Direct RNA sequencing on nanopore arrays redefines the transcriptional complexity of a viral pathogen

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

Herpes Simplex Virus 1 Dramatically Alters Loading and Positioning of RNA Polymerase II on Host Genes Early in Infection

(2018) Claire H. Birkenheuer et al.   JOURNAL OF VIROLOGY

Defining the Role of Stress Granules in Innate Immune Suppression by the Herpes Simplex Virus 1 Endoribonuclease VHS

(2018) Hannah M. Burgess et al.   JOURNAL OF VIROLOGY

Highly parallel direct RNA sequencing on an array of nanopores

(2018) Daniel R Garalde et al.   NATURE METHODS

Translational Control in Virus-Infected Cells

(2018) Noam Stern-Ginossar et al.   Cold Spring Harbor Perspectives in Biology

HSV-1-induced disruption of transcription termination resembles a cellular stress response but selectively increases chromatin accessibility downstream of genes

(2018) Thomas Hennig et al.   PLoS Pathogens

Direct RNA Sequencing of the Coding Complete Influenza A Virus Genome

(2018) Matthew W. Keller et al.   Scientific Reports

Going the Distance: Optimizing RNA-Seq Strategies for Transcriptomic Analysis of Complex Viral Genomes

(2018) Daniel P. Depledge et al.   JOURNAL OF VIROLOGY

The punctilious RNA polymerase II core promoter

(2017) Long Vo ngoc et al.   GENES & DEVELOPMENT

Discovery and characterization of novel trans-spliced products of human polyoma JC virus late transcripts from PML patients

(2017) A. Sami Saribas et al.   JOURNAL OF CELLULAR PHYSIOLOGY

Shared ancestry of herpes simplex virus 1 strain Patton with recent clinical isolates from Asia and with strain KOS63

(2017) Aldo Pourchet et al.   VIROLOGY

Nanopore long-read RNAseq reveals widespread transcriptional variation among the surface receptors of individual B cells

(2017) Ashley Byrne et al.   Nature Communications

Long-Read Isoform Sequencing Reveals a Hidden Complexity of the Transcriptional Landscape of Herpes Simplex Virus Type 1

(2017) Dóra Tombácz et al.   Frontiers in Microbiology

Characterization of the Dynamic Transcriptome of a Herpesvirus with Long-read Single Molecule Real-Time Sequencing

(2017) Dóra Tombácz et al.   Scientific Reports

Gene overlapping and size constraints in the viral world

(2016) Nadav Brandes et al.   Biology Direct

Evolutionary Insights into RNA trans-Splicing in Vertebrates

(2016) Quan Lei et al.   Genome Biology and Evolution

Global transcript structure resolution of high gene density genomes through multi-platform data integration

(2016) Tina O'Grady et al.   NUCLEIC ACIDS RESEARCH

Widespread disruption of host transcription termination in HSV-1 infection

(2015) Andrzej J. Rutkowski et al.   Nature Communications

proovread : large-scale high-accuracy PacBio correction through iterative short read consensus

(2014) Thomas Hackl et al.   BIOINFORMATICS

Transcription of the Herpes Simplex Virus 1 Genome during Productive and Quiescent Infection of Neuronal and Nonneuronal Cells

(2014) J. M. Harkness et al.   JOURNAL OF VIROLOGY

Pervasive Transcription of a Herpesvirus Genome Generates Functionally Important RNAs

(2014) S. P. Canny et al.   mBio

KSHV 2.0: A Comprehensive Annotation of the Kaposi's Sarcoma-Associated Herpesvirus Genome Using Next-Generation Sequencing Reveals Novel Genomic and Functional Features

(2014) Carolina Arias et al.   PLoS Pathogens

IVT-seq reveals extreme bias in RNA sequencing

(2014) Nicholas F Lahens et al.   GENOME BIOLOGY

Homologous SV40 RNA trans-splicing: Special case or prime example of viral RNA trans-splicing?

(2014) Sushmita Poddar et al.   Computational and Structural Biotechnology Journal

Software for Computing and Annotating Genomic Ranges

(2013) Michael Lawrence et al.   PLoS Computational Biology

Decoding Human Cytomegalovirus

(2012) N. Stern-Ginossar et al.   SCIENCE

Chimeric Transcript Generated by cis-Splicing of Adjacent Genes Regulates Prostate Cancer Cell Proliferation

(2012) Yanmei Zhang et al.   Cancer Discovery

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

Ending the message: poly(A) signals then and now

(2011) N. J. Proudfoot   GENES & DEVELOPMENT

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS