Projects

VAT: General and Extensible Algorithmic Framework for Biological Sequence Alignment

VAT: General and Extensible Algorithmic Framework for Biological Sequence Alignment

A general and extensible algorithmic framework to biological sequence alignment across scales and applications, enabling efficient alignment from k-mer to full genome scales.

  • Multi-scale alignment framework
  • Extensible architecture for various biological applications
  • Patent pending
Paper Code Demo
SNAIL: Software Named Entity Identification from Literature

SNAIL: Software Named Entity Identification from Literature

A system for automated identification and extraction of software names and related entities from scientific literature, enabling large-scale software discovery and citation analysis.

  • Named entity recognition for software in biomedical literature
  • Automated citation generation
  • Patent pending
Paper Code Demo
Microbiome + Immunotherapy Embedding for NSCLC Response Prediction

Microbiome + Immunotherapy Embedding for NSCLC Response Prediction

Gut metagenomic k-mer signature-based approach that outperforms traditional taxonomy-based methods for predicting immunotherapy response in non-small cell lung cancer patients.

  • K-mer signature-based prediction
  • Outperforms taxonomy-based methods
  • Clinical application potential
Paper Code Demo
scVAT: Single-Cell RNA-Sequencing Analysis Pipeline

scVAT: Single-Cell RNA-Sequencing Analysis Pipeline

An nf-core compatible single-cell RNA-sequencing analysis pipeline for comprehensive scRNA-seq data processing and analysis.

  • nf-core compatible
  • Comprehensive scRNA-seq analysis
  • Work in progress
Paper Code Demo
Multi-Agent Clinical Intelligence System

Multi-Agent Clinical Intelligence System

Leveraging Model Context Protocol for evidence-based drug discovery through multi-agent reasoning systems.

  • Multi-agent reasoning
  • Evidence-based drug discovery
  • Model Context Protocol integration
Paper Code Demo