Kilannin Krysiak

Searching the Druggable Genome using Large Language Models

The paper develops a server enabling large language models to access drug-gene interaction data through natural language queries.

Multi-Platform Curation in the Development of ACMG/AMP Specifications for Von Hippel Lindau (VHL) Disease

The paper describes the development of variant classification specifications for the VHL gene using ACMG/AMP guidelines, resulting in updated evidence codes and improved classification consistency.

CIViC-Fact: a proof-of-concept framework for AI-assisted verification of cancer variant interpretations

CIViC-Fact evaluates AI models for verifying cancer variant interpretations using full-text evidence, showing abstracts are insufficient for accurate validation.

Neoantigen Landscape Supports Feasibility of Personalized Cancer Vaccine for Follicular Lymphoma

This study identifies high-quality neoantigens in follicular lymphoma patients using WES and RNA-Seq, and initiates a clinical trial of personalized neoantigen vaccines combined with PD-1 blockade.

Ultra Deep Sequencing Reveals the Mutational Landscape of Classical Hodgkin Lymphoma

This study uses ultra-deep exome sequencing to identify recurrent mutations in classical Hodgkin lymphoma HRS cells, demonstrating its utility for analyzing genomic variants in large patient cohorts.

Evolution of the open-access CIViC knowledgebase is driven by the needsof the cancer variant interpretation community

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.

A harmonized meta-knowledgebase of clinical interpretations of cancer genomic variants

The paper harmonizes clinical interpretations of cancer genomic variants across six knowledgebases, improving overlap and matching with patient cohorts.

CIViCpy: a Python software development and analysis toolkit for the CIViC knowledgebase

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

Text-mining clinically relevant cancer biomarkers for curation into the CIViC database

The paper describes the development of CIViCmine, a text-mining tool that extracts clinically relevant cancer biomarkers from literature to aid curation into the CIViC database.

The CIViC knowledge model and standard operating procedures for curation and clinical interpretation of variants in cancer

The paper describes the CIViC knowledge model and curation procedures for systematically organizing and interpreting cancer-related genetic variants.

Identification of community-consensus clinically relevant variants and development of single molecule molecular inversion probes using the CIViC database

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.

Standard operating procedure for somatic variant refinement of tumor sequencing data

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

The prognostic effects of somatic mutations in ER-positive breast cancer

The paper identifies somatic mutations with prognostic effects in ER+ breast cancer using genomic data from multiple cohorts.

CIViC: A knowledgebase for expert-crowdsourcing the clinical interpretation of variants in cancer.

CIViC is a knowledgebase that crowdsources expert input to interpret the clinical significance of cancer variants, providing open-access resources for precision medicine.