VELCRO-IP RNA-seq reveals ribosome expansion segment function in translation genome-wide

MetAP-like Ebp1 occupies the human ribosomal tunnel exit and recruits flexible rRNA expansion segments

(2020) Klemens Wild et al.   Nature Communications

Gene- and Species-Specific Hox mRNA Translation by Ribosome Expansion Segments

(2020) Kathrin Leppek et al.   MOLECULAR CELL

Divergent rRNAs as regulators of gene expression at the ribosome level

(2019) Wooseok Song et al.   Nature Microbiology

Variant ribosomal RNA alleles are conserved and exhibit tissue-specific expression

(2018) Matthew M. Parks et al.   Science Advances

Decoding the Function of Expansion Segments in Ribosomes

(2018) Kotaro Fujii et al.   MOLECULAR CELL

Ribosome–NatA architecture reveals that rRNA expansion segments coordinate N-terminal acetylation

(2018) Alexandra G. Knorr et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Endogenous rRNA Sequence Variation Can Regulate Stress Response Gene Expression and Phenotype

(2018) Chad M. Kurylo et al.   Cell Reports

UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy

(2017) Tom Smith et al.   GENOME RESEARCH

Visualization of chemical modifications in the human 80S ribosome structure

(2017) S. Kundhavai Natchiar et al.   NATURE

Ensembl 2018

(2017) Daniel R Zerbino et al.   NUCLEIC ACIDS RESEARCH

Expression of distinct maternal and somatic 5.8S, 18S, and 28S rRNA types during zebrafish development

(2017) Mauro D. Locati et al.   RNA

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

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Eukaryote-specific rRNA expansion segments function in ribosome biogenesis

(2016) Madhumitha Ramesh et al.   RNA

Systematic discovery of cap-independent translation sequences in human and viral genomes

(2016) Shira Weingarten-Gabbay et al.   SCIENCE

Ribosomal 18S rRNA base pairs with mRNA during eukaryotic translation initiation

(2016) Franck Martin et al.   Nature Communications

MAGED1 Is a Negative Regulator of Bone Remodeling in Mice

(2015) Mei Liu et al.   AMERICAN JOURNAL OF PATHOLOGY

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

Transcriptional profiling of macrophages derived from monocytes and iPS cells identifies a conserved response to LPS and novel alternative transcription

(2015) Kaur Alasoo et al.   Scientific Reports

RNA regulons in Hox 5′ UTRs confer ribosome specificity to gene regulation

(2014) Shifeng Xue et al.   NATURE

Principles of ER cotranslational translocation revealed by proximity-specific ribosome profiling

(2014) C. H. Jan et al.   SCIENCE

voom: precision weights unlock linear model analysis tools for RNA-seq read counts

(2014) Charity W Law et al.   GENOME BIOLOGY

Roquin Promotes Constitutive mRNA Decay via a Conserved Class of Stem-Loop Recognition Motifs

(2013) Kathrin Leppek et al.   CELL

Structures of the human and Drosophila 80S ribosome

(2013) Andreas M. Anger et al.   NATURE

An optimized streptavidin-binding RNA aptamer for purification of ribonucleoprotein complexes identifies novel ARE-binding proteins

(2013) Kathrin Leppek et al.   NUCLEIC ACIDS RESEARCH

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Yeast 18 S rRNA Is Directly Involved in the Ribosomal Response to Stringent AUG Selection during Translation Initiation

(2010) Naoki Nemoto et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Cryo-EM structure and rRNA model of a translating eukaryotic 80S ribosome at 5.5-A resolution

(2010) J.-P. Armache et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A scaling normalization method for differential expression analysis of RNA-seq data

(2010) Mark D Robinson et al.   GENOME BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

A role for ubiquitin in the clearance of nonfunctional rRNAs

(2009) K. Fujii et al.   GENES & DEVELOPMENT