Deep transcriptome annotation enables the discovery and functional characterization of cryptic small proteins

Classification and function of small open reading frames

(2017) Juan-Pablo Couso et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Upstream ORFs are prevalent translational repressors in vertebrates

(2016) Timothy G Johnstone et al.   EMBO JOURNAL

Multiparameter functional diversity of human C2H2 zinc finger proteins

(2016) Frank W. Schmitges et al.   GENOME RESEARCH

MPC1-like Is a Placental Mammal-specific Mitochondrial Pyruvate Carrier Subunit Expressed in Postmeiotic Male Germ Cells

(2016) Benoît Vanderperre et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Ribosome Elongation Stall Directs Gene-specific Translation in the Integrated Stress Response

(2016) Sara K. Young et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Open questions in the study of de novo genes: what, how and why

(2016) Aoife McLysaght et al.   NATURE REVIEWS GENETICS

A peptide encoded by a transcript annotated as long noncoding RNA enhances SERCA activity in muscle

(2016) B. R. Nelson et al.   SCIENCE

Systematic discovery of cap-independent translation sequences in human and viral genomes

(2016) Shira Weingarten-Gabbay et al.   SCIENCE

Thousands of novel translated open reading frames in humans inferred by ribosome footprint profiling

(2016) Anil Raj et al.   eLife

A Micropeptide Encoded by a Putative Long Noncoding RNA Regulates Muscle Performance

(2015) Douglas M. Anderson et al.   CELL

A Human Interactome in Three Quantitative Dimensions Organized by Stoichiometries and Abundances

(2015) Marco Y. Hein et al.   CELL

Found in translation: functions and evolution of a recently discovered alternative proteome

(2015) Christian R Landry et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

The Recent De Novo Origin of Protein C-Termini

(2015) Matthew E. Andreatta et al.   Genome Biology and Evolution

A 5′-upstream short open reading frame encoded peptide regulates angiotensin type 1a receptor production and signalling via the β-arrestin pathway

(2015) Gina L.C. Yosten et al.   JOURNAL OF PHYSIOLOGY-LONDON

Proteogenomics from a bioinformatics angle: A growing field

(2015) Gerben Menschaert et al.   MASS SPECTROMETRY REVIEWS

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

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

PeptideShaker enables reanalysis of MS-derived proteomics data sets

(2015) Marc Vaudel et al.   NATURE BIOTECHNOLOGY

Discovery and characterization of smORF-encoded bioactive polypeptides

(2015) Alan Saghatelian et al.   Nature Chemical Biology

Death of a dogma: eukaryotic mRNAs can code for more than one protein

(2015) Hélène Mouilleron et al.   NUCLEIC ACIDS RESEARCH

Visualization of proteomics data usingRand Bioconductor

(2015) Laurent Gatto et al.   PROTEOMICS

Pri sORF peptides induce selective proteasome-mediated protein processing

(2015) J. Zanet et al.   SCIENCE

Genes from scratch – the evolutionary fate of de novo genes

(2015) Christian Schlötterer   TRENDS IN GENETICS

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

(2015) Zhe Ji et al.   eLife

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

(2015) Dmitry E Andreev et al.   eLife

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

Categorizer: a tool to categorize genes into user-defined biological groups based on semantic similarity

(2014) Dokyun Na et al.   BMC GENOMICS

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

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

Proteomic Analysis of the Epidermal Growth Factor Receptor (EGFR) Interactome and Post-translational Modifications Associated with Receptor Endocytosis in Response to EGF and Stress

(2014) Jiefei Tong et al.   MOLECULAR & CELLULAR PROTEOMICS

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

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

A draft map of the human proteome

(2014) Min-Sik Kim et al.   NATURE

Quantitative profiling of initiating ribosomes in vivo

(2014) Xiangwei Gao et al.   NATURE METHODS

Emerging evidence for functional peptides encoded by short open reading frames

(2014) Shea J. Andrews et al.   NATURE REVIEWS GENETICS

Modified ribosome profiling reveals high abundance of ribosome protected mRNA fragments derived from 3′ untranslated regions

(2014) Teemu P. Miettinen et al.   NUCLEIC ACIDS RESEARCH

The InterPro protein families database: the classification resource after 15 years

