Andrew L. Routh

This study uses a new sequencing method to show that viral RNA is released in an ordered, conserved manner during virus disassembly, with specific genomic regions released first.

This study identifies that reovirus recombination is highly selective, with junction sites determined by gene segment identity rather than polymerase activity.

This study shows SARS-CoV-2 NSP15 (EndoU) regulates RNA recombination and viral fitness, with its loss reducing replication but increasing inflammation and defective genomes.

This study identifies an RNA-RNA heterodimer in Flock House virus that affects genome packaging and virion stability.

This study identifies RpoS as a key regulator of Salmonella Typhi biofilm formation and persistence in the gall bladder, revealing a CsgD-independent mechanism.

ViReMa is updated to detect recombination events in long-read sequencing data and reports various recombinant species in different viral contexts.

ViReMaShiny provides an interactive web tool for visualizing and analyzing viral recombination data in BED format, improving accessibility and downstream analysis.

The paper develops a method to sequence full-length host and viral transcripts by ablating 3' RNA ends and using processive reverse transcriptases, improving coverage and detection of long transcripts.

The paper uses CoVaMa to analyze co-variation between SNVs and recombination events in viral genomes, finding correlations in FHV and HIV datasets.

This study investigates how WT and P301L tau proteins modulate transcription and alternative polyadenylation profiles in neuronal cells, revealing distinct gene expression changes related to chromatin remodeling and splicing.

This study identifies RBFOX2's role in maintaining alternative polyadenylation and mitochondrial health in rat myoblasts, linking it to heart disease pathology.

Tiled-ClickSeq enables complete SARS-CoV-2 genome sequencing with detection of RNA recombination and minority variants in a single assay.

MrHAMER enables accurate long-range viral sequencing, allowing analysis of intra-host evolution and genetic interactions in HIV.

This study identifies differential defective RNA (D-RNA) diversity between intracellular and encapsidated alphavirus compartments, showing that some D-RNAs arise de novo and are not packaged, with subgenomic D-RNAs identified as a novel subtype.

This paper introduces PAR-CL, a method to identify RNA-capsid interactions in virus particles, and shows that these interactions occur preferentially in double-stranded RNA regions.

DPAC analyzes poly(A)-tail targeted RNAseq data to identify differential poly(A) site usage and related gene expression changes.

Poly(A)-ClickSeq enables high-quality RNA-seq libraries of poly(A) site junctions without RNA enrichment or fragmentation, revealing new poly(A) sites and APA regulation.