pathogen-detection

Ultrafast identification of signature sequences in microbial genomes

Reference-free, privacy-preserving wastewater pathogen surveillance for federated hospital networks. DNABERT-2 embeddings + Transformer-encoder VAE detect emerging anomaly clusters in unclassified reads. AIxBio Hackathon Track 2, Apart Research.

Functions for working with NCBI's Pathogen Detection data

Pathogen Identifier and Strain Tagger datasets

Circulating fungal rRNA detection

Sequence Matching fOr REpiratory Diseases, SMORE'D, is a command-line sequence classification tool tailored to meet the needs of the Undiagnosed Respiratory Disease Outbreak (URDO) branch at CDC. SMORE'D is a k-mer based classification tool capable of rapidly classifying read sequences generated by multi-pathogen detection platforms.

MSc thesis: pangenomics + machine learning to cut false positives in metagenomic detection of E. coli O157:H7 (AUROC 0.761 vs 0.552 for BLAST)

ZoonomiX is a bioinformatics pipeline for analyzing microbial genomes, detecting pathogenicity, resistance genes, and mobile elements, and assessing zoonotic risk using BLASTn.

Closed-form sequencing depth bounds for detecting divergent pathogens in clinical metagenomic sequencing (mNGS)

🐹 Metagenomic Alignment and Reporting for Monitoring Of Threats

Multi-omics pipeline for detecting & characterizing Pentatrichomonas hominis as a potential opportunistic pathogen in immunocompromised gut microbiomes — featuring custom genome/marker databases, Nextflow workflows, and machine learning.

Smart Diagnostics Systems — independent third-party profile of a public API surface, by API Evangelist. Smart Diagnostics Systems (SDS) is a food-safety diagnostics company based in Columbia, Missouri, founded in 2016 and backed by Techstars. SDS builds the PathoMeter, a state-of-the-art rapid diagnostic system for the detection of foodborne pathog

Sample6 — independent third-party profile of a public API surface, by API Evangelist. Sample6 was a food-safety technology company (a Canaan Partners portfolio company) that developed rapid, bioluminescence-based pathogen detection and environmental monitoring products for the food industry, aimed at catching contamination such as Listeria, Salmone