Evolutionary origins and interactomes of human, young microproteins and small peptides translated from short open reading frames

De novo genes with an lncRNA origin encode unique human brain developmental functionality

(2023) Ni A. An et al.   Nature Ecology & Evolution

Understudied proteins: opportunities and challenges for functional proteomics

(2022) Georg Kustatscher et al.   NATURE METHODS

A high-resolution map of human RNA translation

(2022) Sonia P. Chothani et al.   MOLECULAR CELL

Standardized annotation of translated open reading frames

(2022) Jonathan M. Mudge et al.   NATURE BIOTECHNOLOGY

De novo birth of functional microproteins in the human lineage

(2022) Nikolaos Vakirlis et al.   Cell Reports

Pan-cancer analysis of transcripts encoding novel open-reading frames (nORFs) and their potential biological functions

(2021) Chaitanya Erady et al.   npj Genomic Medicine

Noncanonical open reading frames encode functional proteins essential for cancer cell survival

(2021) John R. Prensner et al.   NATURE BIOTECHNOLOGY

Trends in peptide drug discovery

(2021) Markus Muttenthaler et al.   NATURE REVIEWS DRUG DISCOVERY

MetamORF: a repository of unique short open reading frames identified by both experimental and computational approaches for gene and metagene analyses

(2021) Sebastien A Choteau et al.   Database-The Journal of Biological Databases and Curation

PRISMA and BioID disclose a motifs-based interactome of the intrinsically disordered transcription factor C/EBPα

(2021) Evelyn Ramberger et al.   iScience

The UCSC Genome Browser database: 2022 update

(2021) Brian T Lee et al.   NUCLEIC ACIDS RESEARCH

The Eukaryotic Linear Motif resource: 2022 release

(2021) Manjeet Kumar et al.   NUCLEIC ACIDS RESEARCH

The dark proteome: translation from noncanonical open reading frames

(2021) Bradley W. Wright et al.   TRENDS IN CELL BIOLOGY

Pervasive functional translation of noncanonical human open reading frames

(2020) Jin Chen et al.   SCIENCE

Internalization mechanisms of cell-penetrating peptides

(2020) Ivana Ruseska et al.   Beilstein Journal of Nanotechnology

Synteny-based analyses indicate that sequence divergence is not the main source of orphan genes

(2020) Nikolaos Vakirlis et al.   eLife

A genome alignment of 120 mammals highlights ultraconserved element variability and placenta-associated enhancers

(2020) Nikolai Hecker et al.   GigaScience

NetMHCpan-4.1 and NetMHCIIpan-4.0: improved predictions of MHC antigen presentation by concurrent motif deconvolution and integration of MS MHC eluted ligand data

(2020) Birkir Reynisson et al.   NUCLEIC ACIDS RESEARCH

Integrated proteogenomic deep sequencing and analytics accurately identify non-canonical peptides in tumor immunopeptidomes

(2020) Chloe Chong et al.   Nature Communications

Mitochondrial peptide BRAWNIN is essential for vertebrate respiratory complex III assembly

(2020) Shan Zhang et al.   Nature Communications

Mitoregulin Controls β-Oxidation in Human and Mouse Adipocytes

(2020) Max Friesen et al.   Stem Cell Reports

Quantification of translation uncovers the functions of the alternative transcriptome

(2020) Lorenzo Calviello et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Mechanisms of drug interactions between translation-inhibiting antibiotics

(2020) Bor Kavčič et al.   Nature Communications

Conserved Upstream Open Reading Frame Nascent Peptides that Control Translation

(2020) Thomas E. Dever et al.   Annual Review of Genetics

EVLncRNAs 2.0: an updated database of manually curated functional long non-coding RNAs validated by low-throughput experiments

(2020) Bailing Zhou et al.   NUCLEIC ACIDS RESEARCH

LINC00116 codes for a mitochondrial peptide linking respiration and lipid metabolism

(2019) Anastasia Chugunova et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

GenTree, an integrated resource for analyzing the evolution and function of primate-specific coding genes

(2019) Yi Shao et al.   GENOME RESEARCH

De novo gene birth

(2019) Stephen Branden Van Oss et al.   PLoS Genetics

The Translational Landscape of the Human Heart

(2019) Sebastiaan van Heesch et al.   CELL

A hidden human proteome encoded by ‘non-coding’ genes

(2019) Shaohua Lu et al.   NUCLEIC ACIDS RESEARCH

Robust prediction of HLA class II epitopes by deep motif deconvolution of immunopeptidomes

(2019) Julien Racle et al.   NATURE BIOTECHNOLOGY

Improved Ribo-seq enables identification of cryptic translation events

(2018) Florian Erhard et al.   NATURE METHODS

The influence of transcript assembly on the proteogenomics discovery of microproteins

(2018) Jiao Ma et al.   PLoS One

Translation of neutrally evolving peptides provides a basis for de novo gene evolution

(2018) Jorge Ruiz-Orera et al.   Nature Ecology & Evolution

MIEF1 Microprotein Regulates Mitochondrial Translation

(2018) Annie Rathore et al.   BIOCHEMISTRY

Mutations in Disordered Regions Can Cause Disease by Creating Dileucine Motifs

(2018) Katrina Meyer et al.   CELL

Flexible and Fast Mapping of Peptides to a Proteome with ProteoMapper

(2018) Luis Mendoza et al.   JOURNAL OF PROTEOME RESEARCH

CORUM: the comprehensive resource of mammalian protein complexes—2019

(2018) Madalina Giurgiu et al.   NUCLEIC ACIDS RESEARCH

The PRIDE database and related tools and resources in 2019: improving support for quantification data

