A vast pool of lineage-specific microproteins encoded by long non-coding RNAs in plants

Most non-canonical proteins uniquely populate the proteome or immunopeptidome

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One-shot analysis of translated mammalian lncRNAs with AHARIBO

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When Long Noncoding Becomes Protein Coding

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SciPy 1.0: fundamental algorithms for scientific computing in Python

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Pervasive functional translation of noncanonical human open reading frames

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De novo emergence of adaptive membrane proteins from thymine-rich genomic sequences

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Nanopore direct RNA sequencing maps the complexity of Arabidopsis mRNA processing and m6A modification

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A Continuum of Evolving De Novo Genes Drives Protein-Coding Novelty in Drosophila

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Large-scale Discovery of Non-conventional Peptides in Maize and Arabidopsis Through an Integrated Peptidogenomic Pipeline

(2020) Shunxi Wang et al.   Molecular Plant

Mass-spectrometry-based draft of the Arabidopsis proteome

(2020) Julia Mergner et al.   NATURE

Full-length transcript characterization of SF3B1 mutation in chronic lymphocytic leukemia reveals downregulation of retained introns

(2020) Alison D. Tang et al.   Nature Communications

Long Non-coding RNA in Plants in the Era of Reference Sequences

(2020) Hikmet Budak et al.   Frontiers in Plant Science

Proteomic analysis of meiosis and characterization of novel short open reading frames in the fission yeast Schizosaccharomyces pombe

(2020) Barbora Huraiova et al.   CELL CYCLE

Translation of small downstream ORFs enhances translation of canonical main open reading frames

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Reconsidering proteomic diversity with functional investigation of small ORFs and alternative ORFs

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New insights into Arabidopsis transcriptome complexity revealed by direct sequencing of native RNAs

(2020) Shoudong Zhang et al.   NUCLEIC ACIDS RESEARCH

smORFunction: a tool for predicting functions of small open reading frames and microproteins

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Functional Long Non-coding RNAs Evolve from Junk Transcripts

(2020) Alexander F. Palazzo et al.   CELL

Prevalence of alternative AUG and non-AUG translation initiators and their regulatory effects across plants

(2020) Ya-Ru Li et al.   GENOME RESEARCH

A hydrophobic ratchet entrenches molecular complexes

(2020) Georg K. A. Hochberg et al.   NATURE

Nanopore RNA Sequencing Revealed Long Non-Coding and LTR Retrotransposon-Related RNAs Expressed at Early Stages of Triticale SEED Development

(2020) Ilya Kirov et al.   Plants-Basel

Phytohormone treatment induces generation of cryptic peptides with antimicrobial activity in the Moss Physcomitrella patens

(2019) Igor Fesenko et al.   BMC PLANT BIOLOGY

SignalP 5.0 improves signal peptide predictions using deep neural networks

(2019) José Juan Almagro Armenteros et al.   NATURE BIOTECHNOLOGY

Unraveling the hidden universe of small proteins in bacterial genomes

(2019) Samuel Miravet‐Verde et al.   Molecular Systems Biology

De novo gene birth

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The Translational Landscape of the Human Heart

(2019) Sebastiaan van Heesch et al.   CELL

Comparative genomic analysis identifies small open reading frames (sORFs) with peptide-encoding features in avian 16S rDNA

(2019) Mathieu Mortz et al.   GENOMICS

Molecular Traits of Long Non-protein Coding RNAs from Diverse Plant Species Show Little Evidence of Phylogenetic Relationships

(2019) Caitlin M. A. Simopoulos et al.   G3-Genes Genomes Genetics

Large-Scale Analyses of Human Microbiomes Reveal Thousands of Small, Novel Genes

(2019) Hila Sberro et al.   CELL

Distinct types of short open reading frames are translated in plant cells

(2019) Igor Fesenko et al.   GENOME RESEARCH

Plant Noncoding RNAs: Hidden Players in Development and Stress Responses

(2019) Yu Yu et al.   Annual Review of Cell and Developmental Biology

MiPepid: MicroPeptide identification tool using machine learning

(2019) Mengmeng Zhu et al.   BMC BIOINFORMATICS

One thousand plant transcriptomes and the phylogenomics of green plants

(2019)   NATURE

Toytree: A minimalist tree visualization and manipulation library for Python

(2019) Deren A. R. Eaton   Methods in Ecology and Evolution

The meanings of 'function' in biology and the problematic case of de novo gene emergence

(2019) Diane Marie Keeling et al.   eLife

Accurate annotation of human protein-coding small open reading frames

(2019) Thomas F. Martinez et al.   Nature Chemical Biology

Identification and analysis of ribosome-associated lncRNAs using ribosome profiling data

(2018) Chao Zeng et al.   BMC GENOMICS

The small peptide world in long noncoding RNAs

(2018) Seo-Won Choi et al.   BRIEFINGS IN BIOINFORMATICS

Functional Classification and Experimental Dissection of Long Noncoding RNAs

(2018) Florian Kopp et al.   CELL

CLAVATA Was a Genetic Novelty for the Morphological Innovation of 3D Growth in Land Plants

(2018) Chris D. Whitewoods et al.   CURRENT BIOLOGY

The Physcomitrella patens chromosome-scale assembly reveals moss genome structure and evolution

