UCD Cancer Data Lab
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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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DOI
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Paralog dispensability shapes homozygous deletion patterns in tumor genomes
Tumor genomes abound with mutations, including homozygous gene deletions, suggesting that tumors are robust to genetic perturbation. In …
Barbara De Kegel
,
Colm J. Ryan
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DOI
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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
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
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
Chemosensitivity profiling of osteosarcoma tumour cell lines identifies a model of BRCAness
Osteosarcoma (OS) is an aggressive sarcoma, where novel treatment approaches are required. Genomic studies suggest that a subset of OS, …
Harriett Holme
,
Aditi Gulati
,
Rachel Brough
,
Emmy DG Fleuren
,
Ilirjana Bajrami
,
James Campbell
,
Irene Y Chong
,
Sara Costa-Cabral
,
Richard Elliott
,
Tim Fenton
,
others
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DOI
Paper
E-cadherin/ROS1 inhibitor synthetic lethality in breast cancer
The cell adhesion glycoprotein E-cadherin (CDH1) is commonly inactivated in breast tumors. Precision medicine approaches that exploit …
Ilirjana Bajrami
,
Rebecca Marlow
,
Marieke van de Ven
,
Rachel Brough
,
Helen N Pemberton
,
Jessica Frankum
,
Feifei Song
,
Rumana Rafiq
,
Asha Konde
,
Dragomir B Krastev
,
others
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DOI
Paper
Identifying genetic dependencies in cancer by analyzing siRNA screens in tumor cell line panels
Loss-of-function screening using RNA interference or CRISPR approaches can be used to identify genes that specific tumor cell lines …
James Campbell
,
Colm J. Ryan
,
Christopher J Lord
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DOI
Paper
A Compendium of Co-regulated Protein Complexes in Breast Cancer Reveals Collateral Loss Events
Protein complexes are responsible for the bulk of activities within the cell, but how their behavior and abundance varies across tumors …
Colm J. Ryan
,
Susan Kennedy
,
Ilirjana Bajrami
,
David Matallanas
,
Christopher J Lord
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