The ribosome-engaged landscape of alternative splicing

Ribosome Footprint Profiling of Translation throughout the Genome

(2016) Nicholas T. Ingolia   CELL

Regulation of Poly(A) Tail and Translation during the Somatic Cell Cycle

(2016) Jong-Eun Park et al.   MOLECULAR CELL

Tunable protein synthesis by transcript isoforms in human cells

(2016) Stephen N Floor et al.   eLife

An extensive program of periodic alternative splicing linked to cell cycle progression

(2016) Daniel Dominguez et al.   eLife

Detained introns are a novel, widespread class of post-transcriptionally spliced introns

(2015) Paul L. Boutz et al.   GENES & DEVELOPMENT

The Evolutionary Fate of Alternatively Spliced Homologous Exons after Gene Duplication

(2015) Federico Abascal et al.   Genome Biology and Evolution

Unmasking alternative splicing inside protein-coding exons defines exitrons and their role in proteome plasticity

(2015) Yamile Marquez et al.   GENOME RESEARCH

Most Highly Expressed Protein-Coding Genes Have a Single Dominant Isoform

(2015) Iakes Ezkurdia et al.   JOURNAL OF PROTEOME RESEARCH

Multiple conformations are a conserved and regulatory feature of theRB15′ UTR

(2015) Katrina M. Kutchko et al.   RNA

Identification and characterization of essential genes in the human genome

(2015) T. Wang et al.   SCIENCE

Alternatively Spliced Homologous Exons Have Ancient Origins and Are Highly Expressed at the Protein Level

(2015) Federico Abascal et al.   PLoS Computational Biology

Regulation of mRNA translation during mitosis

(2015) Marvin E Tanenbaum et al.   eLife

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

(2015) Dmitry E Andreev et al.   eLife

A Highly Conserved Program of Neuronal Microexons Is Misregulated in Autistic Brains

(2014) Manuel Irimia et al.   CELL

Building Robust Transcriptomes with Master Splicing Factors

(2014) Mohini Jangi et al.   CELL

Insights into the anaphase-promoting complex: a molecular machine that regulates mitosis

(2014) Leifu Chang et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Widespread intron retention in mammals functionally tunes transcriptomes

(2014) Ulrich Braunschweig et al.   GENOME RESEARCH

Cyclebase 3.0: a multi-organism database on cell-cycle regulation and phenotypes

(2014) Alberto Santos et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2015

(2014) Fiona Cunningham et al.   NUCLEIC ACIDS RESEARCH

Impact of regulatory variation from RNA to protein

(2014) A. Battle et al.   SCIENCE

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

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

Intron Retention in the 5′UTR of the Novel ZIF2 Transporter Enhances Translation to Promote Zinc Tolerance in Arabidopsis

(2014) Estelle Remy et al.   PLoS Genetics

A proteomic chronology of gene expression through the cell cycle in human myeloid leukemia cells

(2014) Tony Ly et al.   eLife

Orchestrated Intron Retention Regulates Normal Granulocyte Differentiation

(2013) Justin J.-L. Wong et al.   CELL

Frac-seq reveals isoform-specific recruitment to polyribosomes

(2013) T. Sterne-Weiler et al.   GENOME RESEARCH

Status of Large-scale Analysis of Post-translational Modifications by Mass Spectrometry

(2013) Jesper V. Olsen et al.   MOLECULAR & CELLULAR PROTEOMICS

The Translational Landscape of the Mammalian Cell Cycle

(2013) Craig R. Stumpf et al.   MOLECULAR CELL

Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo

(2013) Silvi Rouskin et al.   NATURE

Translational dynamics revealed by genome-wide profiling of ribosome footprints in Arabidopsis

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

Human housekeeping genes, revisited

(2013) Eli Eisenberg et al.   TRENDS IN GENETICS

Ribosome profiling reveals features of normal and disease-associated mitochondrial translation

(2013) Koos Rooijers et al.   Nature Communications

Mass Spectrometry–Based Proteomics and Network Biology

(2012) Ariel Bensimon et al.   Annual Review of Biochemistry

Coordinated regulation of neuronal mRNA steady-state levels through developmentally controlled intron retention

(2012) K. Yap et al.   GENES & DEVELOPMENT

Tissue-Specific Splicing of Disordered Segments that Embed Binding Motifs Rewires Protein Interaction Networks

(2012) Marija Buljan et al.   MOLECULAR CELL

Linear motifs confer functional diversity onto splice variants

(2012) Robert J. Weatheritt 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

Evolutionary Dynamics of Gene and Isoform Regulation in Mammalian Tissues

(2012) J. Merkin et al.   SCIENCE

The Evolutionary Landscape of Alternative Splicing in Vertebrate Species

(2012) N. L. Barbosa-Morais et al.   SCIENCE

A Comparative Transcriptomic Analysis Reveals Conserved Features of Stem Cell Pluripotency in Planarians and Mammals

(2012) Roselyne M. Labbé et al.   STEM CELLS

Linear motifs: lost in (pre)translation

(2012) Robert J. Weatheritt et al.   TRENDS IN BIOCHEMICAL SCIENCES

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

(2011) Nicholas T. Ingolia et al.   CELL

Mammalian microRNAs predominantly act to decrease target mRNA levels

(2010) Huili Guo et al.   NATURE

Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation

(2010) Daniele Merico et al.   PLoS One

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

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

Alternative isoform regulation in human tissue transcriptomes

(2008) Eric T. Wang et al.   NATURE

Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing

(2008) Qun Pan et al.   NATURE GENETICS

Origin of introns by ‘intronization’ of exonic sequences

(2008) Manuel Irimia et al.   TRENDS IN GENETICS