Transcriptome-Wide Cleavage Site Mapping on Cellular mRNAs Reveals Features Underlying Sequence-Specific Cleavage by the Viral Ribonuclease SOX

Viral Nucleases Induce an mRNA Degradation-Transcription Feedback Loop in Mammalian Cells

(2015) Emma Abernathy et al.   Cell Host & Microbe

A Ribonucleoprotein Complex Protects the Interleukin-6 mRNA from Degradation by Distinct Herpesviral Endonucleases

(2015) Mandy Muller et al.   PLoS Pathogens

Human nonsense-mediated RNA decay initiates widely by endonucleolysis and targets snoRNA host genes

(2014) Søren Lykke-Andersen et al.   GENES & DEVELOPMENT

RNase L Targets Distinct Sites in Influenza A Virus RNAs

(2014) Daphne A. Cooper et al.   JOURNAL OF VIROLOGY

Ribonuclease L and metal-ion–independent endoribonuclease cleavage sites in host and viral RNAs

(2014) Daphne A. Cooper et al.   NUCLEIC ACIDS RESEARCH

Identification of SMG6 cleavage sites and a preferred RNA cleavage motif by global analysis of endogenous NMD targets in human cells

(2014) Skye A. Schmidt et al.   NUCLEIC ACIDS RESEARCH

Gammaherpesviral Gene Expression and Virion Composition Are Broadly Controlled by Accelerated mRNA Degradation

(2014) Emma Abernathy et al.   PLoS Pathogens

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

An RNA Element in Human Interleukin 6 Confers Escape from Degradation by the Gammaherpesvirus SOX Protein

(2013) S. Hutin et al.   JOURNAL OF VIROLOGY

Rapid construction of parallel analysis of RNA end (PARE) libraries for Illumina sequencing

(2013) Jixian Zhai et al.   METHODS

Characterization of PA-N terminal domain of Influenza A polymerase reveals sequence specific RNA cleavage

(2013) Kausiki Datta et al.   NUCLEIC ACIDS RESEARCH

Bacterial RNA motif in the 5' UTR of rpsF interacts with an S6:S18 complex

(2013) Y. Fu et al.   RNA

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

A Common Strategy for Host RNA Degradation by Divergent Viruses

(2012) M. M. Gaglia et al.   JOURNAL OF VIROLOGY

NIH Image to ImageJ: 25 years of image analysis

(2012) Caroline A Schneider et al.   NATURE METHODS

Global or local? Predicting secondary structure and accessibility in mRNAs

(2012) Sita J. Lange et al.   NUCLEIC ACIDS RESEARCH

An Overlapping Protein-Coding Region in Influenza A Virus Segment 3 Modulates the Host Response

(2012) B. W. Jagger et al.   SCIENCE

ViennaRNA Package 2.0

(2011) Ronny Lorenz et al.   Algorithms for Molecular Biology

Generation of a doxycycline-inducible KSHV producer cell line of endothelial origin: Maintenance of tight latency with efficient reactivation upon induction

(2011) Jinjong Myoung et al.   JOURNAL OF VIROLOGICAL METHODS

Crystal structure of a KSHV–SOX–DNA complex: insights into the molecular mechanisms underlying DNase activity and host shutoff

(2011) Claire Bagnéris et al.   NUCLEIC ACIDS RESEARCH

Deep Sequencing Reveals Direct Targets of Gammaherpesvirus-Induced mRNA Decay and Suggests That Multiple Mechanisms Govern Cellular Transcript Escape

(2011) Karen Clyde et al.   PLoS One

SARS Coronavirus nsp1 Protein Induces Template-Dependent Endonucleolytic Cleavage of mRNAs: Viral mRNAs Are Resistant to nsp1-Induced RNA Cleavage

(2011) Cheng Huang et al.   PLoS Pathogens

Coordinated Destruction of Cellular Messages in Translation Complexes by the Gammaherpesvirus Host Shutoff Factor and the Mammalian Exonuclease Xrn1

(2011) Sergio Covarrubias et al.   PLoS Pathogens

KSHV and the pathogenesis of Kaposi sarcoma: listening to human biology and medicine

(2010) Don Ganem   JOURNAL OF CLINICAL INVESTIGATION

Diverse Endonucleolytic Cleavage Sites in the Mammalian Transcriptome Depend upon MicroRNAs, Drosha, and Additional Nucleases

(2010) Fedor V. Karginov et al.   MOLECULAR CELL

Host Shutoff Is a Conserved Phenotype of Gammaherpesvirus Infection and Is Orchestrated Exclusively from the Cytoplasm

(2009) S. Covarrubias et al.   JOURNAL OF VIROLOGY

Construction of Parallel Analysis of RNA Ends (PARE) libraries for the study of cleaved miRNA targets and the RNA degradome

(2009) Marcelo A German et al.   Nature Protocols

A two-pronged strategy to suppress host protein synthesis by SARS coronavirus Nsp1 protein

(2009) Wataru Kamitani et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Methods for analyzing deep sequencing expression data: constructing the human and mouse promoterome with deepCAGE data

(2009) Piotr J Balwierz et al.   GENOME BIOLOGY

SMG6 promotes endonucleolytic cleavage of nonsense mRNA in human cells

(2008) Andrea B Eberle et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY