Clinical genomics web app to visualize & prioritize exome VCF variants on protein structures — published in Bioinformatics (2019)

ACMG Assistant is a student-level, research-oriented variant classification tool developed to explore the practical application of ACMG/AMP 2015 and 2023 guidelines. It combines automated retrieval of annotation data from public APIs with structured interactive evidence collection to support systematic variant interpretation.

Calibrate functional/in-silico variant scores into ACMG clinical evidence strengths (ClinGen-SVI), with LDLR/AlphaMissense worked example

Drafts ACMG/AMP variant classifications for a human curator: gathers genomics evidence, adjudicates each criterion with Claude, computes the label in code via ClinGen points, and shows every source.

MCP gateway federating 21 biomedical MCP servers — gnomAD, ClinVar, HPO, UniProt, Ensembl VEP, PanelApp and more — behind one Streamable-HTTP endpoint, with collision-free namespaced tools and BM25 tool search.

Mechanism-aware variant interpretation pipeline for monogenic epilepsy: RF + ESM-2 LoRA pathogenicity heads, gain-vs-loss-of-function mechanism classifier, sodium-channel prescribing rule, leave-one-out dynamic-evidence framework.

MCP server for GeneReviews: the expert-authored, peer-reviewed gene–disease chapters on NCBI Bookshelf, served as a searchable corpus of individually citable passages.

Interactive web-based tool for visualizing gene variants, protein domains & annotations – no coding required. Customize maps, highlight variants, export SVG/PNG.

Research tool for exploring carrier frequencies and recurrence risks for autosomal recessive conditions using gnomAD population data. For research use only.

MCP server for PanelApp: consensus diagnostic gene panels and gene–disease ratings from Genomics England (UK) and PanelApp Australia — as typed tools for LLM agents.

MCP server for NCBI ClinVar: variant clinical significance and gene-level classifications, served from a local SQLite index built from the ClinVar weekly bulk release — not the eUtils API.

MCP server for AutoPVS1: automated ACMG PVS1 loss-of-function evidence for sequence variants and copy-number variants — variant interpretation as typed tools for LLM agents.

MCP server for GenCC (Gene Curation Coalition): harmonized gene–disease validity classifications across member submitters, with consensus and conflict detection per gene–disease pair.

MCP server for ClinGen (Clinical Genome Resource): gene–disease validity, dosage sensitivity, clinical actionability, and expert-panel variant pathogenicity (ERepo) — as typed tools for LLM agents.