(2018) Yasset Perez-Riverol et al.   NUCLEIC ACIDS RESEARCH

STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets

(2018) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

Translation of Small Open Reading Frames: Roles in Regulation and Evolutionary Innovation

(2018) Jorge Ruiz-Orera et al.   TRENDS IN GENETICS

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

(2017) Andy T Kong et al.   NATURE METHODS

The eukaryotic linear motif resource – 2018 update

(2017) Marc Gouw et al.   NUCLEIC ACIDS RESEARCH

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

(2017) Volodimir Olexiouk et al.   NUCLEIC ACIDS RESEARCH

Functional screening in human cardiac organoids reveals a metabolic mechanism for cardiomyocyte cell cycle arrest

(2017) Richard J. Mills et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mining for Micropeptides

(2017) Catherine A. Makarewich et al.   TRENDS IN CELL BIOLOGY

Random sequences are an abundant source of bioactive RNAs or peptides

(2017) Rafik Neme et al.   Nature Ecology & Evolution

Extracellular matrix endocytosis in controlling matrix turnover and beyond: emerging roles in cancer

(2016) Elena Rainero   BIOCHEMICAL SOCIETY TRANSACTIONS

Tiered Human Integrated Sequence Search Databases for Shotgun Proteomics

(2016) Eric W. Deutsch et al.   JOURNAL OF PROTEOME RESEARCH

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

(2016) Aoife McLysaght et al.   NATURE REVIEWS GENETICS

Expansion of the Gene Ontology knowledgebase and resources

(2016)   NUCLEIC ACIDS RESEARCH

g:Profiler—a web server for functional interpretation of gene lists (2016 update)

(2016) Jüri Reimand et al.   NUCLEIC ACIDS RESEARCH

Genomic analysis reveals hidden biodiversity within colugos, the sister group to primates

(2016) V. C. Mason et al.   Science Advances

The Mitochondrial-Derived Peptide MOTS-c Promotes Metabolic Homeostasis and Reduces Obesity and Insulin Resistance

(2015) Changhan Lee et al.   Cell Metabolism

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

Detecting actively translated open reading frames in ribosome profiling data

(2015) Lorenzo Calviello et al.   NATURE METHODS

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

Trans-Proteomic Pipeline, a standardized data processing pipeline for large-scale reproducible proteomics informatics

(2015) Eric W. Deutsch et al.   Proteomics Clinical Applications

Gene essentiality and synthetic lethality in haploid human cells

(2015) V. A. Blomen et al.   SCIENCE

Origins of De Novo Genes in Human and Chimpanzee

(2015) Jorge Ruiz-Orera et al.   PLoS Genetics

Accurate Protein Complex Retrieval by Affinity Enrichment Mass Spectrometry (AE-MS) Rather than Affinity Purification Mass Spectrometry (AP-MS)

(2014) Eva C. Keilhauer et al.   MOLECULAR & CELLULAR PROTEOMICS

A draft map of the human proteome

(2014) Min-Sik Kim et al.   NATURE

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

(2014) Sibylle Schleich et al.   NATURE

ProteomeXchange provides globally coordinated proteomics data submission and dissemination

(2014) Juan A Vizcaíno et al.   NATURE BIOTECHNOLOGY

NCYM, a Cis-Antisense Gene of MYCN, Encodes a De Novo Evolved Protein That Inhibits GSK3β Resulting in the Stabilization of MYCN in Human Neuroblastomas

(2014) Yusuke Suenaga et al.   PLoS Genetics

Differential protein occupancy profiling of the mRNA transcriptome

(2014) Markus Schueler et al.   GENOME BIOLOGY

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Insights into RNA Biology from an Atlas of Mammalian mRNA-Binding Proteins

(2012) Alfredo Castello et al.   CELL

A Tandem Di-hydrophobic Motif Mediates Clathrin-dependent Endocytosis via Direct Binding to the AP-2 ασ2 Subunits

(2012) Bernardo Ortega et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Proto-genes and de novo gene birth

(2012) Anne-Ruxandra Carvunis et al.   NATURE

Fiji: an open-source platform for biological-image analysis

(2012) Johannes Schindelin et al.   NATURE METHODS

NIH Image to ImageJ: 25 years of image analysis

(2012) Caroline A Schneider et al.   NATURE METHODS

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

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

Aberrations of NEGR1 on 1p31 and MYEOV on 11q13 in neuroblastoma

(2011) Junko Takita et al.   CANCER SCIENCE

Attributes of short linear motifs

(2011) Norman E. Davey et al.   Molecular BioSystems

The evolutionary origin of orphan genes

(2011) Diethard Tautz et al.   NATURE REVIEWS GENETICS

Hundreds of putatively functional small open reading frames in Drosophila

(2011) Emmanuel Ladoukakis et al.   GENOME BIOLOGY

Skyline: an open source document editor for creating and analyzing targeted proteomics experiments

(2010) Brendan MacLean et al.   BIOINFORMATICS

Systems survey of endocytosis by multiparametric image analysis

(2010) Claudio Collinet et al.   NATURE

Endocytosis and signalling: intertwining molecular networks

(2009) Alexander Sorkin et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

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

(2009) N. T. Ingolia et al.   SCIENCE

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

(2008) Jürgen Cox et al.   NATURE BIOTECHNOLOGY