Recognition of the polycistronic nature of human genes is critical to understanding the genotype-phenotype relationship

Synonymous Somatic Variants in Human Cancer Are Not Infamous: A Plea for Full Disclosure in Databases and Publications

(2017) Thierry Soussi et al.   HUMAN MUTATION

Apelin/APJ system: A novel potential therapy target for kidney disease

(2017) Zhen Huang et al.   JOURNAL OF CELLULAR PHYSIOLOGY

Mitochondrially derived peptides as novel regulators of metabolism

(2017) Su-Jeong Kim et al.   JOURNAL OF PHYSIOLOGY-LONDON

Improved Reversed Phase Chromatography of Hydrophilic Peptides from Spatial and Temporal Changes in Column Temperature

(2017) Clifford Young et al.   JOURNAL OF PROTEOME RESEARCH

A recurrent synonymous mutation in the human androgen receptor gene causing complete androgen insensitivity syndrome

(2017) Rafael Loch Batista et al.   JOURNAL OF STEROID BIOCHEMISTRY AND MOLECULAR BIOLOGY

Mass Spectral Library Quality Assurance by Inter-Library Comparison

(2017) William E. Wallace et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

Renal cell tumors with clear cell histology and intact VHL and chromosome 3p: a histological review of tumors from the Cancer Genome Atlas database

(2017) Laura Favazza et al.   MODERN PATHOLOGY

N-terminal Proteomics Assisted Profiling of the Unexplored Translation Initiation Landscape in Arabidopsis thaliana

(2017) Patrick Willems et al.   MOLECULAR & CELLULAR PROTEOMICS

Annotation-free quantification of RNA splicing using LeafCutter

(2017) Yang I. Li et al.   NATURE GENETICS

MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry–based proteomics

(2017) Andy T Kong et al.   NATURE METHODS

Classification and function of small open reading frames

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

Polyglutamine spinocerebellar ataxias — from genes to potential treatments

(2017) Henry L. Paulson et al.   NATURE REVIEWS NEUROSCIENCE

Synonymous mutation in TP53 results in a cryptic splice site affecting its DNA-binding site in an adolescent with two primary sarcomas

(2017) Frances Austin et al.   PEDIATRIC BLOOD & CANCER

Small but Mighty: Functional Peptides Encoded by Small ORFs in Plants

(2017) Polly Yingshan Hsu et al.   PROTEOMICS

Small Proteins Encoded by Unannotated ORFs are Rising Stars of the Proteome, Confirming Shortcomings in Genome Annotations and Current Vision of an mRNA

(2017) Vivian Delcourt et al.   PROTEOMICS

The Relationship between Alternative Splicing and Proteomic Complexity

(2017) Benjamin J. Blencowe   TRENDS IN BIOCHEMICAL SCIENCES

Mammalian Polycistronic mRNAs and Disease

(2017) Timofey A. Karginov et al.   TRENDS IN GENETICS

Beyond Read-Counts: Ribo-seq Data Analysis to Understand the Functions of the Transcriptome

(2017) Lorenzo Calviello et al.   TRENDS IN GENETICS

Identification of Unannotated Small Genes in Salmonella

(2017) Jonghwan Baek et al.   G3-Genes Genomes Genetics

The Mitochondrial-Derived Peptides, HumaninS14G and Small Humanin-like Peptide 2, Exhibit Chaperone-like Activity

(2017) Alan K. Okada et al.   Scientific Reports

Improved Identification and Analysis of Small Open Reading Frame Encoded Polypeptides

(2016) Jiao Ma et al.   ANALYTICAL CHEMISTRY

SPECtre: a spectral coherence-­based classifier of actively translated transcripts from ribosome profiling sequence data

(2016) Sang Y. Chun et al.   BMC BIOINFORMATICS

Ribosome Footprint Profiling of Translation throughout the Genome

(2016) Nicholas T. Ingolia   CELL

Ultra-deep sequencing of ribosome-associated poly-adenylated RNA in earlyDrosophilaembryos reveals hundreds of conserved translated sORFs

