Publications

Where an Open Access PDF of a paper is available I have linked to it. I have also linked to the journal hosted version of the paper, as the formatting is usually better than the ‘author submitted’ versions.

Journal Articles:

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. (2017). Cell Systems 5, 82-86

[PDF]  [Journal page]

There’s a blog post from Systems Biology Ireland describing this work here and a preview piece from Cell Systems here 


CancerGD: a resource for identifying and interpreting genetic dependencies in cancer.
Bridgett, S., Campbell, J., Lord, C.J., Ryan, C.J. (2017). Cell Systems 5, 82-86

[PDF]  [Journal page]

There’s a blog post from Systems Biology Ireland describing this work here


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. (2017). Genes & Development 31, 688-701

[PDF]  [Journal page]


ATR inhibitors as a synthetic lethal therapy for tumours deficient in ARID1A.
Williamson, C.T., Miller, R., Pemberton, H.N., Jones, S.E., Campbell, J., Konde, A., Badham, N., Rafiq, R., Brough, R., Gulati, A., Ryan, C.J., Francis, J., Vermulen, P.B., Reynolds, A.R., Reaper, P.M., Pollard, J.R., Ashworth, A., Lord, C.J. (2016). Nature Communications

[PDF]  [Journal page]

There’s a writeup from the Institute of Cancer Research here


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., Costa-Cabral, S., Frankum, J., Gulati, A., Holme, H., Miller, R., Postel-Vinay, S., Rafiq, R., Wei, W., Williamson, C.T., Quigley, D.A., Tym, J., Al-Lazikani, B., Fenton, T., Natrajan, R., Strauss, S.J., Ashworth, A., Lord, C.J. (2016). Cell Reports 14, 10 * Equal Contribution

[PDF]  [Journal page]

I have written a lay summary of this paper here and there’s a writeup from the Institute of Cancer Research here


Genetic Interaction Mapping Reveals a Role for the SWI/SNF Nucleosome Remodeler in Spliceosome Activation in Fission Yeast.
Patrick, K.L., Ryan, C.J., Xu, J., Lipp, J.J., Nissen, K.E., Roguev, A., Shales, M., Krogan, N.J., and Guthrie, C. (2015). PLoS Genetics 11, 3

[PDF]  [Journal page]


Genome-wide epistatic expression quantitative trait loci discovery in four human tissues reveals the importance of local chromosomal interactions governing gene expression.
Fitzpatrick, D.J., Ryan, C.J., Shah, N., Greene, D., Molony, D., and Shields, D.C. (2015). BMC Genomics 16, 109

[PDF]  [Journal page]

This paper has been identified as Highly Accessed by Biomed Central.


Evolutionarily conserved genetic interactions with budding and fission yeast MutS identify orthologous relationships in mismatch repair-deficient cancer cells.
Tosti, E., Katakowski, J.A., Schaetzlein, S., Kim, H., Ryan, C.J., Shales, M., Roguev, A., Krogan, N.J., Palliser, D., Keogh, M., and Edelmann, W. (2014). Genome Medicine 6, 68

[PDF]  [Journal page]


DAISY: Picking Synthetic Lethals from Cancer Genomes.
Ryan, C.J., Lord, C.J., and Ashworth, A. (2014). Cancer Cell 26, 306–308

[PDF]  [Journal page]


Identification of a BET Family Bromodomain/Casein Kinase II/TAF-Containing Complex as a Regulator of Mitotic Condensin Function.
Kim, H., Mukhopadhyay, R., Rothbart, S.B., Silva, A.C., Vanoosthuyse, V., Radovani, E., Kislinger, T., Roguev, A., Ryan, C.J., Xu, J., Jahari, H., Hardwick, K.G., Greenblatt, J.F., Krogan, N.J., Fillingham, J.S., Strahl, B.D., Bouhassira, E.E., Edelmann, W., and Keogh, M.C. (2013). Cell Reports 6, 892–905

[PDF]  [Journal page]


Chemical Genetics of Rapamycin-Insensitive TORC2 in S. cerevisiae.
Kliegman, J.I., Fiedler, D., Ryan, C.J. , Xu, Y., Su, X., Thomas, D., Caccese, M.C., Cheng, A., Shales, M., Rabinowitz, J.D., Krogan, N.J., and Shokat, K.M. (2013). Cell Reports 5, 1725–1736

[PDF] [Journal page]


High-resolution network biology: connecting sequence with function.
Ryan, C.J., Cimermančič, P., Szpiech, Z.A., Sali, A., Hernandez, R.D., and Krogan, N.J. (2013). Nature Reviews Genetics 14, 865–879

[PDF][Journal page]

The Conway Institute have an article this paper here.


