Genome-wide maps of ribosomal occupancy provide insights into adaptive evolution and regulatory roles of uORFs during Drosophila development

Pervasive, Coordinated Protein-Level Changes Driven by Transcript Isoform Switching during Meiosis

(2018) Ze Cheng et al.   CELL

N 6 -Methyladenosine Guides mRNA Alternative Translation during Integrated Stress Response

(2018) Jun Zhou et al.   MOLECULAR CELL

Translational profiling of B cells infected with the Epstein-Barr virus reveals 5′ leader ribosome recruitment through upstream open reading frames

(2018) Maja Bencun et al.   NUCLEIC ACIDS RESEARCH

Loss-of-function uORF mutations in human malignancies

(2018) Julia Schulz et al.   Scientific Reports

Conserved non-AUG uORFs revealed by a novel regression analysis of ribosome profiling data

(2017) Pieter Spealman et al.   GENOME RESEARCH

Discovery of noncanonical translation initiation sites through mass spectrometric analysis of protein N termini

(2017) Chan Hyun Na et al.   GENOME RESEARCH

Global translational reprogramming is a fundamental layer of immune regulation in plants

(2017) Guoyong Xu et al.   NATURE

uORF-mediated translation allows engineered plant disease resistance without fitness costs

(2017) Guoyong Xu et al.   NATURE

A uORF Represses the Transcription Factor AtHB1 in Aerial Tissues to Avoid a Deleterious Phenotype

(2017) Pamela A. Ribone et al.   PLANT PHYSIOLOGY

asymptoticMK: A Web-Based Tool for the Asymptotic McDonald–Kreitman Test

(2017) Benjamin C. Haller et al.   G3-Genes Genomes Genetics

Development of a tissue-specific ribosome profiling approach in Drosophila enables genome-wide evaluation of translational adaptations

(2017) Xun Chen et al.   PLoS Genetics

Kinetochore inactivation by expression of a repressive mRNA

(2017) Jingxun Chen et al.   eLife

A mutation creating an upstream initiation codon in the SOX9 5′ UTR causes acampomelic campomelic dysplasia

(2017) Anna E. von Bohlen et al.   Molecular Genetics & Genomic Medicine

RiboDiff: detecting changes of mRNA translation efficiency from ribosome footprints

(2016) Yi Zhong et al.   BIOINFORMATICS

Inferring the Frequency Spectrum of Derived Variants to Quantify Adaptive Molecular Evolution in Protein-Coding Genes of Drosophila melanogaster

(2016) Peter D. Keightley et al.   GENETICS

microRNAs in the Same Clusters Evolve to Coordinately Regulate Functionally Related Genes

(2016) Yirong Wang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

Translation from the 5' untranslated region shapes the integrated stress response

(2016) S. R. Starck et al.   SCIENCE

Translational control by 5'-untranslated regions of eukaryotic mRNAs

(2016) A. G. Hinnebusch et al.   SCIENCE

Conservation of uORF repressiveness and sequence features in mouse, human and zebrafish

(2016) Guo-Liang Chew et al.   Nature Communications

Genome-wide assessment of differential translations with ribosome profiling data

(2016) Zhengtao Xiao et al.   Nature Communications

mRNA poly(A)-tail changes specified by deadenylation broadly reshape translation in Drosophila oocytes and early embryos

(2016) Stephen W Eichhorn et al.   eLife

Inferring the Frequency Spectrum of Derived Variants to Quantify Adaptive Molecular Evolution in Protein-Coding Genes of Drosophila melanogaster

(2016) Peter D. Keightley et al.   GENETICS

Integrative analysis of RNA, translation, and protein levels reveals distinct regulatory variation across humans

(2015) Can Cenik et al.   GENOME RESEARCH

DrosophilaX-Linked Genes Have Lower Translation Rates than Autosomal Genes

(2015) Zhenguo Zhang et al.   MOLECULAR BIOLOGY AND EVOLUTION

A Regression-Based Analysis of Ribosome-Profiling Data Reveals a Conserved Complexity to Mammalian Translation

