The UCD Cancer Data Lab, led by Dr. Colm J. Ryan, use large-scale data analysis to understand how genetic variation in cancer alters molecular interaction networks and to identify ways to target these alterations therapeutically.


Research Overview

Recent News

Olivier's paper evaluating alternative protein representations for predicting shared paralog functions

Olivier’s paper evaluating alternative protein representations for predicting shared paralog functions

Congrats to Olivier on his first publication with the lab, Evaluating Sequence and Structural Similarity Metrics for Predicting Shared Paralog Functions, up now on biorXiv.

Anjan's paper on proteomic compensation between paralogs in cancer

Anjan’s paper on proteomic compensation between paralogs in cancer

Compensation between duplicate genes (paralogs) allows cancer cells to tolerate genetic mutations that might otherwise be lethal. We wanted to know what this compensation looked at a molecular level – what are the proteins involved doing? How come losing functional genes doesn’t just just break the protein-protein interaction networks operating inside cancer cells?

Conway Festival 2024!

Conway Festival 2024!

The lab was well represented at the Conway Festival of Research 2024. Colm gave an invite lectured, Cosmin was a runner up in the Gold Medal competition for his NAR Cancer paper and Narod, Metin, Olivier and Hamda all presented posters. We didn’t take enough photos, but managed to capture Metin and Olivier in action.

Congratulations to Dr. Swathi Upadhya

Congratulations to Dr. Swathi Upadhya

Congratulations to Dr. Swathi Upadhya, who successfully defended her thesis ‘On the predictability and prediction of protein abundances in tumours’ on December 12th.

Barbara's paper on homozygous deletions of paralogs in cancer

Barbara’s paper on homozygous deletions of paralogs in cancer

Congrats to Dr. Barbara De Kegel on the publication of her work to understand how the dispensability of paralogs shapes homozygous deletion patterns in tumors.

Swathi's paper on the influence of antibody quality on mRNA-protein correlations

Swathi’s paper on the influence of antibody quality on mRNA-protein correlations

Congrats to Swathi on the publication of her work to understand the influence of antibody quality on the mRNA-protein correlations observed in tumour cohorts.

Congratulations to Dr. Thomas Lefeivre

Congratulations to Dr. Thomas Lefeivre

Congratulations to Dr. Thomas Lefeivre, who successfully defended his thesis ‘Investigation of the functional interplay between signalling pathways and epigenetic factors in acute leukaemia’ on April 18th.

Cosmin's paper on using Gene Regulatory Networks to predict gene essentiality in cancer

Cosmin’s paper on using Gene Regulatory Networks to predict gene essentiality in cancer

Gene regulatory networks (GRNs) are widely used to understand how driver mutations in tumours alter transcriptional networks and to identify new therapeutic targets. Here, we use genome-wide CRISPR screen data to systematically evaluate the ability of GRNs to predict sensitivity to genetic perturbation in cancer.

End of year symposium - ICBG2022

End of year symposium - ICBG2022

Just approaching the end of the year, we had the opportunity to present our work at #ICGB2022.

We are hiring!

We are hiring!

We are currently looking for computational postdoctoral fellows! More details here Photo above is from a lab hike during COVID times. In Dublin we cannot promise constant sunshine, but we can promise the benefits of living in a capital city coupled with close proximity to the sea and some lovely scenery.

The return of in person conferences!

The return of in person conferences!

After more than two years with conference travel halted due to COVID-19, lab members have finally had the opportunity to attend in person conferences.

Swathi's paper on the relationship between mRNA and protein abundances

Swathi’s paper on the relationship between mRNA and protein abundances

Everyone knows that there is an imperfect correlation between mRNA and protein abundances. In Swathi’s recent paper we analysed how much measurement (ir)reproducibility contributes to this.

Thomas presents at Spetses Summer School

Thomas presents at Spetses Summer School

Congratulations to Thomas Lefeivre, who is a member of both the Bond Group and the Ryan group for giving a talk titled ‘The loss of PRC2 function diversely impacts signalling pathway activity in acute leukaemia’ at the Spetses Summer School 2022.

Congratulations to Dr. Barbara De Kegel!

Congratulations to Dr. Barbara De Kegel!

Congratulations to Dr. Barbara De Kegel, who passed her viva with flying colours last week.

Our group are affiliated with the UCD School of Medicine and based in the Conway Institute of Biomolecular and Biomedical Research. Various lab members are also affiliated with Systems Biology Ireland and the SFI Centre for Research Training in Genomics Data Science.