Systematic Triple-Mutant Analysis Uncovers Functional Connectivity between Pathways Involved in Chromosome Regulation.
Haber, J.E., Braberg, H., Wu, Q., Alexander, R., Haase, J., Ryan, C., Lipkin-Moore, Z., Franks-Skiba, K.E., Johnson, T., Shales, M., Lenstra, T.L., Holstege, F.C., Johnson, J.R., Bloom, K., and Krogan, N.J. (2013). Cell Reports 3, 2168-2178 

[PDF]  [Journal page]


All or Nothing: Protein Complexes Flip Essentiality between Distantly Related Eukaryotes.
Ryan, C.J., Krogan, N.J., Cunningham, P., and Cagney, G. (2013). Genome Biology and Evolution 5, 1049-1059.

[PDF]  [Journal page]

 The Yeast Genome Database (SGD) have a post on this paper here.


The yeast SR-like protein Npl3 links chromatin modification to mRNA processing.
Moehle, E.A., Ryan, C.J., Krogan, N.J., Kress, T.L., and Guthrie, C. (2012). PLoS Genetics 8, e1003101.

[PDF]  [Journal page]

 This paper is recommended by the Faculty of 1000 here.


Hierarchical modularity and the evolution of genetic interactomes across species
Ryan, C.J.*, Roguev, A.*, Patrick, K., Xu, J., Jahari, H., Tong, Z., Beltrao, P., Shales, M., Qu, H., Collins, S.R., Kliegman, J.I., Jiang, L., Kuo, D., Tosti, E., Kim, H.S., Edelmann, W., Keogh, M.C., Greene, D., Tang, C., Cunningham, P., Shokat, K.M., Cagney, G., Svensson, J.P., Guthrie, C., Espenshade, P.J., Ideker, T., and Krogan, N.J. (2012). Molecular Cell 46, 691-704. * Equal Contribution

[PDF]  [Journal page] [Supplementary Site With Databases]


Key functional regions in the histone variant H2A.Z C-terminal docking domain.
Wang, A.Y., Aristizabal, M.J., Ryan, C., Krogan, N.J., and Kobor, M.S. (2011). Molecular and Cellular Biology 31, 3871-3884.

[PDF]  [Journal page]


Improved functional overview of protein complexes using inferred epistatic relationships.
Ryan, C., Greene, D., Guenole, A., van Attikum, H., Krogan, N.J., Cunningham, P., and Cagney, G. (2011). BMC Systems Biology 5, 80.

[PDF]  [Journal page]


Missing value imputation for epistatic MAPs.
Ryan, C., Greene, D., Cagney, G., and Cunningham, P. (2010). BMC Bioinformatics 11, 197.

[PDF]  [Journal page] [Supplementary Site With Code]


Book Chapters:

High-throughput quantitative genetic interaction mapping in the fission yeast Schizosaccharomyces pombe

Roguev, A., Ryan, C.J., Hartsuiker, E., Krogan, N. (2017). Cold Spring Harbor Protocols

 [Journal page]


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

Roguev, A., Ryan, C.J., Xu, J., Colson, I., Hartsuiker, E., Krogan, N. (2017). Cold Spring Harbor Protocols

 [Journal page]


Comparative interaction networks: bridging genotype to phenotype.
Beltrao, P., Ryan, C., and Krogan, N.J. (2012). Advances in Experimental Medicine and Biology 751, 139-156.

[PDF]  [Journal page]


Imputing and predicting quantitative genetic interactions in epistatic MAPs.
Ryan, C., Cagney, G., Krogan, N., Cunningham, P., and Greene, D. (2011). Methods Mol Biol 781, 353-361.

[PDF]  [Journal page] [Supplementary Site With Code]