UCD Cancer Data Lab
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Genetic interactions under the microscope
Traditional genetic interaction screens profile phenotypes at aggregate level, missing interactions that may influence the distribution …
Colm J. Ryan
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DOI
Paper
Antibody reliability influences observed mRNA–protein correlations in tumour samples
Reverse phase protein arrays (RPPA) have been used to quantify the abundance of hundreds of proteins across thousands of tumour samples …
Swathi Ramachandra Upadhya
,
Colm J. Ryan
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Targeting synthetic lethal paralogs in cancer
Synthetic lethal interactions, where mutation of one gene renders cells sensitive to inhibition of another gene, can be exploited for …
Colm J. Ryan
,
Ishan Mehta
,
Narod Kebabci
,
David J. Adams
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DOI
Paper
Experimental reproducibility limits the correlation between mRNA and protein abundances in tumour proteomic profiles
Large-scale studies of human proteomes have revealed only a moderate correlation between mRNA and protein abundances. It is unclear to …
Swathi Ramachandra Upadhya
,
Colm J. Ryan
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DOI
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Comprehensive prediction of robust synthetic lethality between paralog pairs in cancer cell lines
Pairs of paralogs may share common functionality and, hence, display synthetic lethal interactions. As the majority of human genes have …
Barbara De Kegel
,
Niall Quinn
,
Nicola A Thompson
,
David J Adams
,
Colm J. Ryan
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DOI
Paper
Predictions and Supplementary Data
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Proteomic signatures of radioresistance: Alteration of inflammation, angiogenesis and metabolism-related factors in radioresistant oesophageal adenocarcinoma
The clinical management of locally advanced oesophageal adenocarcinoma (OAC) involves neoadjuvant chemoradiotherapy (CRT), but as …
Simone Marcone
,
Amy Buckley
,
Colm J. Ryan
,
Mark McCabe
,
Niamh Lynam-Lennon
,
David Matallanas
,
OSullivan Jacintha
,
Susan Kennedy
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DOI
Paper
Cross-species identification of PIP5K1-, splicing-and ubiquitin-related pathways as potential targets for RB1-deficient cells
The
RB1
tumor suppressor is recurrently mutated in a variety of cancers including retinoblastomas, small cell lung cancers, …
Andrey A Parkhitko
,
Arashdeep Singh
,
Sharon Hsieh
,
Yanhui Hu
,
Richard Binari
,
Christopher J Lord
,
Sridhar Hannenhalli
,
Colm J. Ryan
,
Norbert Perrimon
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DOI
Paper
Accurate prediction of kinase-substrate networks using knowledge graphs
Phosphorylation of specific substrates by protein kinases is a key control mechanism for vital cell-fate decisions and other cellular …
Vı́t Nováček
,
Gavin McGauran
,
David Matallanas
,
Adrián Vallejo Blanco
,
Piero Conca
,
Emir Muñoz
,
Luca Costabello
,
Kamalesh Kanakaraj
,
Zeeshan Nawaz
,
Brian Walsh
,
others
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Integrative analysis of large-scale loss-of-function screens identifies robust cancer-associated genetic interactions
Genetic interactions, including synthetic lethal effects, can now be systematically identified in cancer cell lines using …
Christopher J Lord
,
Niall Quinn
,
Colm J. Ryan
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DOI
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Extensive rewiring of the EGFR network in colorectal cancer cells expressing transforming levels of KRASᴳ¹³ᴰ
Protein-protein-interaction networks (PPINs) organize fundamental biological processes, but how oncogenic mutations impact these …
Susan A Kennedy
,
Mohamed-Ali Jarboui
,
Sriganesh Srihari
,
Cinzia Raso
,
Kenneth Bryan
,
Layal Dernayka
,
Theodosia Charitou
,
Manuel Bernal-Llinares
,
Carlos Herrera-Montavez
,
Aleksandar Krstic
,
others
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