Ryan Group

Targeting Gene Loss in Cancer

Group Members

Colm Ryan
Assistant Professor
Narod Kebabci
Ph.D. Student, Ryan Group
Thomas Lefeivre
Ph.D. Student, Bond/Ryan Groups
Sutanu Nandi
Postdoctoral Researcher, Ryan Group
Cosmin Tudose
Ph.D. Student, Bond/Ryan Groups
Swathi Ramachandra Upadhya
Ph.D. Student, Ryan Group
Anjan Venkatesh
Ph.D. Student, Ryan Group

About the Group

What we do 

We are interested in how gene loss rewires tumour cells and how this may be exploited to target them therapeutically. A particular focus of the group is the identification of synthetic lethality - a phenomenon whereby mutation of one gene renders tumour cells especially sensitive to the perturbation of a second gene. We have developed computational methods to identify synthetic lethal interactions from genetic screens and interpret them using protein-protein interaction networks (see our resource www.cancergd.org). Through the integration of whole proteome expression profiling (see bit.ly/brca_complexes), protein interaction mapping, and high-content screening we are hoping to gain a mechanistic understanding of how gene loss rewires molecular networks. We anticipate that this will aid us in the identification and mechanistic interpretation of novel synthetic lethal interactions. In collaboration with Prof. Walter Kolch we are applying similar approaches to understand how gene loss can lead to drug resistance in BRAF mutant melanoma 


Work with us 

We will shortly be advertising positions for a computational postdoctoral fellow. A PhD in computational biology is required for this role, preferably with some experience in machine learning, statistics or network biology. If you are interested in either position, please send me an email and we can discuss further. 

I am also interested in supporting applications for PhD studentships - either through the Irish Research Council's postgraduate schemes or the UCD School of Computer Science PhD Scholarship Programme


Recent publications 

Comprehensive prediction of robust synthetic lethality between paralog pairs in cancer cell lines
De Kegel, B., Quinn, N., Thompson, N.A., Adams, D. J., Ryan, C.J. * Cell Systems 2021

Integrative analysis of large-scale loss-of-function screens identifies robust cancer-associated genetic interactions 
Lord, C.J., Quinn, N., Ryan, C.J.* eLife 2020

Paralog buffering contributes to the variable essentiality of genes in cancer cell lines
De Kegel, B., Ryan, C.J.* PLoS Genetics 2019

Synthetic Lethality and Cancer – Penetrance as the Major Barrier
Ryan, C.J.*, Bajrami, I.*, Lord, C.J.* Trends in Cancer, 2018

A compendium of co-regulated protein complexes in breast cancer reveals collateral loss events
Ryan, C.J.*, Kennedy, S., Bajrami, I., Matallanas, D., Lord, C.J. Cell Systems 2017

* Corresponding Author


Irish Research Council: ‘Using data science to identify better therapeutic targets in cancer’ | 12 June 2020

SBI Blog: ‘Spare tire genes’ explain why some genes can be lost by cancer cells | 27 November 2019

SBI Blog: ‘Uncovering How the Machinery of Life is Rewired in Breast Cancer’ | 06 November 2017

New online tool launched to speed up development of novel, therapeutic, targeted approaches to cancer | 12 July 2017 

SBI Blog: ‘SBI at the Irish Association for Cancer Research Meeting 2017’ | 27 February 2017 

Genetic screening of cancer cell lines to identify new targeted treatments | 23 May 2016 

SBI Blog: 2 + 4 = 6, 4 + 2 = 7? | 25 November 2015 

UCD scientist receives €300,000 in international funding for cancer research | 17 June 2014