(2018) Daniel Lang et al.   PLANT JOURNAL

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

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

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

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lncRNAs are associated with polysomes during adipose-derived stem cell differentiation

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A Molecular Portrait of De Novo Genes in Yeasts

(2017) Nikolaos Vakirlis et al.   MOLECULAR BIOLOGY AND EVOLUTION

Classification and function of small open reading frames

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

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Global analysis of ribosome-associated noncoding RNAs unveils new modes of translational regulation

(2017) Jérémie Bazin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Diversity of Long Noncoding RNAs and Their Generation

(2017) Huang Wu et al.   TRENDS IN GENETICS

High GC content causes orphan proteins to be intrinsically disordered

(2017) Walter Basile et al.   PLoS Computational Biology

Prosurvival long noncoding RNA PINCR regulates a subset of p53 targets in human colorectal cancer cells by binding to Matrin 3

(2017) Ritu Chaudhary et al.   eLife

Young genes are highly disordered as predicted by the preadaptation hypothesis of de novo gene birth

(2017) Benjamin A. Wilson et al.   Nature Ecology & Evolution

Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences

(2016) Heng Li   BIOINFORMATICS

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

(2016) Akinobu Matsumoto et al.   NATURE

The MaxQuant computational platform for mass spectrometry-based shotgun proteomics

(2016) Stefka Tyanova et al.   Nature Protocols

Evolution to the rescue: using comparative genomics to understand long non-coding RNAs

(2016) Igor Ulitsky   NATURE REVIEWS GENETICS

Cytoplasmic long noncoding RNAs are frequently bound to and degraded at ribosomes in human cells

(2016) Joana Carlevaro-Fita et al.   RNA

Transmembrane Domain Lengths Serve as Signatures of Organismal Complexity and Viral Transport Mechanisms

(2016) Snigdha Singh et al.   Scientific Reports

Overexpression of theArabidopsis thalianasignalling peptide TAXIMIN1 affects lateral organ development

(2015) Janine Colling et al.   JOURNAL OF EXPERIMENTAL BOTANY

Gene-Wide Identification of Episodic Selection

(2015) Ben Murrell et al.   MOLECULAR BIOLOGY AND EVOLUTION

Primary transcripts of microRNAs encode regulatory peptides

(2015) Dominique Lauressergues et al.   NATURE

Determinants of the rate of protein sequence evolution

(2015) Jianzhi Zhang et al.   NATURE REVIEWS GENETICS

The Plant Peptidome: An Expanding Repertoire of Structural Features and Biological Functions

(2015) Patrizia Tavormina et al.   PLANT CELL

Principles of Long Noncoding RNA Evolution Derived from Direct Comparison of Transcriptomes in 17 Species

(2015) Hadas Hezroni et al.   Cell Reports

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

(2015) Zhe Ji et al.   eLife

Computational approach for calculating the probability of eukaryotic translation initiation from ribo-seq data that takes into account leaky scanning

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UpSet: Visualization of Intersecting Sets

(2014) Alexander Lex et al.   IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS

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

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

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Quantitative profiling of initiating ribosomes in vivo

(2014) Xiangwei Gao et al.   NATURE METHODS

Proteogenomics: concepts, applications and computational strategies

(2014) Alexey I Nesvizhskii   NATURE METHODS

Pervasive transcription: illuminating the dark matter of bacterial transcriptomes

(2014) Joseph T. Wade et al.   NATURE REVIEWS MICROBIOLOGY

Evolution at protein ends: major contribution of alternative transcription initiation and termination to the transcriptome and proteome diversity in mammals

(2014) S. A. Shabalina et al.   NUCLEIC ACIDS RESEARCH

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

(2014) Julie L Aspden et al.   eLife

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

System for Stable β-Estradiol-Inducible Gene Expression in the Moss Physcomitrella patens

(2013) Minoru Kubo et al.   PLoS One

The Vast, Conserved Mammalian lincRNome

(2013) David Managadze et al.   PLoS Computational Biology

Dissecting the role of low-complexity regions in the evolution of vertebrate proteins

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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

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

Systemin, Hydroxyproline-Rich Systemin and the Induction of Protease Inhibitors

(2011) Gregory Pearce   CURRENT PROTEIN & PEPTIDE SCIENCE

Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis

(2011) A. Pauli et al.   GENOME RESEARCH

Role of Low-Complexity Sequences in the Formation of Novel Protein Coding Sequences

(2011) M. Toll-Riera et al.   MOLECULAR BIOLOGY AND EVOLUTION

lncRNAs transactivate STAU1-mediated mRNA decay by duplexing with 3′ UTRs via Alu elements

(2011) Chenguang Gong et al.   NATURE

Hundreds of putatively functional small open reading frames in Drosophila

(2011) Emmanuel Ladoukakis et al.   GENOME BIOLOGY

Distinct Patterns of Expression and Evolution of Intronless and Intron-Containing Mammalian Genes

(2010) Svetlana A. Shabalina et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evidence That Mutation Is Universally Biased towards AT in Bacteria

(2010) Ruth Hershberg et al.   PLoS Genetics

The Sequence Alignment/Map format and SAMtools

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Evolution of alternative and constitutive regions of mammalian 5'UTRs

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