Detecting actively translated open reading frames in ribosome profiling data

RiboTools: a Galaxy toolbox for qualitative ribosome profiling analysis

(2015) Rachel Legendre et al.   BIOINFORMATICS

Translational regulation shapes the molecular landscape of complex disease phenotypes

(2015) Sebastian Schafer et al.   Nature Communications

Translation of 5′ leaders is pervasive in genes resistant to eIF2 repression

(2015) Dmitry E Andreev et al.   eLife

Identification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservation

(2014) A. A. Bazzini et al.   EMBO JOURNAL

Accounting for biases in riboprofiling data indicates a major role for proline in stalling translation

(2014) Carlo G. Artieri et al.   GENOME RESEARCH

A Review of Multitaper Spectral Analysis

(2014) Behtash Babadi et al.   IEEE TRANSACTIONS ON BIOMEDICAL ENGINEERING

Causal signals between codon bias, mRNA structure, and the efficiency of translation and elongation

(2014) C. Pop et al.   Molecular Systems Biology

Quantitative profiling of initiating ribosomes in vivo

(2014) Xiangwei Gao et al.   NATURE METHODS

The translational landscape of fission-yeast meiosis and sporulation

(2014) Caia D S Duncan et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

PROTEOFORMER: deep proteome coverage through ribosome profiling and MS integration

(2014) Jeroen Crappé et al.   NUCLEIC ACIDS RESEARCH

Translation inhibitors cause abnormalities in ribosome profiling experiments

(2014) Maxim V. Gerashchenko et al.   NUCLEIC ACIDS RESEARCH

Detecting translational regulation by change point analysis of ribosome profiling data sets

(2014) Anze Zupanic et al.   RNA

Toddler: An Embryonic Signal That Promotes Cell Movement via Apelin Receptors

(2014) A. Pauli et al.   SCIENCE

Ribosome Profiling Reveals Pervasive Translation Outside of Annotated Protein-Coding Genes

(2014) Nicholas T. Ingolia et al.   Cell Reports

Distinct stages of the translation elongation cycle revealed by sequencing ribosome-protected mRNA fragments

(2014) Liana F Lareau et al.   eLife

Extensive translation of small Open Reading Frames revealed by Poly-Ribo-Seq

(2014) Julie L Aspden et al.   eLife

Differential protein occupancy profiling of the mRNA transcriptome

(2014) Markus Schueler et al.   GENOME BIOLOGY

IVT-seq reveals extreme bias in RNA sequencing

(2014) Nicholas F Lahens et al.   GENOME BIOLOGY

Assessing gene-level translational control from ribosome profiling

(2013) Adam B. Olshen et al.   BIOINFORMATICS

A fast Peptide Match service for UniProt Knowledgebase

(2013) Chuming Chen et al.   BIOINFORMATICS

Ribosome Profiling Provides Evidence that Large Noncoding RNAs Do Not Encode Proteins

(2013) Mitchell Guttman et al.   CELL

Ribosome profiling reveals resemblance between long non-coding RNAs and 5′ leaders of coding RNAs

(2013) Guo-Liang Chew et al.   DEVELOPMENT

uORFdb—a comprehensive literature database on eukaryotic uORF biology

(2013) Klaus Wethmar et al.   NUCLEIC ACIDS RESEARCH

GWIPS-viz: development of a ribo-seq genome browser

(2013) Audrey M. Michel et al.   NUCLEIC ACIDS RESEARCH

CPAT: Coding-Potential Assessment Tool using an alignment-free logistic regression model

(2013) Liguo Wang et al.   NUCLEIC ACIDS RESEARCH

Gene Expression Regulation by Upstream Open Reading Frames and Human Disease

(2013) Cristina Barbosa et al.   PLoS Genetics

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Long noncoding RNAs are rarely translated in two human cell lines

(2012) B. Banfai et al.   GENOME RESEARCH

Observation of dually decoded regions of the human genome using ribosome profiling data

(2012) A. M. Michel et al.   GENOME RESEARCH

Genome-wide search for novel human uORFs and N-terminal protein extensions using ribosomal footprinting

(2012) C. Fritsch et al.   GENOME RESEARCH

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

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

PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions

(2011) M. F. Lin et al.   BIOINFORMATICS

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

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

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

(2008) Jürgen Cox et al.   NATURE BIOTECHNOLOGY