Publications | UCD Cancer Data Lab https://cancerdata.ucd.ie/publication/ Publications Wowchemy (https://wowchemy.com)en-usTue, 01 Jul 2025 00:00:00 +0000 https://cancerdata.ucd.ie/media/sharing.png Publications https://cancerdata.ucd.ie/publication/ The synthetic lethal interaction between CDS1 and CDS2 is a vulnerability in uveal melanoma and across multiple tumor types https://cancerdata.ucd.ie/publication/chan-2025/ Tue, 01 Jul 2025 00:00:00 +0000 https://cancerdata.ucd.ie/publication/chan-2025/ Proteomic compensation by paralogs preserves protein interaction networks after gene loss in cancer https://cancerdata.ucd.ie/publication/venkatesh-2025/ Wed, 28 May 2025 15:19:22 +0000 https://cancerdata.ucd.ie/publication/venkatesh-2025/ Benchmarking Genetic Interaction Scoring Methods for Identifying Synthetic Lethality from Combinatorial CRISPR Screens https://cancerdata.ucd.ie/publication/ajmal-2025-evaluating/ Tue, 01 Apr 2025 00:00:00 +0000 https://cancerdata.ucd.ie/publication/ajmal-2025-evaluating/ Evaluating Sequence and Structural Similarity Metrics for Predicting Shared Paralog Functions https://cancerdata.ucd.ie/publication/dennler-2024-evaluating/ Mon, 14 Oct 2024 00:00:00 +0000 https://cancerdata.ucd.ie/publication/dennler-2024-evaluating/ Complex synthetic lethality in cancer https://cancerdata.ucd.ie/publication/ryan-2023-sl/ Thu, 30 Nov 2023 00:00:00 +0000 https://cancerdata.ucd.ie/publication/ryan-2023-sl/ Gene essentiality in cancer is better predicted by mRNA abundance than by gene regulatory network-inferred activity https://cancerdata.ucd.ie/publication/tudose-2023-gnr/ Tue, 28 Nov 2023 00:00:00 +0000 https://cancerdata.ucd.ie/publication/tudose-2023-gnr/ Exploiting Cancer Synthetic Lethality in Cancer---Lessons Learnt from PARP Inhibitors https://cancerdata.ucd.ie/publication/pettitt-2023-parp/ Sat, 18 Nov 2023 00:00:00 +0000 https://cancerdata.ucd.ie/publication/pettitt-2023-parp/ Paralog dispensability shapes homozygous deletion patterns in tumor genomes https://cancerdata.ucd.ie/publication/de-2022-paralog/ Tue, 14 Nov 2023 00:00:00 +0000 https://cancerdata.ucd.ie/publication/de-2022-paralog/ Genetic interactions under the microscope https://cancerdata.ucd.ie/publication/ryan-2023-gi/ Wed, 17 May 2023 00:00:00 +0000 https://cancerdata.ucd.ie/publication/ryan-2023-gi/ Antibody reliability influences observed mRNA–protein correlations in tumour samples https://cancerdata.ucd.ie/publication/upadhya-2023-antibody/ Thu, 11 May 2023 00:00:00 +0000 https://cancerdata.ucd.ie/publication/upadhya-2023-antibody/ Targeting synthetic lethal paralogs in cancer https://cancerdata.ucd.ie/publication/ryan-2023-targeting/ Mon, 06 Mar 2023 00:00:00 +0000 https://cancerdata.ucd.ie/publication/ryan-2023-targeting/ Experimental reproducibility limits the correlation between mRNA and protein abundances in tumour proteomic profiles https://cancerdata.ucd.ie/publication/upadhya-2021-experimental/ Thu, 08 Sep 2022 00:00:00 +0000 https://cancerdata.ucd.ie/publication/upadhya-2021-experimental/ Comprehensive prediction of robust synthetic lethality between paralog pairs in cancer cell lines https://cancerdata.ucd.ie/publication/de-2021-comprehensive/ Wed, 15 Dec 2021 00:00:00 +0000 https://cancerdata.ucd.ie/publication/de-2021-comprehensive/ Proteomic signatures of radioresistance: Alteration of inflammation, angiogenesis and metabolism-related factors in radioresistant oesophageal adenocarcinoma https://cancerdata.ucd.ie/publication/marcone-2021-proteomic/ Sun, 18 Apr 2021 00:00:00 +0000 https://cancerdata.ucd.ie/publication/marcone-2021-proteomic/ Cross-species identification of PIP5K1-, splicing-and ubiquitin-related pathways as potential targets for RB1-deficient cells https://cancerdata.ucd.ie/publication/parkhitko-2021-cross/ Tue, 16 Feb 2021 00:00:00 +0000 https://cancerdata.ucd.ie/publication/parkhitko-2021-cross/ Accurate prediction of kinase-substrate networks using knowledge graphs https://cancerdata.ucd.ie/publication/novavcek-2020-accurate/ Thu, 03 Dec 2020 