Devika Ganesamoorthy

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

This study uses CRISPR-Cas9 to enrich specific transcripts for long-read sequencing, enabling efficient and accurate isoform discovery and low abundance transcript detection.

The paper compares Nanopore direct RNA-seq and Illumina cDNA-seq in sepsis patients, finding strong correlation and identifying post- and co-transcriptional biomarkers.

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

The paper analyzes polyclonal vector integration sites using Nanopore sequencing to provide a scalable and cost-effective method for tracking gene-modified cells.

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.

This paper introduces qCNV and sCNA-seq tools to profile somatic copy number alterations in cell-free DNA without a reference panel, showing effectiveness in detecting clinically relevant mutations from plasma samples.

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

sCNAphase improves copy number alteration analysis in low-cellularity tumors by using haplotype-resolved read depth to genotype somatic copy number alterations.

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

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