Obi L. Griffith

Refinement of the Pathogenic T Cell Receptor Motif Suggests Type 17 CD8+ T Cells Initiate HLA-B*27-associated Autoimmunity

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.

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.

Personalized Neoantigen Vaccines Synergize with Immune Checkpoint Therapy and CD8-Targeted Cytokines to Control B-Cell Lymphoma

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.

dgiLIT: A Method for Prioritization and AI Curation of Drug-Gene Interactions

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.

CIViC MCP: Integrating Large Language Models with the Clinical Interpretations of Variants in Cancer

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.

Clonal dynamics of monozygotic twinning in early human embryogenesis

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

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.

Single-Cell Transcriptomic Analysis of Kaposi Sarcoma

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.

The Hao-Fountain syndrome protein USP7 regulates neuronal connectivity in the brain via a novel p53-independent ubiquitin signaling pathway

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

Whole-genome sequences reveal zygotic composition in chimeric twins

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.

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.

Single Cell T Cell Receptor Repertoire Profiling for Dogs

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

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.

Computational prediction of MHC anchor locations guide neoantigen identification and prioritization

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: Integrated analysis of genomic and transcriptomic data for the discovery of splice-associated variants in cancer

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

The GA4GH Variation Representation Specification (VRS): a Computational Framework for the Precise Representation and Federated Identification of Molecular Variation

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.

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.

Integration of the Drug-Gene Interaction Database (DGIdb) with open crowdsource efforts

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.

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.

Wikidata as a FAIR knowledge graph for the life sciences

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: a computational toolkit to identify and visualize cancer neoantigens

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

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.

Clingen Cancer Somatic Working Group: standardizing and democratizing access to cancer molecular diagnostic data to drive translational research

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

DGIdb 3.0: a redesign and expansion of the drug-gene interaction database

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