UCD Cancer Data Lab
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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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Video
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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Video
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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DOI
Paper
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
Paper
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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Cells lacking the RB1 tumor suppressor gene are hyperdependent on Aurora B kinase for survival
Small cell lung cancer (SCLC) accounts for 15% of lung cancers and is almost always linked to inactivating
RB1
and
TP53
mutations. SCLC …
Matthew G Oser
,
Raquel Fonseca
,
Abhishek A Chakraborty
,
Rachel Brough
,
Alexander Spektor
,
Rebecca B Jennings
,
Abdallah Flaifel
,
Jesse S Novak
,
Aditi Gulati
,
Elizabeth Buss
,
others
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DOI
Paper
Paralog buffering contributes to the variable essentiality of genes in cancer cell lines
What makes a gene essential for cellular survival? In model organisms, such as budding yeast, systematic gene deletion studies have …
Barbara De Kegel
,
Colm J. Ryan
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DOI
Paper
Synthetic Lethality and Cancer – Penetrance as the Major Barrier
Synthetic lethality has long been proposed as an approach for targeting genetic defects in tumours. Despite a decade of screening …
Colm J. Ryan
,
Ilirjana Bajrami
,
Christopher J Lord
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