dnabert

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.

DeepVRegulome is an end‑to‑end framework for predicting the functional impact of small somatic variants in non‑coding regulatory regions (splice sites and transcription‑factor‑binding sites) using fine‑tuned DNABERT models.

Assessing LLMs—AAM, DNABERT, DNABERT-2, GROVER—to improve the prediction of COVID-19 status ("Positive" or "Not detected") using microbiome data

Code and datasets for studying how negative dataset selection impacts ML-based promoter predictors across multiple bacterial species (Random Forest, CNN, DNABERT, Nucleotide Transformer).

From Raw DNA to Real Action. An AI-powered platform that translates raw river eDNA datasets into instant, plain-English biodiversity intelligence and automatically alerts government agencies of ecological risks in minutes instead of years.

Mosquito Virome Emergence Framework — companion code for Hoyos-López (2026), Briefings in Bioinformatics

Predict antomicrobial resistance (AMR) for a pathogen (Staphylococcus aureus) against an antibiotic (Cefoxitin) using encoder-only transformer given the genomic sequence of one of its genes (gene pbp4) as input.