(2016) Hongmei Li et al.   DNA RESEARCH

MOTS-c: A novel mitochondrial-derived peptide regulating muscle and fat metabolism

(2016) Changhan Lee et al.   FREE RADICAL BIOLOGY AND MEDICINE

Search for Genetic Variant in the Apelin Gene by Resequencing and Association Study in European Subjects

(2016) Federica Sentinelli et al.   Genetic Testing and Molecular Biomarkers

Upstream Open Reading Frames Differentially Regulate Gene-specific Translation in the Integrated Stress Response

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

Apelin/APJ system as a therapeutic target in diabetes and its complications

(2016) Haoliang Hu et al.   MOLECULAR GENETICS AND METABOLISM

mTORC1 and muscle regeneration are regulated by the LINC00961-encoded SPAR polypeptide

(2016) Akinobu Matsumoto et al.   NATURE

Mass-spectrometric exploration of proteome structure and function

(2016) Ruedi Aebersold et al.   NATURE

A human microprotein that interacts with the mRNA decapping complex

(2016) Nadia G D'Lima et al.   Nature Chemical Biology

The state of play in higher eukaryote gene annotation

(2016) Jonathan M. Mudge et al.   NATURE REVIEWS GENETICS

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

(2016) Aoife McLysaght et al.   NATURE REVIEWS GENETICS

Coming of age: ten years of next-generation sequencing technologies

(2016) Sara Goodwin et al.   NATURE REVIEWS GENETICS

Comprehensive Molecular Characterization of Papillary Renal-Cell Carcinoma

(2016)   NEW ENGLAND JOURNAL OF MEDICINE

NCBI prokaryotic genome annotation pipeline

(2016) Tatiana Tatusova et al.   NUCLEIC ACIDS RESEARCH

Evaluating the evaluation of cancer driver genes

(2016) Collin J. Tokheim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

The Rise and Rise of Exome Sequencing

(2016) Chee-Seng Ku et al.   Public Health Genomics

Decoding sORF translation – from small proteins to gene regulation

(2016) Luis Enrique Cabrera-Quio et al.   RNA Biology

In-depth analysis ofcis-determinants that either promote or inhibit reinitiation onGCN4mRNA after translation of its four short uORFs

(2016) Stanislava Gunišová et al.   RNA

New Peptides Under the s(ORF)ace of the Genome

(2016) Jose I. Pueyo et al.   TRENDS IN BIOCHEMICAL SCIENCES

The Emerging World of Small ORFs

(2016) Roger P. Hellens et al.   TRENDS IN PLANT SCIENCE

Improving GENCODE reference gene annotation using a high-stringency proteogenomics workflow

(2016) James C. Wright et al.   Nature Communications

The Ensembl gene annotation system

(2016) Bronwen L. Aken et al.   Database-The Journal of Biological Databases and Curation

Proteomic profiling of NCI-60 extracellular vesicles uncovers common protein cargo and cancer type-specific biomarkers

(2016) Stephanie N. Hurwitz et al.   Oncotarget

Hemotin, a Regulator of Phagocytosis Encoded by a Small ORF and Conserved across Metazoans

(2016) José I. Pueyo et al.   PLOS BIOLOGY

Single Synonymous Mutations in KRAS Cause Transformed Phenotypes in NIH3T3 Cells

(2016) Andrew M. Waters et al.   PLoS One

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

The BioPlex Network: A Systematic Exploration of the Human Interactome

(2015) Edward L. Huttlin et al.   CELL

small ORFs: A new class of essential genes for development

(2015) João Paulo Albuquerque et al.   GENETICS AND MOLECULAR BIOLOGY

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology

(2015) Sue Richards et al.   GENETICS IN MEDICINE

The Generating Function Approach for Peptide Identification in Spectral Networks

(2015) Adrian Guthals et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

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

Advanced Proteogenomic Analysis Reveals Multiple Peptide Mutations and Complex Immunoglobulin Peptides in Colon Cancer

(2015) Sunghee Woo et al.   JOURNAL OF PROTEOME RESEARCH

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

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

Defining a minimal cell: essentiality of small ORFs and ncRNAs in a genome-reduced bacterium

(2015) M. Lluch-Senar et al.   Molecular Systems Biology

A mass-tolerant database search identifies a large proportion of unassigned spectra in shotgun proteomics as modified peptides

(2015) Joel M Chick et al.   NATURE BIOTECHNOLOGY

Discovery and characterization of smORF-encoded bioactive polypeptides

(2015) Alan Saghatelian et al.   Nature Chemical Biology

Detecting actively translated open reading frames in ribosome profiling data

(2015) Lorenzo Calviello et al.   NATURE METHODS

A-to-I editing of coding and non-coding RNAs by ADARs

(2015) Kazuko Nishikura   NATURE REVIEWS MOLECULAR CELL BIOLOGY

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

(2015) Hélène Mouilleron et al.   NUCLEIC ACIDS RESEARCH

Identification of novel Arabidopsis thaliana upstream open reading frames that control expression of the main coding sequences in a peptide sequence-dependent manner

(2015) Isao Ebina et al.   NUCLEIC ACIDS RESEARCH

RPFdb: a database for genome wide information of translated mRNA generated from ribosome profiling

(2015) Shang-Qian Xie et al.   NUCLEIC ACIDS RESEARCH

sORFs.org: a repository of small ORFs identified by ribosome profiling

(2015) Volodimir Olexiouk et al.   NUCLEIC ACIDS RESEARCH

Whisper mutations: cryptic messages within the genetic code

(2015) R Fåhraeus et al.   ONCOGENE

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

Best practices for evaluating single nucleotide variant calling methods for microbial genomics

(2015) Nathan D. Olson et al.   Frontiers in Genetics

Small Proteins Can No Longer Be Ignored

(2014) Gisela Storz et al.   Annual Review of Biochemistry

Identifying (non-)coding RNAs and small peptides: Challenges and opportunities

(2014) Andrea Pauli et al.   BIOESSAYS

Synonymous Mutations Frequently Act as Driver Mutations in Human Cancers

(2014) Fran Supek et al.   CELL

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

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

A Large Nonconserved Region of the Tethering Protein Leashin Is Involved in Regulating the Position, Movement, and Function of Woronin Bodies in Aspergillus oryzae

(2014) Pei Han et al.   EUKARYOTIC CELL

Transition from metabolic adaptation to maladaptation of the heart in obesity: role of apelin

(2014) C Alfarano et al.   INTERNATIONAL JOURNAL OF OBESITY

Discovery of Human sORF-Encoded Polypeptides (SEPs) in Cell Lines and Tissue

(2014) Jiao Ma et al.   JOURNAL OF PROTEOME RESEARCH

Principles of regulatory information conservation between mouse and human

(2014) Yong Cheng et al.   NATURE

Population genomics of Populus trichocarpa identifies signatures of selection and adaptive trait associations

(2014) Luke M Evans et al.   NATURE GENETICS

Proteogenomics: concepts, applications and computational strategies

(2014) Alexey I Nesvizhskii   NATURE METHODS

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

(2014) Nicholas T. Ingolia   NATURE REVIEWS GENETICS

Emerging evidence for functional peptides encoded by short open reading frames

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

PROTEOFORMER: deep proteome coverage through ribosome profiling and MS integration

(2014) Jeroen Crappé et al.   NUCLEIC ACIDS RESEARCH

OMIM.org: Online Mendelian Inheritance in Man (OMIM®), an online catalog of human genes and genetic disorders

(2014) Joanna S. Amberger 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

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

(2014) Julie L Aspden et al.   eLife

Long non-coding RNAs as a source of new peptides

(2014) Jorge Ruiz-Orera et al.   eLife

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

(2013) Mitchell Guttman et al.   CELL

Pathogenic variants in non-protein-coding sequences

(2013) P Makrythanasis et al.   CLINICAL GENETICS

On the Immortality of Television Sets: "Function" in the Human Genome According to the Evolution-Free Gospel of ENCODE

