signalling. Nolan et al. Genes (Basel), 2021 10 April 

 

The Cancer Stem Cell Niche in Ovarian Cancer and Its Impact on Immune Surveillance. Jain et al. Int J Mol Sci, 2021 15 Apr

 

The Role of Gut Barrier Dysfunction and Microbiome Dysbiosis in Colorectal Cancer. Genua et al. Front Oncol., 2021 15 Apr

 

Personalized Medicine for Neuroblastoma: Moving from Static Genotypes to Dynamic Simulations of Drug Response. Han et al. J Pers Med. 2021 11 May

 

Future of biomarker evaluation in the realm of artificial intelligence algorithms: application in improved therapeutic stratification of patients with breast and prostate cancer. Fitzgerald et al.  J Clin Pathol., 2021 18 June

 

Emerging Evidence of the Functional Impact of the miR379/miR656 Cluster (C14MC) in Breast Cancer. McCarthy et al. Biomedicines, 2021 16 Jul 

 

MicroRNAs in Molecular Classification and Pathogenesis of Breast Tumors. Richard et al. Cancers (Basel), 2021 23 Oct 

 

Emerging role for the Serum Response Factor (SRF) as a potential therapeutic target in cancer. Azam et al. Expert Opin Ther Targets, 2022 11 Feb

 

The double agents in liquid biopsy: promoter and informant biomarkers of early metastases in breast cancer. Richard et al. Mol Cancer., 2022 4 Apr

 

Overview of MicroRNA Expression in Predicting Response to Neoadjuvant Therapies in Human Epidermal Growth Receptor-2 Enriched Breast Cancer – A Systematic Review. Davey et al. Breast Cancer (Auckl), 2022 22 Mar

 

New insights into IRE1α activation and function in anti-tumor immunity Logue et al. J Cell Biol., 2022 11 May

 

Application of Artificial Intelligence Techniques to Predict Risk of Recurrence of Breast Cancer: A Systematic Review. Mazo et al. J Pers Med., 2022 13 Sep

 

Unfolded protein response at the cross roads of tumourigenesis, oxygen sensing and drug resistance in clear cell renal cell carcinoma. Chee et al. Biochim Biophys Acta Rev Cancer,  2022 3 October

 

Targeting KRAS in Pancreatic Cancer. Cowzer et al. J Pers Med., 2022 8 Nov

 

Understanding and harnessing triple-negative breast cancer-related microbiota in oncology. Devoy, et al. Front Oncol., 2022 24 Nov

 

Dynamic regulation of RAS and RAS signaling. Kolch et al. Biochem J., 2023 6 Jan

 

Oncotherapeutic Strategies in Early Onset Colorectal Cancer. O'Reilly et al. Cancers (Basel), 2023 16 Jan

 

Deciphering the tumour immune microenvironment cell by cell. Nabhan et al. Immunooncol Technol.,  2023 7 Apr

 

Obesity, non-alcoholic fatty liver disease and hepatocellular carcinoma: current status and therapeutic targets. Chen et al. Front Endocrinol (Lausanne),  2023 8 Jun

 

Pitfalls in machine learning-based assessment of tumor-infiltrating lymphocytes in breast cancer: A report of the International Immuno-Oncology Biomarker Working Group on Breast Cancer. Thagaard et al. J Pathol., 2023 23 August

 

Spatial analyses of immune cell infiltration in cancer: current methods and future directions: A report of the International Immuno-Oncology Biomarker Working Group on Breast Cancer. Page et al. J Pathol., 2023 23 August

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