C. J. Ryan

ATOMDANCE: kernel-based denoising and allosteric resonance analysis for functional and evolutionary comparisons of protein dynamics

ATOMDANCE compares and denoises protein motion dynamics between functional or evolutionary states using kernel-based methods to identify key sites and functional shifts.

Paralog dispensability shapes homozygous deletion patterns in tumor genomes

The paper shows that paralog dispensability influences homozygous deletion patterns in tumors, with more dispensable paralogs being more frequently deleted.

Integrative analysis of large-scale loss-of-function screens identifies robust cancer-associated genetic interactions

The paper identifies robust cancer-associated genetic interactions across multiple studies and finds that protein-protein interactions are enriched among these interactions.

A compendium of co-regulated protein complexes in breast cancer reveals collateral loss events

The paper identifies 258 protein complexes in breast cancer and finds that mutations in one subunit often lead to reduced expression of other complex members, a phenomenon observed in proteomic but not transcriptomic data.

CancerGD: a resource for identifying and interpreting genetic dependencies in cancer

CancerGD identifies and interprets genetic dependencies in cancer by integrating genotypic profiling with loss-of-function screens in tumor cell lines.