(2013) D. Graur et al.   Genome Biology and Evolution

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

The apelin receptor APJ: journey from an orphan to a multifaceted regulator of homeostasis

(2013) Anne-Marie O'Carroll et al.   JOURNAL OF ENDOCRINOLOGY

Comprehensive molecular characterization of clear cell renal cell carcinoma

(2013)   NATURE

Rare-disease genetics in the era of next-generation sequencing: discovery to translation

(2013) Kym M. Boycott et al.   NATURE REVIEWS GENETICS

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

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

TISdb: a database for alternative translation initiation in mammalian cells

(2013) Ji Wan et al.   NUCLEIC ACIDS RESEARCH

Activities at the Universal Protein Resource (UniProt)

(2013)   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

Small open reading frames associated with morphogenesis are hidden in plant genomes

(2013) K. Hanada et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

The next level of complexity: Crosstalk of posttranslational modifications

(2013) A. Saskia Venne et al.   PROTEOMICS

Conserved Regulation of Cardiac Calcium Uptake by Peptides Encoded in Small Open Reading Frames

(2013) E. G. Magny et al.   SCIENCE

Cancer Genome Landscapes

(2013) B. Vogelstein et al.   SCIENCE

De Novo ORFs in Drosophila Are Important to Organismal Fitness and Evolved Rapidly from Previously Non-coding Sequences

(2013) Josephine A. Reinhardt et al.   PLoS Genetics

Gene Expression Regulation by Upstream Open Reading Frames and Human Disease

(2013) Cristina Barbosa et al.   PLoS Genetics

Ribosome profiling reveals pervasive and regulated stop codon readthrough in Drosophila melanogaster

(2013) Joshua G Dunn et al.   eLife

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

The emerging role of the mitochondrial-derived peptide humanin in stress resistance

(2012) Kelvin Yen et al.   JOURNAL OF MOLECULAR ENDOCRINOLOGY

Analysis of High Accuracy, Quantitative Proteomics Data in the MaxQB Database

(2012) Christoph Schaab et al.   MOLECULAR & CELLULAR PROTEOMICS

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

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

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

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

Insights into the regulation of protein abundance from proteomic and transcriptomic analyses

(2012) Christine Vogel et al.   NATURE REVIEWS GENETICS

SNP Calling, Genotype Calling, and Sample Allele Frequency Estimation from New-Generation Sequencing Data

(2012) Rasmus Nielsen et al.   PLoS One

Interactive Association of Five Candidate Polymorphisms in Apelin/APJ Pathway with Coronary Artery Disease among Chinese Hypertensive Patients

(2012) Wei Jin et al.   PLoS One

Computational analysis of functional long noncoding RNAs reveals lack of peptide-coding capacity and parallels with 3' UTRs

(2012) F. Niazi et al.   RNA

Apelin, a promising target for type 2 diabetes treatment?

(2012) Isabelle Castan-laurell et al.   TRENDS IN ENDOCRINOLOGY AND METABOLISM

Apelin gene polymorphism influences apelin expression and obesity phenotypes in Chinese women

(2011) Y.-C. Liao et al.   AMERICAN JOURNAL OF CLINICAL NUTRITION

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

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

A novel hybrid gene prediction method employing protein multiple sequence alignments

