Malachi Griffith

The paper identifies a broader pathogenic T cell receptor motif linked to HLA-B*27-associated autoimmune diseases and shows these T cells express a Type 17 program.

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

This study shows that personalized neoantigen vaccines combined with immune checkpoint therapy and CD8-targeted cytokines effectively control B-cell lymphoma by enhancing T-cell responses and preventing dysfunction.

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.

The paper introduces dgiLIT, an AI-driven method to prioritize and curate drug-gene interactions from biomedical literature for inclusion in DGIdb, achieving high validation rates.

The paper introduces CIViC MCP, a system that uses large language models to interface with the CIViC knowledgebase, enabling natural language queries for cancer variant interpretations.

The paper uses post-zygotic mutations to analyze clonal dynamics in monozygotic twins and finds three clonal categories correlated with amnionicity, not chorionicity.

This study shows that the CTCF binding site in HTLV-1 regulates viral pathogenesis by affecting proviral load, Tax expression, and T-cell activation in humanized mice.

This study uses single-cell RNA sequencing to analyze Kaposi Sarcoma tumors and blood samples, identifying KSHV-infected cell types and their biomarkers, and showing changes with therapy.

This study shows that USP7 deletion in mice causes neurological phenotypes, including synaptic proteome changes and dendritic spine defects, independent of p53.

The paper uses whole-genome sequencing to determine zygotic composition in chimeric twins, finding asymmetrical contributions from two zygotes in blood but not in buccal tissues.

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.

This paper develops species-specific single-cell T cell receptor sequencing (scTCRseq) for dogs, enabling analysis of T cell repertoires in cancer immunotherapy trials.

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.

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 introduces the GA4GH Variation Representation Specification (VRS), a framework for precise and federated representation of molecular variation, with a reference implementation and community resources available online.

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.

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

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

The paper describes Wikidata as a FAIR knowledge graph for life sciences, showcasing its breadth, tools for integration, and use cases in biomedical analysis.

pVACtools provides a suite of tools for neoantigen prediction, prioritization, and vaccine design in cancer immunotherapy.

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

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.

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

The paper describes the development of standards for cancer variant interpretation and sharing through the ClinGen Cancer Somatic Working Group.

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