(2014) Alex Mitchell et al.   NUCLEIC ACIDS RESEARCH

InParanoid 8: orthology analysis between 273 proteomes, mostly eukaryotic

(2014) Erik L.L. Sonnhammer et al.   NUCLEIC ACIDS RESEARCH

Proteogenomic strategies for identification of aberrant cancer peptides using large-scale next-generation sequencing data

(2014) Sunghee Woo et al.   PROTEOMICS

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

(2014) A. Pauli et al.   SCIENCE

Quantitative profiling of peptides from RNAs classified as noncoding

(2014) Sudhakaran Prabakaran et al.   Nature Communications

MS-GF+ makes progress towards a universal database search tool for proteomics

(2014) Sangtae Kim et al.   Nature Communications

Ultradeep Human Phosphoproteome Reveals a Distinct Regulatory Nature of Tyr and Ser/Thr-Based Signaling

(2014) Kirti Sharma et al.   Cell Reports

A repository of assays to quantify 10,000 human proteins by SWATH-MS

(2014) George Rosenberger et al.   Scientific Data

Phylogenetic patterns of emergence of new genes support a model of frequent de novo evolution

(2013) Rafik Neme et al.   BMC GENOMICS

Inflammation-Induced Alteration of Astrocyte Mitochondrial Dynamics Requires Autophagy for Mitochondrial Network Maintenance

(2013) Elisa Motori et al.   Cell Metabolism

The A2AAdenosine Receptor Is a Dual Coding Gene

(2013) Chien-fei Lee et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

An Out-of-frame Overlapping Reading Frame in the Ataxin-1 Coding Sequence Encodes a Novel Ataxin-1 Interacting Protein

(2013) Danny Bergeron et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Fis1, Mff, MiD49, and MiD51 mediate Drp1 recruitment in mitochondrial fission

(2013) Oliver C. Losón et al.   MOLECULAR BIOLOGY OF THE CELL

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

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

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

(2013) Benoît Vanderperre et al.   PLoS One

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

(2012) C. Fritsch et al.   GENOME RESEARCH

Evolution of Viral Proteins Originated De Novo by Overprinting

(2012) Niv Sabath et al.   MOLECULAR BIOLOGY AND EVOLUTION

Proto-genes and de novo gene birth

(2012) Anne-Ruxandra Carvunis et al.   NATURE

Peptidomic discovery of short open reading frame–encoded peptides in human cells

(2012) Sarah A Slavoff et al.   Nature Chemical Biology

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

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

Comet: An open-source MS/MS sequence database search tool

(2012) Jimmy K. Eng et al.   PROTEOMICS

Decoding Human Cytomegalovirus

(2012) N. Stern-Ginossar et al.   SCIENCE

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

(2011) Nicholas T. Ingolia et al.   CELL

MiD49 and MiD51, new components of the mitochondrial fission machinery

(2011) Catherine S Palmer et al.   EMBO REPORTS

An overlapping reading frame in the PRNP gene encodes a novel polypeptide distinct from the prion protein

(2011) Benoît Vanderperre et al.   FASEB JOURNAL

Widespread Polymorphism in the Positions of Stop Codons in Drosophila melanogaster

(2011) Yuh Chwen G. Lee et al.   Genome Biology and Evolution

iProphet: Multi-level Integrative Analysis of Shotgun Proteomic Data Improves Peptide and Protein Identification Rates and Error Estimates

(2011) David Shteynberg et al.   MOLECULAR & CELLULAR PROTEOMICS

SearchGUI: An open-source graphical user interface for simultaneous OMSSA and X!Tandem searches

(2011) Marc Vaudel et al.   PROTEOMICS

Molecular Symbiosis of CHOP and C/EBP  Isoform LIP Contributes to Endoplasmic Reticulum Stress-Induced Apoptosis

(2010) C.-B. Chiribau et al.   MOLECULAR AND CELLULAR BIOLOGY

Recent de novo origin of human protein-coding genes

(2009) D. G. Knowles et al.   GENOME RESEARCH

Detection of nonneutral substitution rates on mammalian phylogenies

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