(2011) Oliver Keller et al.   BIOINFORMATICS

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

(2011) Nicholas T. Ingolia et al.   CELL

Small Open Reading Frames: Current Prediction Techniques and Future Prospect

(2011) Haoyu Cheng et al.   CURRENT PROTEIN & PEPTIDE SCIENCE

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

(2011) Benoît Vanderperre et al.   FASEB JOURNAL

Understanding the contribution of synonymous mutations to human disease

(2011) Zuben E. Sauna et al.   NATURE REVIEWS GENETICS

Genotype and SNP calling from next-generation sequencing data

(2011) Rasmus Nielsen et al.   NATURE REVIEWS GENETICS

NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy

(2011) K. D. Pruitt et al.   NUCLEIC ACIDS RESEARCH

Hundreds of putatively functional small open reading frames in Drosophila

(2011) Emmanuel Ladoukakis et al.   GENOME BIOLOGY

Searching in microbial genomes for encoded small proteins

(2011) Jos Boekhorst et al.   Microbial Biotechnology

Association of Genetic Variants in the Apelin-APJ System and ACE2 With Blood Pressure Responses to Potassium Supplementation: The GenSalt Study

(2010) Q. Zhao et al.   AMERICAN JOURNAL OF HYPERTENSION

Apelin and APJ regulation in adipose tissue and skeletal muscle of type 2 diabetic mice and humans

(2010) Cédric Dray et al.   AMERICAN JOURNAL OF PHYSIOLOGY-ENDOCRINOLOGY AND METABOLISM

tsORFdb: Theoretical Small Open Reading Frames (ORFs) database and massProphet: Peptide Mass Fingerprinting (PMF) tool for unknown small functional ORFs

(2010) Hyoung-Sam Heo et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Brick1 Is an Essential Regulator of Actin Cytoskeleton Required for Embryonic Development and Cell Transformation

(2010) B. Escobar et al.   CANCER RESEARCH

Identifying a High Fraction of the Human Genome to be under Selective Constraint Using GERP++

(2010) Eugene V. Davydov et al.   PLoS Computational Biology

Plasma apelin levels and apelin/APJ mRNA expression in patients with gestational diabetes mellitus

(2009) Beata Telejko et al.   DIABETES RESEARCH AND CLINICAL PRACTICE

The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes

(2009) K. D. Pruitt et al.   GENOME RESEARCH

Detection of nonneutral substitution rates on mammalian phylogenies

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

The Unreasonable Effectiveness of Data

(2009) Alon Halevy et al.   IEEE INTELLIGENT SYSTEMS

Small Stress Response Proteins in Escherichia coli: Proteins Missed by Classical Proteomic Studies

(2009) M. R. Hemm et al.   JOURNAL OF BACTERIOLOGY

Effect of diet-induced weight loss on plasma apelin and cytokine levels in individuals with the metabolic syndrome

(2009) M.V. Heinonen et al.   NUTRITION METABOLISM AND CARDIOVASCULAR DISEASES

Apelin Levels Are Increased in Morbidly Obese Subjects with Type 2 Diabetes Mellitus

(2009) Federico Soriguer et al.   OBESITY SURGERY

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

(2009) N. T. Ingolia et al.   SCIENCE

Apelin Stimulates Glucose Utilization in Normal and Obese Insulin-Resistant Mice

(2008) Cédric Dray et al.   Cell Metabolism

Effect of hypocaloric diet-induced weight loss in obese women on plasma apelin and adipose tissue expression of apelin and APJ.

(2008) Isabelle Castan-Laurell et al.   EUROPEAN JOURNAL OF ENDOCRINOLOGY

Low Plasma Apelin Levels in Newly Diagnosed Type 2 Diabetes Mellitus

(2008) G. Erdem et al.   EXPERIMENTAL AND CLINICAL ENDOCRINOLOGY & DIABETES

Small membrane proteins found by comparative genomics and ribosome binding site models

(2008) Matthew R. Hemm et al.   MOLECULAR MICROBIOLOGY

Drosophila Pgc protein inhibits P-TEFb recruitment to chromatin in primordial germ cells

(2008) Kazuko Hanyu-Nakamura et al.   NATURE

Opposing effects of polyglutamine expansion on native protein complexes contribute to SCA1

(2008) Janghoo Lim et al.   NATURE

An ancient genetic link between vertebrate mitochondrial fatty acid synthesis and RNA processing

(2007) Kaija J. Autio et al.   FASEB JOURNAL