Assessing the translational landscape of myogenic differentiation by ribosome profiling

Gene Regulatory Networks and Transcriptional Mechanisms that Control Myogenesis

(2014) Margaret Buckingham et al.   DEVELOPMENTAL CELL

Affinity proteomics within rare diseases: a BIO-NMD study for blood biomarkers of muscular dystrophies

(2014) B. Ayoglu et al.   EMBO Molecular Medicine

Crystallin-αB Regulates Skeletal Muscle Homeostasis via Modulation of Argonaute2 Activity

(2014) Ronald L. Neppl et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Ribosome Profiling Reveals a Cell-Type-Specific Translational Landscape in Brain Tumors

(2014) C. Gonzalez et al.   JOURNAL OF NEUROSCIENCE

A promoter-level mammalian expression atlas

(2014)   NATURE

Ribosome profiling: new views of translation, from single codons to genome scale

(2014) Nicholas T. Ingolia   NATURE REVIEWS GENETICS

Proteomic Analysis of C2C12 Myoblast and Myotube Exosome-Like Vesicles: A New Paradigm for Myoblast-Myotube Cross Talk?

(2014) Alexis Forterre et al.   PLoS One

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

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

Extensive localization of long noncoding RNAs to the cytosol and mono- and polyribosomal complexes

(2014) Sebastiaan van Heesch et al.   GENOME BIOLOGY

Translation and silencing in RNA granules: a tale of sand grains

(2014) Jerónimo Pimentel et al.   Frontiers in Molecular Neuroscience

System wide analyses have underestimated protein abundances and the importance of transcription in mammals

(2014) Jingyi Jessica Li et al.   PeerJ

Assessing gene-level translational control from ribosome profiling

(2013) Adam B. Olshen et al.   BIOINFORMATICS

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

(2013) Mitchell Guttman et al.   CELL

A perspective on mammalian upstream open reading frame function

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

Deep Proteome Coverage Based on Ribosome Profiling Aids Mass Spectrometry-based Protein and Peptide Discovery and Provides Evidence of Alternative Translation Products and Near-cognate Translation Initiation Events*

(2013) Gerben Menschaert et al.   MOLECULAR & CELLULAR PROTEOMICS

Protein synthesis rate is the predominant regulator of protein expression during differentiation

(2013) A. R. Kristensen et al.   Molecular Systems Biology

HiRIEF LC-MS enables deep proteome coverage and unbiased proteogenomics

(2013) Rui M M Branca et al.   NATURE METHODS

Direct Detection of Alternative Open Reading Frames Translation Products in Human Significantly Expands the Proteome

(2013) Benoît Vanderperre et al.   PLoS One

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Widespread uncoupling between transcriptome and translatome variations after a stimulus in mammalian cells

(2012) Toma Tebaldi et al.   BMC GENOMICS

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

TGFBR2 but not SPP1 genotype modulates osteopontin expression in Duchenne muscular dystrophy muscle

(2012) Luisa Piva et al.   JOURNAL OF PATHOLOGY

The translational landscape of mTOR signalling steers cancer initiation and metastasis

(2012) Andrew C. Hsieh et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

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

miRNAs' strict schedule

(2012) Rachel David   NATURE REVIEWS GENETICS

Poly(A) binding protein nuclear 1 levels affect alternative polyadenylation

(2012) Eleonora de Klerk 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

Ribosome Profiling Shows That miR-430 Reduces Translation Before Causing mRNA Decay in Zebrafish

(2012) A. A. Bazzini et al.   SCIENCE

Building Muscle: Molecular Regulation of Myogenesis

(2012) C. F. Bentzinger et al.   Cold Spring Harbor Perspectives in Biology

New methods for next generation sequencing based microRNA expression profiling

(2011) Henk PJ Buermans et al.   BMC GENOMICS

Selective Ribosome Profiling Reveals the Cotranslational Chaperone Action of Trigger Factor In Vivo

(2011) Eugene Oh 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

Proteomics-based investigation in C2C12 myoblast differentiation

(2011) L. Casadei et al.   EUROPEAN JOURNAL OF HISTOCHEMISTRY

The C Terminus of Bax Inhibitor-1 Forms a Ca2+-permeable Channel Pore

(2011) Geert Bultynck et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Global quantification of mammalian gene expression control

(2011) Björn Schwanhäusser et al.   NATURE

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

C/EBP  uORF mice--a genetic model for uORF-mediated translational control in mammals

(2010) K. Wethmar et al.   GENES & DEVELOPMENT

Sequence signatures and mRNA concentration can explain two-thirds of protein abundance variation in a human cell line

(2010) Christine Vogel et al.   Molecular Systems Biology

Defining the transcriptome and proteome in three functionally different human cell lines

(2010) Emma Lundberg et al.   Molecular Systems Biology

Real-time tRNA transit on single translating ribosomes at codon resolution

(2010) Sotaro Uemura et al.   NATURE

Mammalian microRNAs predominantly act to decrease target mRNA levels

(2010) Huili Guo et al.   NATURE

Tissue-specific transcript annotation and expression profiling with complementary next-generation sequencing technologies

(2010) Matthew S. Hestand et al.   NUCLEIC ACIDS RESEARCH

A guided tour of the Trans-Proteomic Pipeline

(2010) Eric W. Deutsch et al.   PROTEOMICS

Ubiquitin–proteasome-mediated degradation and synthesis of MyoD is modulated by αB-crystallin, a small heat shock protein, during muscle differentiation

(2009) Bhairab N. Singh et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH

Probabilistic resolution of multi-mapping reads in massively parallel sequencing data using MuMRescueLite

(2009) T. Hashimoto et al.   BIOINFORMATICS

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Correlation of mRNA and protein in complex biological samples

(2009) Tobias Maier et al.   FEBS LETTERS

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

UTRdb and UTRsite (RELEASE 2010): a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs

(2009) Giorgio Grillo et al.   NUCLEIC ACIDS RESEARCH

Transcriptome analysis by strand-specific sequencing of complementary DNA

(2009) Dmitri Parkhomchuk et al.   NUCLEIC ACIDS RESEARCH

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

BI-1 Regulates Endoplasmic Reticulum Ca2+Homeostasis Downstream of Bcl-2 Family Proteins

(2008) Chunyan Xu et al.   JOURNAL OF BIOLOGICAL CHEMISTRY