Daniel Pearce Depledge

An ONT sequencing framework for hantavirus genome assembly, variant analysis, and defective viral genome characterization from whole-segment amplicons

This paper introduces an Oxford Nanopore sequencing framework for hantavirus genome assembly and variant analysis, revealing defective viral genomes as a new feature of hantavirus populations.

Extended poly(A) tails are a shared feature of herpesvirus mRNAs

The paper uses nanopore sequencing to show herpesvirus mRNAs have longer poly(A) tails than cellular or other viral transcripts, suggesting a unique mechanism for enhancing gene expression.

Defining expansions and perturbations to the RNA polymerase III transcriptome and epitranscriptome by modified direct RNA nanopore sequencing

This paper introduces DRAP3R, a method for analyzing Pol III transcribed RNAs and their modifications, revealing new transcripts and epitranscriptomic changes in infected cells.

Calibrated analysis framework for nanopore direct RNA sequencing uncovers cell-specific m6A proportions at conserved sites

The paper evaluates Dorado basecalling for nanopore DRS to detect m6A modifications in RNA, finding that stringent filtering improves accuracy and revealing cell-type differences in m6A proportions at conserved sites.

Repression of varicella zoster virus gene expression during quiescent infection in the absence of detectable histone deposition

This study investigates VZV gene repression in neuronal cells, finding that histone deposition is absent at quiescent viral genomes.

Nanopore Guided Annotation of Transcriptome Architectures

The paper develops a novel method for high-resolution transcriptome annotation from Nanopore DRS data, demonstrating its effectiveness on both synthetic and real datasets, including a new annotation of human adenovirus type F 41.

The influence of human genetic variation on Epstein-Barr virus sequence diversity

The paper investigates how human genetic variation influences Epstein-Barr virus (EBV) sequence diversity by analyzing paired viral and human genomic data from HIV-coinfected individuals.

Direct RNA sequencing reveals m6A modifications on adenovirus RNA are necessary for efficient splicing

The paper uses direct RNA long-read sequencing to show m6A modifications on adenovirus RNA are necessary for efficient splicing.

A unique, spliced varicella-zoster virus latency transcript represses expression of the viral transactivator gene 61

The paper identifies and characterizes a unique VZV latency transcript (VLT) that represses the viral transactivator gene ORF61 during latency, unifying VZV latency with other herpesviruses.