Publications | UCD Cancer Data Lab

Evaluating Sequence and Structural Similarity Metrics for Predicting Shared Paralog Functions

Olivier Dennler, Colm J. Ryan

Paralog protein compensation preserves protein-protein interaction networks following gene loss in cancer

Anjan Venkatesh, Niall Quinn, Swathi Ramachandra Upadhya, Barbara De Kegel, Alfonso Bolado Carrancio, Thomas Lefeivre, Olivier Dennler, Kieran Wynne, Alexander von Kriegsheim, Colm J. Ryan

Complex synthetic lethality in cancer

Colm J. Ryan, Lovely Paul Solomon Devakumar, Stephan J. Pettitt, Christopher J. Lord

Gene essentiality in cancer is better predicted by mRNA abundance than by gene regulatory network-inferred activity

Cosmin Tudose, Jonathan Bond, Colm J. Ryan

Exploiting Cancer Synthetic Lethality in Cancer---Lessons Learnt from PARP Inhibitors

Stephan J. Pettitt, Colm J. Ryan, Christopher J. Lord

Paralog dispensability shapes homozygous deletion patterns in tumor genomes

Barbara De Kegel, Colm J. Ryan

Genetic interactions under the microscope

Colm J. Ryan

Antibody reliability influences observed mRNA–protein correlations in tumour samples

Swathi Ramachandra Upadhya, Colm J. Ryan

Targeting synthetic lethal paralogs in cancer

Colm J. Ryan, Ishan Mehta, Narod Kebabci, David J. Adams

Experimental reproducibility limits the correlation between mRNA and protein abundances in tumour proteomic profiles

Swathi Ramachandra Upadhya, Colm J. Ryan

Comprehensive prediction of robust synthetic lethality between paralog pairs in cancer cell lines

Barbara De Kegel, Niall Quinn, Nicola A Thompson, David J Adams, Colm J. Ryan

Proteomic signatures of radioresistance: Alteration of inflammation, angiogenesis and metabolism-related factors in radioresistant oesophageal adenocarcinoma

Simone Marcone, Amy Buckley, Colm J. Ryan, Mark McCabe, Niamh Lynam-Lennon, David Matallanas, OSullivan Jacintha, Susan Kennedy

Cross-species identification of PIP5K1-, splicing-and ubiquitin-related pathways as potential targets for RB1-deficient cells

Andrey A Parkhitko, Arashdeep Singh, Sharon Hsieh, Yanhui Hu, Richard Binari, Christopher J Lord, Sridhar Hannenhalli, Colm J. Ryan, Norbert Perrimon

Accurate prediction of kinase-substrate networks using knowledge graphs

Vı́t Nováček, Gavin McGauran, David Matallanas, Adrián Vallejo Blanco, Piero Conca, Emir Muñoz, Luca Costabello, Kamalesh Kanakaraj, Zeeshan Nawaz, Brian Walsh, others

Integrative analysis of large-scale loss-of-function screens identifies robust cancer-associated genetic interactions

Christopher J Lord, Niall Quinn, Colm J. Ryan

Extensive rewiring of the EGFR network in colorectal cancer cells expressing transforming levels of KRAS&#7475&#185&#179&#7472

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

Paralog buffering contributes to the variable essentiality of genes in cancer cell lines

Barbara De Kegel, Colm J. Ryan

Cells lacking the RB1 tumor suppressor gene are hyperdependent on Aurora B kinase for survival

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

Synthetic Lethality and Cancer – Penetrance as the Major Barrier

Colm J. Ryan, Ilirjana Bajrami, Christopher J Lord

Systems biology: old news or new stimulus for biochemistry

Walter Kolch, Dirk Fey, Colm J. Ryan

Chemosensitivity profiling of osteosarcoma tumour cell lines identifies a model of BRCAness

Harriett Holme, Aditi Gulati, Rachel Brough, Emmy DG Fleuren, Ilirjana Bajrami, James Campbell, Irene Y Chong, Sara Costa-Cabral, Richard Elliott, Tim Fenton, others

Identification of highly penetrant Rb-related synthetic lethal interactions in triple negative breast cancer

Rachel Brough, Aditi Gulati, Syed Haider, Rahul Kumar, James Campbell, Erik Knudsen, Stephen J Pettitt, Colm J. Ryan, Christopher J Lord

E-cadherin/ROS1 inhibitor synthetic lethality in breast cancer

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

Identifying genetic dependencies in cancer by analyzing siRNA screens in tumor cell line panels

James Campbell, Colm J. Ryan, Christopher J Lord

A Compendium of Co-regulated Protein Complexes in Breast Cancer Reveals Collateral Loss Events

Colm J. Ryan, Susan Kennedy, Ilirjana Bajrami, David Matallanas, Christopher J Lord

CancerGD: a resource for identifying and interpreting genetic dependencies in cancer

Stephen Bridgett, James Campbell, Christopher J Lord, Colm J. Ryan

High-Throughput Quantitative Genetic Interaction Mapping in the Fission Yeast Schizosaccharomyces pombe

