DHX9 suppresses RNA processing defects originating from the Alu invasion of the human genome

Global RNA recognition patterns of post‐transcriptional regulators Hfq and CsrA revealed by UV crosslinkingin vivo

(2016) Erik Holmqvist et al.   EMBO JOURNAL

deepTools2: a next generation web server for deep-sequencing data analysis

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

REDIportal: a comprehensive database of A-to-I RNA editing events in humans

(2016) Ernesto Picardi et al.   NUCLEIC ACIDS RESEARCH

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update

(2016) Enis Afgan et al.   NUCLEIC ACIDS RESEARCH

Accessory Factors of Cytoplasmic Viral RNA Sensors Required for Antiviral Innate Immune Response

(2016) Hiroyuki Oshiumi et al.   Frontiers in Immunology

A Human Interactome in Three Quantitative Dimensions Organized by Stoichiometries and Abundances

(2015) Marco Y. Hein et al.   CELL

Identification and characterization of essential genes in the human genome

(2015) T. Wang et al.   SCIENCE

Nanobody-targeted E3-ubiquitin ligase complex degrades nuclear proteins

(2015) Yeong Ju Shin et al.   Scientific Reports

JAMM: a peak finder for joint analysis of NGS replicates

(2014) Mahmoud M. Ibrahim et al.   BIOINFORMATICS

Complementary Sequence-Mediated Exon Circularization

(2014) Xiao-Ou Zhang et al.   CELL

Revealing long noncoding RNA architecture and functions using domain-specific chromatin isolation by RNA purification

(2014) Jeffrey J Quinn et al.   NATURE BIOTECHNOLOGY

Repetitive RNA unwinding by RNA helicase A facilitates RNA annealing

(2014) Hye Ran Koh et al.   NUCLEIC ACIDS RESEARCH

UniProt: a hub for protein information

(2014)   NUCLEIC ACIDS RESEARCH

MOF-associated complexes ensure stem cell identity and Xist repression

(2014) Tomasz Chelmicki et al.   eLife

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

RepeatExplorer: a Galaxy-based web server for genome-wide characterization of eukaryotic repetitive elements from next-generation sequence reads

(2013) P. Novak et al.   BIOINFORMATICS

Direct Competition between hnRNP C and U2AF65 Protects the Transcriptome from the Exonization of Alu Elements

(2013) Kathi Zarnack et al.   CELL

STAU1 binding 3' UTR IRAlus complements nuclear retention to protect cells from PKR-mediated translational shutdown

(2013) R. A. Elbarbary et al.   GENES & DEVELOPMENT

Tandem Stem-Loops in roX RNAs Act Together to Mediate X Chromosome Dosage Compensation in Drosophila

(2013) Ibrahim Avsar Ilik et al.   MOLECULAR CELL

Circular RNAs are a large class of animal RNAs with regulatory potency

(2013) Sebastian Memczak et al.   NATURE

Genome engineering using the CRISPR-Cas9 system

(2013) F Ann Ran et al.   Nature Protocols

Staufen1 senses overall transcript secondary structure to regulate translation

(2013) Emiliano P Ricci et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

(2013) Daehwan Kim et al.   GENOME BIOLOGY

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Detecting differential usage of exons from RNA-seq data

(2012) S. Anders et al.   GENOME RESEARCH

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Not All Sequence Tags Are Created Equal: Designing and Validating Sequence Identification Tags Robust to Indels

(2012) Brant C. Faircloth et al.   PLoS One

Circular RNAs are abundant, conserved, and associated with ALU repeats

(2012) W. R. Jeck et al.   RNA

Origin and evolution of SINEs in eukaryotic genomes

(2011) D A Kramerov et al.   HEREDITY

Repetitive Elements May Comprise Over Two-Thirds of the Human Genome

(2011) A. P. Jason de Koning et al.   PLoS Genetics

Graph-based clustering and characterization of repetitive sequences in next-generation sequencing data

(2010) Petr Novák et al.   BMC BIOINFORMATICS

Phenotypic profiling of the human genome by time-lapse microscopy reveals cell division genes

(2010) Beate Neumann et al.   NATURE

iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution

(2010) Julian König et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Estimating enrichment of repetitive elements from high-throughput sequence data

(2010) Daniel S Day et al.   GENOME BIOLOGY

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Aurora B-Mediated Abscission Checkpoint Protects against Tetraploidization

(2009) Patrick Steigemann et al.   CELL

Use of in vivo biotinylation to study protein–protein and protein–DNA interactions in mouse embryonic stem cells

(2009) Jonghwan Kim et al.   Nature Protocols

Mechanism of PKR Activation by dsRNA

(2008) Peter A. Lemaire et al.   JOURNAL OF MOLECULAR BIOLOGY