00:00:00 +0000 https://cancerdata.ucd.ie/publication/novavcek-2020-accurate/ Integrative analysis of large-scale loss-of-function screens identifies robust cancer-associated genetic interactions https://cancerdata.ucd.ie/publication/lord-2020-integrative/ Thu, 28 May 2020 00:00:00 +0000 https://cancerdata.ucd.ie/publication/lord-2020-integrative/ Extensive rewiring of the EGFR network in colorectal cancer cells expressing transforming levels of KRASG13D https://cancerdata.ucd.ie/publication/kennedy-2020-extensive/ Fri, 24 Jan 2020 00:00:00 +0000 https://cancerdata.ucd.ie/publication/kennedy-2020-extensive/ Cells lacking the RB1 tumor suppressor gene are hyperdependent on Aurora B kinase for survival https://cancerdata.ucd.ie/publication/oser-2019-cells/ Tue, 01 Jan 2019 00:00:00 +0000 https://cancerdata.ucd.ie/publication/oser-2019-cells/ Paralog buffering contributes to the variable essentiality of genes in cancer cell lines https://cancerdata.ucd.ie/publication/de-2019-paralog/ Tue, 01 Jan 2019 00:00:00 +0000 https://cancerdata.ucd.ie/publication/de-2019-paralog/ Synthetic Lethality and Cancer – Penetrance as the Major Barrier https://cancerdata.ucd.ie/publication/ryan-2018-synthetic/ Sat, 15 Sep 2018 00:00:00 +0000 https://cancerdata.ucd.ie/publication/ryan-2018-synthetic/ Systems biology: old news or new stimulus for biochemistry https://cancerdata.ucd.ie/publication/kolch-2018-systems/ Mon, 13 Aug 2018 00:00:00 +0000 https://cancerdata.ucd.ie/publication/kolch-2018-systems/ Chemosensitivity profiling of osteosarcoma tumour cell lines identifies a model of BRCAness https://cancerdata.ucd.ie/publication/holme-2018-chemosensitivity/ Fri, 13 Jul 2018 00:00:00 +0000 https://cancerdata.ucd.ie/publication/holme-2018-chemosensitivity/ Identification of highly penetrant Rb-related synthetic lethal interactions in triple negative breast cancer https://cancerdata.ucd.ie/publication/brough-2018-identification/ Mon, 18 Jun 2018 00:00:00 +0000 https://cancerdata.ucd.ie/publication/brough-2018-identification/ E-cadherin/ROS1 inhibitor synthetic lethality in breast cancer https://cancerdata.ucd.ie/publication/bajrami-2018-cadherin/ Sun, 01 Apr 2018 00:00:00 +0000 https://cancerdata.ucd.ie/publication/bajrami-2018-cadherin/ Identifying genetic dependencies in cancer by analyzing siRNA screens in tumor cell line panels https://cancerdata.ucd.ie/publication/campbell-2018-identifying/ Mon, 01 Jan 2018 00:00:00 +0000 https://cancerdata.ucd.ie/publication/campbell-2018-identifying/ A Compendium of Co-regulated Protein Complexes in Breast Cancer Reveals Collateral Loss Events https://cancerdata.ucd.ie/publication/ryan-2017-compendium/ Wed, 25 Oct 2017 00:00:00 +0000 https://cancerdata.ucd.ie/publication/ryan-2017-compendium/ CancerGD: a resource for identifying and interpreting genetic dependencies in cancer https://cancerdata.ucd.ie/publication/bridgett-2017-cancergd/ Wed, 26 Jul 2017 00:00:00 +0000 https://cancerdata.ucd.ie/publication/bridgett-2017-cancergd/ Genetic Interaction Score (S-Score) Calculation, Clustering, and Visualization of Genetic Interaction Profiles for Yeast https://cancerdata.ucd.ie/publication/roguev-2018-genetic/ Fri, 21 Jul 2017 00:00:00 +0000 https://cancerdata.ucd.ie/publication/roguev-2018-genetic/ High-Throughput Quantitative Genetic Interaction Mapping in the Fission Yeast Schizosaccharomyces pombe https://cancerdata.ucd.ie/publication/roguev-2018-high/ Fri, 21 Jul 2017 00:00:00 +0000 https://cancerdata.ucd.ie/publication/roguev-2018-high/ The histone variant H2A. Z promotes splicing of weak introns https://cancerdata.ucd.ie/publication/nissen-2017-histone/ Sat, 01 Apr 2017 00:00:00 +0000 https://cancerdata.ucd.ie/publication/nissen-2017-histone/ ATR inhibitors as a synthetic lethal therapy for tumours deficient in ARID1A https://cancerdata.ucd.ie/publication/williamson-2016-atr/ Tue, 13 Dec 2016 00:00:00 +0000 https://cancerdata.ucd.ie/publication/williamson-2016-atr/ Large-scale profiling of kinase dependencies in cancer cell lines