Widespread disruption of host transcription termination in HSV-1 infection

Molecular Profiling of Neurons Based on Connectivity

(2014) Mats I. Ekstrand et al.   CELL

Quantitative Temporal Viromics: An Approach to Investigate Host-Pathogen Interaction

(2014) Michael P. Weekes et al.   CELL

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

Mouse TU tagging: a chemical/genetic intersectional method for purifying cell type-specific nascent RNA

(2013) L. Gay et al.   GENES & DEVELOPMENT

Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories

(2013) Peter A C 't Hoen et al.   NATURE BIOTECHNOLOGY

Mining RNA–Seq Data for Infections and Contaminations

(2013) Thomas Bonfert et al.   PLoS One

Means to an end: mechanisms of alternative polyadenylation of messenger RNA precursors

(2013) Andreas R. Gruber et al.   Wiley Interdisciplinary Reviews-RNA

The non-coding snRNA 7SK controls transcriptional termination, poising, and bidirectionality in embryonic stem cells

(2013) Gonçalo Castelo-Branco et al.   GENOME BIOLOGY

Molecular Profiling of Activated Neurons by Phosphorylated Ribosome Capture

(2012) Zachary A. Knight et al.   CELL

Co-transcriptional degradation of aberrant pre-mRNA by Xrn2

(2012) Lee Davidson et al.   EMBO JOURNAL

The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments

(2012) Nicholas T Ingolia et al.   Nature Protocols

A Comprehensive Evaluation of Alignment Algorithms in the Context of RNA-Seq

(2012) Robert Lindner et al.   PLoS One

Decoding Human Cytomegalovirus

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

Real-time Transcriptional Profiling of Cellular and Viral Gene Expression during Lytic Cytomegalovirus Infection

(2012) Lisa Marcinowski et al.   PLoS Pathogens

DREME: motif discovery in transcription factor ChIP-seq data

(2011) Timothy L. Bailey   BIOINFORMATICS

The many roles of the highly interactive HSV protein ICP27, a key regulator of infection

(2011) Rozanne M Sandri-Goldin   Future Microbiology

Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses

(2011) M. N. Cabili et al.   GENES & DEVELOPMENT

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

(2011) N. J. Proudfoot   GENES & DEVELOPMENT

Dynamic transcriptome analysis measures rates of mRNA synthesis and decay in yeast

(2011) C. Miller et al.   Molecular Systems Biology

Role of Herpes Simplex Virus ICP27 in the Degradation of mRNA by Virion Host Shutoff RNase

(2010) B. Taddeo et al.   JOURNAL OF VIROLOGY

Most “Dark Matter” Transcripts Are Associated With Known Genes

(2010) Harm van Bakel et al.   PLOS BIOLOGY

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

TU-tagging: cell type–specific RNA isolation from intact complex tissues

(2009) Michael R Miller et al.   NATURE METHODS

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

Herpesvirus protein ICP27 switches PML isoform by altering mRNA splicing

(2009) Takayuki Nojima et al.   NUCLEIC ACIDS RESEARCH

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH

Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling

(2009) N. T. Ingolia et al.   SCIENCE

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

The many roles of the regulatory protein ICP27 during herpes simplex virus infection

(2008) Rozanne et al.   Frontiers in Bioscience-Landmark

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

High-resolution gene expression profiling for simultaneous kinetic parameter analysis of RNA synthesis and decay

(2008) L. Dolken et al.   RNA