Kelsy C. Cotto

The paper predicts MHC anchor positions for 328 HLA alleles and shows that incorporating these improves neoantigen identification by correcting misclassified candidates in tumor samples.

RegTools identifies splice-associated variants in cancer by integrating genomic and transcriptomic data across 9,000 tumor samples, discovering 235,778 splicing events.

The paper describes the evolution of the CIViC knowledgebase to meet the needs of the cancer variant interpretation community by expanding its functionality and data types.

DGIdb 4.0 aggregates drug-gene interaction and druggability claims from 41 sources, adding crowd-sourced Drug Target Commons, Wikidata-based drug normalization, search-relative query scores, and NDEx export.

CIViCpy is a Python SDK for accessing and analyzing the CIViC knowledgebase, enabling efficient variant annotation in cancer genomics.

The paper designs single molecule molecular inversion probes targeting clinically relevant variants using the CIViC database, demonstrating high sensitivity and discovering missed variants in cancer samples.

This paper establishes a standard operating procedure for manual refinement of somatic variants in tumor sequencing data to improve consistency and reproducibility.

DGIdb 3.0 updates and expands the drug-gene interaction database by adding new sources, improving the codebase, and enhancing API features.