Minh Duc Cao

This study evaluates in vitro resistance development in MRSA to vancomycin, daptomycin, and linezolid, identifying mutations and mechanisms associated with resistance.

PanTA efficiently constructs large bacterial pangenomes, outperforming existing tools in speed while maintaining accuracy and enabling progressive updates without rebuilding from scratch.

AMRomics is a scalable pipeline for analyzing large microbial genome collections, showing better performance than existing tools.

Pasa improves genome scaffolding by using population pangenome graphs, enhancing accuracy and efficiency for bacterial genome assemblies.

This paper introduces npGraph, a streaming hybrid assembly tool that improves genome assembly accuracy using ONT long reads and an assembly graph, while maintaining low computational cost.

This paper develops a method to assemble whole-chromosome pseudomolecules for polyploid plant genomes using genotyping-by-sequencing and reference genome data, showing improved accuracy over existing tools.

This paper develops a targeted long-read sequencing method for high-throughput tandem repeat genotyping, achieving high accuracy and scalability.

The paper uses BioNano and nanopore data to analyze human chromosome ends, revealing heritable extensions and sequence duplications across primate lineages.

GtTR is a Bayesian method for estimating absolute tandem repeat copy numbers using targeted sequencing and reference data, achieving high accuracy in population-scale genotyping.

npInv detects and genotypes NAHR inversions using long read sub-alignment, identifying 30 inversions in NA12878 with 94% accuracy, including 15 novel ones.

Chiron is a deep learning model that directly translates nanopore raw signals into DNA sequences without segmentation, achieving high accuracy and speed with minimal training data.

CapSim simulates targeted sequencing dynamics to evaluate probe design efficiency and sequencing pipeline performance.

npBarcode enables real-time demultiplexing of nanopore barcoded sequencing data with comparable accuracy to existing tools.

This paper introduces a real-time method using nanopore sequencing to scaffold and complete genome assemblies, improving accuracy and reducing data and resource requirements.

This paper presents streaming algorithms for real-time MinION sequencing to identify pathogens and antibiotic resistance, demonstrating rapid species and resistance profile detection.