(2015) Alexander P. Fields et al.   MOLECULAR CELL

Detecting actively translated open reading frames in ribosome profiling data

(2015) Lorenzo Calviello et al.   NATURE METHODS

Determinants of the rate of protein sequence evolution

(2015) Jianzhi Zhang et al.   NATURE REVIEWS GENETICS

CAGEr: precise TSS data retrieval and high-resolution promoterome mining for integrative analyses

(2015) Vanja Haberle et al.   NUCLEIC ACIDS RESEARCH

Global Diversity Lines–A Five-Continent Reference Panel of Sequenced Drosophila melanogaster Strains

(2015) Jennifer K. Grenier et al.   G3-Genes Genomes Genetics

Gene Model Annotations for Drosophila melanogaster : Impact of High-Throughput Data

(2015) Beverley B. Matthews et al.   G3-Genes Genomes Genetics

Upstream open reading frames and Kozak regions of assembled transcriptome sequences from the spider Cupiennius salei. Selection or chance?

(2014) Andrew S. French et al.   GENE

Natural variation in genome architecture among 205 Drosophila melanogaster Genetic Reference Panel lines

(2014) W. Huang et al.   GENOME RESEARCH

Diversity and dynamics of the Drosophila transcriptome

(2014) James B. Brown et al.   NATURE

DENR–MCT-1 promotes translation re-initiation downstream of uORFs to control tissue growth

(2014) Sibylle Schleich et al.   NATURE

Quantitative profiling of initiating ribosomes in vivo

(2014) Xiangwei Gao et al.   NATURE METHODS

The UCSC Genome Browser database: 2015 update

(2014) Kate R. Rosenbloom et al.   NUCLEIC ACIDS RESEARCH

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

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

Widespread Changes in the Posttranscriptional Landscape at the Drosophila Oocyte-to-Embryo Transition

(2014) Iva Kronja et al.   Cell Reports

The regulatory potential of upstream open reading frames in eukaryotic gene expression

(2014) Klaus Wethmar   Wiley Interdisciplinary Reviews-RNA

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

(2014) Julie L Aspden et al.   eLife

Engineering ribosomal leaky scanning and upstream open reading frames for precise control of protein translation

(2014) Joshua P Ferreira et al.   Bioengineered

The role of Dichaete in transcriptional regulation during Drosophila embryonic development

(2013) Jelena Aleksic et al.   BMC GENOMICS

Strong Mutational Bias Toward Deletions in the Drosophila melanogaster Genome Is Compensated by Selection

(2013) Evgeny V. Leushkin et al.   Genome Biology and Evolution

Ribosome profiling reveals post-transcriptional buffering of divergent gene expression in yeast

(2013) C. J. McManus et al.   GENOME RESEARCH

Evolution at two levels of gene expression in yeast

(2013) C. G. Artieri et al.   GENOME RESEARCH

Roles for transcript leaders in translation and mRNA decay revealed by transcript leader sequencing

(2013) J. A. Arribere et al.   GENOME RESEARCH

A perspective on mammalian upstream open reading frame function

(2013) Joanna Somers et al.   INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY

Coordinate regulation of eIF2  phosphorylation by PPP1R15 and GCN2 is required during Drosophila development

(2013) E. Malzer et al.   JOURNAL OF CELL SCIENCE

In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features

(2013) Yiliang Ding et al.   NATURE

Regulation of plant translation by upstream open reading frames

(2013) Albrecht G. von Arnim et al.   PLANT SCIENCE

Differential requirements for mRNA folding partially explain why highly expressed proteins evolve slowly

(2013) C. Park et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Tuning gene expression with synthetic upstream open reading frames

(2013) J. P. Ferreira et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Frequent adaptation and the McDonald-Kreitman test

(2013) P. W. Messer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Gene Expression Regulation by Upstream Open Reading Frames and Human Disease

(2013) Cristina Barbosa et al.   PLoS Genetics

Transcriptome analysis of human tissues and cell lines reveals one dominant transcript per gene

(2013) Mar Gonzàlez-Porta et al.   GENOME BIOLOGY

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

The Drosophila melanogaster Genetic Reference Panel

(2012) Trudy F. C. Mackay et al.   NATURE

A mechanistic overview of translation initiation in eukaryotes

(2012) Colin Echeverría Aitken et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation

(2012) Davis J. McCarthy et al.   NUCLEIC ACIDS RESEARCH

Global mapping of translation initiation sites in mammalian cells at single-nucleotide resolution

(2012) S. Lee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Protein misinteraction avoidance causes highly expressed proteins to evolve slowly

(2012) J.-R. Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

Translational Control via Protein-Regulated Upstream Open Reading Frames

(2011) Jan Medenbach et al.   CELL

Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity and Dynamics of Mammalian Proteomes

(2011) Nicholas T. Ingolia et al.   CELL

A Method for Inferring the Rate of Occurrence and Fitness Effects of Advantageous Mutations

(2011) Adrian Schneider et al.   GENETICS

BigWig and BigBed: enabling browsing of large distributed datasets

(2010) W. J. Kent et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

An Evolutionarily Conserved Mechanism for Controlling the Efficiency of Protein Translation

(2010) Tamir Tuller et al.   CELL

Genome-wide analysis of promoter architecture in Drosophila melanogaster

(2010) R. A. Hoskins et al.   GENOME RESEARCH

Functional analysis of CDKN2A/p16INK4a 5′-UTR variants predisposing to melanoma

(2010) Alessandra Bisio et al.   HUMAN MOLECULAR GENETICS

On the Utility of Short Intron Sequences as a Reference for the Detection of Positive and Negative Selection in Drosophila

(2010) J. Parsch et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genome-wide measurement of RNA secondary structure in yeast

(2010) Michael Kertesz et al.   NATURE

The developmental transcriptome of Drosophila melanogaster

(2010) Brenton R. Graveley et al.   NATURE

Mammalian microRNAs predominantly act to decrease target mRNA levels

(2010) Huili Guo et al.   NATURE

The mechanism of eukaryotic translation initiation and principles of its regulation

(2010) Richard J. Jackson et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Evolutionary Roles of Upstream Open Reading Frames in Mediating Gene Regulation in Fungi

(2009) Heather M. Hood et al.   Annual Review of Microbiology

Regulation of Translation Initiation by RNA Binding Proteins

(2009) Paul Babitzke et al.   Annual Review of Microbiology

Noisy splicing, more than expression regulation, explains why some exons are subject to nonsense-mediated mRNA decay

(2009) Zhenguo Zhang et al.   BMC BIOLOGY

Evolution of alternative and constitutive regions of mammalian 5'UTRs

(2009) Alissa M Resch et al.   BMC GENOMICS

Regulation of Translation Initiation in Eukaryotes: Mechanisms and Biological Targets

(2009) Nahum Sonenberg et al.   CELL

Detection of nonneutral substitution rates on mammalian phylogenies

(2009) K. S. Pollard et al.   GENOME RESEARCH

Estimating the Rate of Adaptive Molecular Evolution in the Presence of Slightly Deleterious Mutations and Population Size Change

(2009) A. Eyre-Walker et al.   MOLECULAR BIOLOGY AND EVOLUTION

Effective population size and patterns of molecular evolution and variation

(2009) Brian Charlesworth   NATURE REVIEWS GENETICS

Small silencing RNAs: an expanding universe

(2009) Megha Ghildiyal et al.   NATURE REVIEWS GENETICS

The complex eukaryotic transcriptome: unexpected pervasive transcription and novel small RNAs

(2009) Alain Jacquier   NATURE REVIEWS GENETICS

Upstream open reading frames cause widespread reduction of protein expression and are polymorphic among humans

(2009) S. E. Calvo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2009) N. T. Ingolia et al.   SCIENCE

uShuffle: A useful tool for shuffling biological sequences while preserving the k-let counts

(2008) Minghui Jiang et al.   BMC BIOINFORMATICS

uORFs, reinitiation and alternative translation start sites in human mRNAs

(2008) Alex V. Kochetov et al.   FEBS LETTERS

The McDonald-Kreitman Test and Slightly Deleterious Mutations

(2008) J. Charlesworth et al.   MOLECULAR BIOLOGY AND EVOLUTION