Tânia Duarte

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

This study compares DNA and RNA nanopore sequencing for detecting drug resistance in XDR K. pneumoniae, finding RNA sequencing identifies more resistance genes and shows strong correlation with qRT-PCR.

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.

The paper assembles a complete genome of an XDR M. tuberculosis strain using Nanopore sequencing, identifies novel genetic variations in repetitive PE/PPE regions, and links these to drug resistance and virulence.

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.

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