RiboPlotR: a visualization tool for periodic Ribo-seq reads

Prevalence of alternative AUG and non-AUG translation initiators and their regulatory effects across plants

(2020) Ya-Ru Li et al.   GENOME RESEARCH

The tomato translational landscape revealed by transcriptome assembly and ribosome profiling

(2019) Hsin-Yen Larry Wu et al.   PLANT PHYSIOLOGY

Ribosome elongating footprints denoised by wavelet transform comprehensively characterize dynamic cellular translation events

(2018) Zhiyu Xu et al.   NUCLEIC ACIDS RESEARCH

Trips-Viz: a transcriptome browser for exploring Ribo-Seq data

(2018) Stephen J Kiniry et al.   NUCLEIC ACIDS RESEARCH

Super-resolution ribosome profiling reveals unannotated translation events inArabidopsis

(2016) Polly Yingshan Hsu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-wide assessment of differential translations with ribosome profiling data

(2016) Zhengtao Xiao et al.   Nature Communications

Gene-Specific Translation Regulation Mediated by the Hormone-Signaling Molecule EIN2

(2015) Catharina Merchante et al.   CELL

Detecting actively translated open reading frames in ribosome profiling data

(2015) Lorenzo Calviello et al.   NATURE METHODS

Many lncRNAs, 5’UTRs, and pseudogenes are translated and some are likely to express functional proteins

(2015) Zhe Ji et al.   eLife

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

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

Software for Computing and Annotating Genomic Ranges

(2013) Michael Lawrence et al.   PLoS Computational Biology

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

rtracklayer: an R package for interfacing with genome browsers

(2009) M. Lawrence et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

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

(2009) N. T. Ingolia et al.   SCIENCE