Assen Roguev, Colm J. Ryan, Edgar Hartsuiker, Nevan J Krogan

Genetic Interaction Score (S-Score) Calculation, Clustering, and Visualization of Genetic Interaction Profiles for Yeast

Assen Roguev, Colm J. Ryan, Jiewei Xu, Isabelle Colson, Edgar Hartsuiker, Nevan Krogan

The histone variant H2A. Z promotes splicing of weak introns

Kelly E Nissen, Christina M Homer, Colm J. Ryan, Michael Shales, Nevan J Krogan, Kristin L Patrick, Christine Guthrie

ATR inhibitors as a synthetic lethal therapy for tumours deficient in ARID1A

Chris T. Williamson, Rowan Miller, Helen N. Pemberton, Samuel E. Jones, James Campbell, Asha Konde, Nicholas Badham, Rumana Rafiq, Rachel Brough, Aditi Gulati, Colm J. Ryan, Andrew R. Reynolds, others

Large-scale profiling of kinase dependencies in cancer cell lines

James Campbell, Colm J. Ryan, Rachel Brough, Ilirjana Bajrami, Helen N Pemberton, Irene Y Chong, Sara Costa-Cabral, Jessica Frankum, Aditi Gulati, Harriet Holme, others

Genetic Interaction Mapping Reveals a Role for the SWI/SNF Nucleosome Remodeler in Spliceosome Activation in Fission Yeast

Kristin L. Patrick, Colm J. Ryan, Jiewei Xu, Jesse J. Lipp, Kelly E. Nissen, Assen Roguev, Michael Shales, Nevan J. Krogan, Christine Guthrie

Genome-wide epistatic expression quantitative trait loci discovery in four human tissues reveals the importance of local chromosomal interactions governing gene expression

Darren J Fitzpatrick, Colm J. Ryan, Naisha Shah, Derek Greene, Cliona Molony, Denis C Shields

Evolutionarily conserved genetic interactions with budding and fission yeast &#119872&#119906&#119905&#119878 identify orthologous relationships in mismatch repair-deficient cancer cells

Elena Tosti, Joseph A Katakowski, Sonja Schaetzlein, Hyun-Soo Kim, Colm J. Ryan, Michael Shales, Assen Roguev, Nevan J Krogan, Deborah Palliser, Michael-Christopher Keogh, others

DAISY: picking synthetic lethals from cancer genomes

Colm J. Ryan, Christopher J Lord, Alan Ashworth

Identification of a BET family bromodomain/casein kinase II/TAF-containing complex as a regulator of mitotic condensin function

Hyun-Soo Kim, Rituparna Mukhopadhyay, Scott B Rothbart, Andrea C Silva, Vincent Vanoosthuyse, Ernest Radovani, Thomas Kislinger, Assen Roguev, Colm J. Ryan, Jiewei Xu, others

Chemical genetics of rapamycin-insensitive TORC2 in S. cerevisiae

Joseph I Kliegman, Dorothea Fiedler, Colm J. Ryan, Yi-Fan Xu, Xiao-yang Su, David Thomas, Max C Caccese, Ada Cheng, Michael Shales, Joshua D Rabinowitz, others

High-resolution network biology: connecting sequence with function

Colm J. Ryan, Peter Cimermančič, Zachary A Szpiech, Andrej Sali, Ryan D Hernandez, Nevan J Krogan

Systematic triple-mutant analysis uncovers functional connectivity between pathways involved in chromosome regulation

James E Haber, Hannes Braberg, Qiuqin Wu, Richard Alexander, Julian Haase, Colm J. Ryan, Zach Lipkin-Moore, Kathleen E Franks-Skiba, Tasha Johnson, Michael Shales, others

All or nothing: protein complexes flip essentiality between distantly related eukaryotes

Colm J. Ryan, Nevan J Krogan, Pádraig Cunningham, Gerard Cagney

The yeast SR-like protein Npl3 links chromatin modification to mRNA processing

Erica A Moehle, Colm J. Ryan, Nevan J Krogan, Tracy L Kress, Christine Guthrie

Hierarchical Modularity and the Evolution of Genetic Interactomes across Species

Colm J. Ryan, Assen Roguev, Kristin Patrick, Jiewei Xu, Harlizawati Jahari, Zongtian Tong, Pedro Beltrao, Michael Shales, Hong Qu, Sean R Collins, others

Comparative interaction networks: bridging genotype to phenotype

Pedro Beltrao, Colm J. Ryan, Nevan J Krogan

Key Functional Regions in the Histone Variant H2A.Z C-Terminal Docking Domain

Alice Y Wang, Maria J Aristizabal, Colm J. Ryan, Nevan J Krogan, Michael S Kobor

Improved functional overview of protein complexes using inferred epistatic relationships

Colm J. Ryan, Derek Greene, Aude Guénolé, Haico van Attikum, Nevan J Krogan, Pádraig Cunningham, Gerard Cagney

Imputing and predicting quantitative genetic interactions in epistatic MAPs

Colm J. Ryan, Gerard Cagney, Nevan J Krogan, Pádraig Cunningham, Derek Greene

Missing value imputation for epistatic MAPs

Colm J. Ryan, Derek Greene, Gerard Cagney, Pádraig Cunningham