https://cancerdata.ucd.ie/publication/campbell-2016-large/ Thu, 03 Mar 2016 00:00:00 +0000 https://cancerdata.ucd.ie/publication/campbell-2016-large/ Genetic Interaction Mapping Reveals a Role for the SWI/SNF Nucleosome Remodeler in Spliceosome Activation in Fission Yeast https://cancerdata.ucd.ie/publication/krogan-2015-genetic/ Tue, 31 Mar 2015 00:00:00 +0000 https://cancerdata.ucd.ie/publication/krogan-2015-genetic/ Genome-wide epistatic expression quantitative trait loci discovery in four human tissues reveals the importance of local chromosomal interactions governing gene expression https://cancerdata.ucd.ie/publication/fitzpatrick-2015-genome/ Sat, 21 Feb 2015 00:00:00 +0000 https://cancerdata.ucd.ie/publication/fitzpatrick-2015-genome/ Evolutionarily conserved genetic interactions with budding and fission yeast &#119872&#119906&#119905&#119878 identify orthologous relationships in mismatch repair-deficient cancer cells https://cancerdata.ucd.ie/publication/tosti-2014-evolutionarily/ Wed, 17 Sep 2014 00:00:00 +0000 https://cancerdata.ucd.ie/publication/tosti-2014-evolutionarily/ DAISY: picking synthetic lethals from cancer genomes https://cancerdata.ucd.ie/publication/ryan-2014-daisy/ Mon, 08 Sep 2014 00:00:00 +0000 https://cancerdata.ucd.ie/publication/ryan-2014-daisy/ Identification of a BET family bromodomain/casein kinase II/TAF-containing complex as a regulator of mitotic condensin function https://cancerdata.ucd.ie/publication/kim-2014-identification/ Fri, 21 Feb 2014 00:00:00 +0000 https://cancerdata.ucd.ie/publication/kim-2014-identification/ Chemical genetics of rapamycin-insensitive TORC2 in S. cerevisiae https://cancerdata.ucd.ie/publication/kliegman-2013-chemical/ Thu, 19 Dec 2013 00:00:00 +0000 https://cancerdata.ucd.ie/publication/kliegman-2013-chemical/ High-resolution network biology: connecting sequence with function https://cancerdata.ucd.ie/publication/ryan-2013-high/ Thu, 07 Nov 2013 00:00:00 +0000 https://cancerdata.ucd.ie/publication/ryan-2013-high/ Systematic triple-mutant analysis uncovers functional connectivity between pathways involved in chromosome regulation https://cancerdata.ucd.ie/publication/haber-2013-systematic/ Thu, 27 Jun 2013 00:00:00 +0000 https://cancerdata.ucd.ie/publication/haber-2013-systematic/ All or nothing: protein complexes flip essentiality between distantly related eukaryotes https://cancerdata.ucd.ie/publication/ryan-2013-all/ Wed, 08 May 2013 00:00:00 +0000 https://cancerdata.ucd.ie/publication/ryan-2013-all/ The yeast SR-like protein Npl3 links chromatin modification to mRNA processing https://cancerdata.ucd.ie/publication/moehle-2012-yeast/ Thu, 29 Nov 2012 00:00:00 +0000 https://cancerdata.ucd.ie/publication/moehle-2012-yeast/ Hierarchical Modularity and the Evolution of Genetic Interactomes across Species https://cancerdata.ucd.ie/publication/ryan-2012-hierarchical/ Fri, 08 Jun 2012 00:00:00 +0000 https://cancerdata.ucd.ie/publication/ryan-2012-hierarchical/ Comparative interaction networks: bridging genotype to phenotype https://cancerdata.ucd.ie/publication/beltrao-2012-comparative/ Sun, 01 Jan 2012 00:00:00 +0000 https://cancerdata.ucd.ie/publication/beltrao-2012-comparative/ Key Functional Regions in the Histone Variant H2A.Z C-Terminal Docking Domain https://cancerdata.ucd.ie/publication/wang-2011-key/ Thu, 25 Aug 2011 00:00:00 +0000 https://cancerdata.ucd.ie/publication/wang-2011-key/ Improved functional overview of protein complexes using inferred epistatic relationships https://cancerdata.ucd.ie/publication/ryan-2011-improved/ Mon, 23 May 2011 00:00:00 +0000 https://cancerdata.ucd.ie/publication/ryan-2011-improved/ Imputing and predicting quantitative genetic interactions in epistatic MAPs https://cancerdata.ucd.ie/publication/ryan-2011-imputing/ Sat, 01 Jan 2011 00:00:00 +0000 https://cancerdata.ucd.ie/publication/ryan-2011-imputing/ Missing value imputation for epistatic MAPs https://cancerdata.ucd.ie/publication/ryan-2010-missing/ Tue, 20 Apr 2010 00:00:00 +0000 https://cancerdata.ucd.ie/publication/ryan-2010-missing/