Ryan Group: Targeting gene loss in cancer
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.
Networks | data integration | synthetic lethality | cancer | computational biology | proteogenomics
Work with us
We will shortly be advertising positions for a computational PhD student and a lab-based research assistant. For the PhD studentship some programming experience is required and someone with an undergraduate degree in computer science, statistics, genetics or bioinformatics may be suitable. A background in biology is not required for this role. 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. The next deadline for the Computer Science PhD Scholarship is May 2018.
Colm J. Ryan is an Assistant Professor in the UCD School of Computer Science and Junior Group Leader in Systems Biology Ireland. He has a degree in Computer Science from Trinity College Dublin, and a PhD in computational biology from University College Dublin (2013). He has worked in industry as a software developer for IBM, and as a visiting scientist at the University of California, San Francisco and the Institute of Cancer Research in London. He was the first recipient of the Sir Henry Wellcome fellowship to be funded under the SFI/HRB/Wellcome Trust Partnership and was previously the ICON Newman Fellow in Genomics.
I obtained my BSc(Hons) in Genetics in 2012 from University College Dublin (UCD). Subsequently, I was awarded funding from the Irish Research Council to pursue a PhD under the supervision of Dr. Gerard Cagney in the Conway Institute of UCD and Prof. Nevan J. Krogan in University of California, San Francisco. My PhD involved the use of proteomics and genomic screening approaches to investigate the physical and functional interactome of developmentally important protein complexes (UCD), as well as in dissecting the genetic interaction landscape of HIV-infected human cells (UCSF).
Following completion of my PhD in 2016, I was awarded a postdoctoral fellowship under the Marie Skłodowska-Curie COFUND Action through System Biology Ireland's TOPMed10 programme. Under the supervision of Prof. Walter Kolch and Dr. Colm Ryan, I am currently investigating the role of crosstalk between epigenetic machinery and canonical signalling pathways in facilitating the development of drug resistance in late stage melanoma.
Barbara De Kegel
I'm a computational biology PhD student at Systems Biology Ireland. Under the supervision of Dr. Colm Ryan, I'm investigating the contribution of paralog buffering to tumour robustness. I have a BSc(Hons) Computer Science degree from University College Dublin and an MSc Computer Science degree from Trinity College Dublin. Prior to joining SBI, I worked in industry as a software engineer at Havok (Microsoft), who specialize in 3D physics simulation for video games.
Ryan Group: Targeting gene loss in cancer
CancerGD: a resource for identifying and interpreting genetic dependencies in cancer
Bridgett, S., Campbell, J., Lord, C.J., Ryan, C.J
Cell Systems 2017
The histone variant H2A. Z promotes splicing of weak introns
Nissen, K.E., Homer, C.M, Ryan, C.J., Shales, M., Krogan, N.J., Patrick, K.L., Guthrie, C.
Genes & Development 2017
ATR inhibitors as a Synthetic Lethal Therapy for Tumors Deficient in ARID1A
Williamson, C., Miller, R., Pemberton, H., Jones, S., Campbell, J., Konde, A., Badham, N., Rafiq, M.R., Brough, R., Gulati, A., Ryan, C.J., Francis, J., Vermulen, P., Reynolds, A., Reaper, P., Pollard, J.R., Ashworth, A., Lord, C.J. (2016)
Nature Communications 2016
Large-Scale Profiling of Kinase Dependencies in Cancer Cell Lines
Campbell, J.,* Ryan, C.J.*, Brough, R., Bajrami, I., Pemberton, H.N., Chong, I.Y., Frankum, J., Gulati, A., Holme, H., Miller, R., Postel-Vinay, S., Rafiq, R., Wei, W., Williamson, C.T., Quigley, D.A., Fenton, T., Natrajan, R., Strauss, S.J., Ashworth, A., Lord, C.J.
Cell Reports 2016 * Equal Contribution
- New online tool launched to speed up development of novel, therapeutic, targeted approaches to cancer | 12 July 2017
- 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
- 2 + 4 = 6, 4 + 2 = 7? | 25 November 2015
- UCD scientist receives €300,000 in international funding for cancer research | 17 June 2014