Roham Razaghi

Uncalled4 improves nanopore signal alignment for DNA and RNA modification detection, identifying more modifications than existing tools in human cell lines.

The paper introduces modbamtools, a tool for analyzing single-molecule epigenetic data, enabling visualization, manipulation, and downstream analysis of base modifications in long-read sequencing data.

The paper uses a complete human genome assembly to analyze epigenetic patterns in previously uncharacterized genomic regions, revealing methylation and chromatin accessibility features in satellite DNA and centromeres.

This paper demonstrates direct detection of RNA modifications and structure using single molecule nanopore sequencing, showing it can identify endogenous and exogenous modifications in rRNA from E. coli and S. cerevisiae.

This paper presents a new, more continuous and accurate reference genome for the Tobacco Hornworm moth using modern assembly techniques.

This study introduces nanoNOMe, a method combining NOMe-seq and nanopore sequencing to profile chromatin accessibility and methylation in human cell lines, revealing phased methylation, large-scale patterns, and structural variations.

StringTie2 assembles error-prone long reads, recovering on average 8.3 and 2.6 times as many correct transcripts as FLAIR and Traphlor, and outperforms Scallop on short reads.

The paper uses nanopore sequencing to analyze poly(A) RNA from human cells, identifying long transcripts and modifications not captured by traditional methods.