Publications

Evaluating Sequence and Structural Similarity Metrics for Predicting Shared Paralog Functions
Olivier Dennler, Colm J. Ryan
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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
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Complex synthetic lethality in cancer
Colm J. Ryan, Lovely Paul Solomon Devakumar, Stephan J. Pettitt, Christopher J. Lord
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Gene essentiality in cancer is better predicted by mRNA abundance than by gene regulatory network-inferred activity
Cosmin Tudose, Jonathan Bond, Colm J. Ryan
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Exploiting Cancer Synthetic Lethality in Cancer---Lessons Learnt from PARP Inhibitors
Stephan J. Pettitt, Colm J. Ryan, Christopher J. Lord
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Paralog dispensability shapes homozygous deletion patterns in tumor genomes
Barbara De Kegel, Colm J. Ryan
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Genetic interactions under the microscope
Colm J. Ryan
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Antibody reliability influences observed mRNA–protein correlations in tumour samples
Swathi Ramachandra Upadhya, Colm J. Ryan
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Targeting synthetic lethal paralogs in cancer
Colm J. Ryan, Ishan Mehta, Narod Kebabci, David J. Adams
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Experimental reproducibility limits the correlation between mRNA and protein abundances in tumour proteomic profiles
Swathi Ramachandra Upadhya, Colm J. Ryan
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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
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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
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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
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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
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Integrative analysis of large-scale loss-of-function screens identifies robust cancer-associated genetic interactions
Christopher J Lord, Niall Quinn, Colm J. Ryan
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Extensive rewiring of the EGFR network in colorectal cancer cells expressing transforming levels of KRASG13D
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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Paralog buffering contributes to the variable essentiality of genes in cancer cell lines
Barbara De Kegel, Colm J. Ryan
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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
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Synthetic Lethality and Cancer – Penetrance as the Major Barrier
Colm J. Ryan, Ilirjana Bajrami, Christopher J Lord
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Systems biology: old news or new stimulus for biochemistry
Walter Kolch, Dirk Fey, Colm J. Ryan
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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
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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
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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
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Identifying genetic dependencies in cancer by analyzing siRNA screens in tumor cell line panels
James Campbell, Colm J. Ryan, Christopher J Lord
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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
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CancerGD: a resource for identifying and interpreting genetic dependencies in cancer
Stephen Bridgett, James Campbell, Christopher J Lord, Colm J. Ryan
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High-Throughput Quantitative Genetic Interaction Mapping in the Fission Yeast Schizosaccharomyces pombe
Assen Roguev, Colm J. Ryan, Edgar Hartsuiker, Nevan J Krogan
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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
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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
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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
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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
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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
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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
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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
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DAISY: picking synthetic lethals from cancer genomes
Colm J. Ryan, Christopher J Lord, Alan Ashworth
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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
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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
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High-resolution network biology: connecting sequence with function
Colm J. Ryan, Peter Cimermančič, Zachary A Szpiech, Andrej Sali, Ryan D Hernandez, Nevan J Krogan
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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
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All or nothing: protein complexes flip essentiality between distantly related eukaryotes
Colm J. Ryan, Nevan J Krogan, Pádraig Cunningham, Gerard Cagney
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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
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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
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Comparative interaction networks: bridging genotype to phenotype
Pedro Beltrao, Colm J. Ryan, Nevan J Krogan
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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
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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
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Imputing and predicting quantitative genetic interactions in epistatic MAPs
Colm J. Ryan, Gerard Cagney, Nevan J Krogan, Pádraig Cunningham, Derek Greene
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Missing value imputation for epistatic MAPs
Colm J. Ryan, Derek Greene, Gerard Cagney, Pádraig Cunningham
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