pathogenicity

Characterization of Germline variants

ClassifyCNV: a tool for clinical annotation of copy-number variants

Cancer Predisposition Sequencing Reporter (CPSR)

POSTRE: Prediction Of STRuctural variant Effects

LieFold-AI: Lie-Dynamics Geometric Biology

MetaDome is aimed at professionals in the (bio-)medical field of human genetics who wish to visualize the position of their variant of interest in the context of general population-based genetic variation, and provides detailed information on pathogenic variants found across homologous protein domain positions, for GRCh37 and GRCh38.

TAD-aware annotation of CNVs

[MLCB 2024] [ICML AI4Science 2024] PathoLM: Identifying pathogenicity from the DNA sequence through the Genome Foundation Model

Predicting pathogenic potentials of short DNA reads with reverse-complement deep neural networks.

A weakly supervised regression approach to directly predict the probability of pathogenicity based on categorized pathogenicity classes

Assessing the performance of 28 pathogenicity prediction methods on rare single nucleotide variants in coding regions

Deep multiple instance learning model for predicting deletion pathogenicity and gene haploinsufficiency.

Collection of 1069 Escherichia coli virulence factors

Calibrated confidence layer for variant-effect pathogenicity (AlphaMissense/ESM-1v/EVE)

Variant pathogenicity classifier with calibrated probabilities, gene-grouped cross-validation

Evidence-aware somatic variant pathogenicity classifier. Benchmarks a Cross-Attention fusion network over ESM-2 protein embeddings against LightGBM, with gene-disjoint external validation and a leakage-audit for Type-1 circularity.

Computational analysis and classification of Variants of Unknown Significance (VUS) in the BCS1L gene associated with Björnstad Syndrome. Implements a conservation score-based algorithm using BLASTp homologous sequences, MUSCLE alignment, and phylogenetic analysis to classify variants as pathogenic or benign.

SGG (Soupirr's Global Genotyper) is a bioinformatics tool designed to identify the genotype and predict the pathogenicity of Virus by using reference sequences. It compares user input sequence against a curated reference database.

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.