Pervasive functional translation of noncanonical human open reading frames

Molecular recording of mammalian embryogenesis

(2019) Michelle M. Chan et al.   NATURE

MOXI Is a Mitochondrial Micropeptide That Enhances Fatty Acid β-Oxidation

(2018) Catherine A. Makarewich et al.   Cell Reports

Mitoregulin: A lncRNA-Encoded Microprotein that Supports Mitochondrial Supercomplexes and Respiratory Efficiency

(2018) Colleen S. Stein et al.   Cell Reports

MIEF1 Microprotein Regulates Mitochondrial Translation

(2018) Annie Rathore et al.   BIOCHEMISTRY

The protein coded by a short open reading frame, not by the annotated coding sequence is the main gene product of the dual-coding gene MIEF1

(2018) Vivian Delcourt et al.   MOLECULAR & CELLULAR PROTEOMICS

The translation of non-canonical open reading frames controls mucosal immunity

(2018) Ruaidhrí Jackson et al.   NATURE

Transcriptome-wide measurement of translation by ribosome profiling

(2017) Nicholas J. McGlincy et al.   METHODS

Loss-less Nano-fractionator for High Sensitivity, High Coverage Proteomics

(2017) Nils A. Kulak et al.   MOLECULAR & CELLULAR PROTEOMICS

Combined CRISPRi/a-Based Chemical Genetic Screens Reveal that Rigosertib Is a Microtubule-Destabilizing Agent

(2017) Marco Jost et al.   MOLECULAR CELL

A Peptide Encoded by a Putative lncRNA HOXB-AS3 Suppresses Colon Cancer Growth

(2017) Jin-Zhou Huang et al.   MOLECULAR CELL

Translation from unconventional 5′ start sites drives tumour initiation

(2017) Ataman Sendoel et al.   NATURE

GuideScan software for improved single and paired CRISPR guide RNA design

(2017) Alexendar R Perez et al.   NATURE BIOTECHNOLOGY

Pooled CRISPR screening with single-cell transcriptome readout

(2017) Paul Datlinger et al.   NATURE METHODS

The ClusPro web server for protein–protein docking

(2017) Dima Kozakov et al.   Nature Protocols

GibbsCluster: unsupervised clustering and alignment of peptide sequences

(2017) Massimo Andreatta et al.   NUCLEIC ACIDS RESEARCH

LncATLAS database for subcellular localization of long noncoding RNAs

(2017) David Mas-Ponte et al.   RNA

Control of muscle formation by the fusogenic micropeptide myomixer

(2017) Pengpeng Bi et al.   SCIENCE

Improved split fluorescent proteins for endogenous protein labeling

(2017) Siyu Feng et al.   Nature Communications

The microprotein Minion controls cell fusion and muscle formation

(2017) Qiao Zhang et al.   Nature Communications

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

(2017) Sondos Samandi et al.   eLife

MIEF1/2 function as adaptors to recruit Drp1 to mitochondria and regulate the association of Drp1 with Mff

(2017) Rong Yu et al.   Scientific Reports

Plastid: nucleotide-resolution analysis of next-generation sequencing and genomics data

(2016) Joshua G. Dunn et al.   BMC GENOMICS

A Multiplexed Single-Cell CRISPR Screening Platform Enables Systematic Dissection of the Unfolded Protein Response

(2016) Britt Adamson et al.   CELL

CRISPR Interference Efficiently Induces Specific and Reversible Gene Silencing in Human iPSCs

(2016) Mohammad A. Mandegar et al.   Cell Stem Cell

Upstream ORFs are prevalent translational repressors in vertebrates

(2016) Timothy G Johnstone et al.   EMBO JOURNAL

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

(2016) Akinobu Matsumoto et al.   NATURE

Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9

(2016) John G Doench et al.   NATURE BIOTECHNOLOGY

A human microprotein that interacts with the mRNA decapping complex

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

The MaxQuant computational platform for mass spectrometry-based shotgun proteomics

(2016) Stefka Tyanova et al.   Nature Protocols

A scalable strategy for high-throughput GFP tagging of endogenous human proteins

(2016) Manuel D. Leonetti et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2016) B. R. Nelson et al.   SCIENCE

Translation from the 5' untranslated region shapes the integrated stress response

(2016) S. R. Starck et al.   SCIENCE

CRISPRi-based genome-scale identification of functional long noncoding RNA loci in human cells

(2016) S. John Liu et al.   SCIENCE

Conservation of uORF repressiveness and sequence features in mouse, human and zebrafish

(2016) Guo-Liang Chew et al.   Nature Communications

Compact and highly active next-generation libraries for CRISPR-mediated gene repression and activation

(2016) Max A Horlbeck et al.   eLife

Gapped sequence alignment using artificial neural networks: application to the MHC class I system

(2015) Massimo Andreatta et al.   BIOINFORMATICS

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

(2015) Douglas M. Anderson et al.   CELL

Sequence determinants of improved CRISPR sgRNA design

(2015) Han Xu et al.   GENOME RESEARCH

Mass Spectrometry of Human Leukocyte Antigen Class I Peptidomes Reveals Strong Effects of Protein Abundance and Turnover on Antigen Presentation

(2015) Michal Bassani-Sternberg et al.   MOLECULAR & CELLULAR PROTEOMICS

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

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

The landscape of long noncoding RNAs in the human transcriptome

(2015) Matthew K Iyer et al.   NATURE GENETICS

Single-nucleotide-resolution mapping of m6A and m6Am throughout the transcriptome

(2015) Bastian Linder et al.   NATURE METHODS

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

(2015) Zhe Ji et al.   eLife

Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation

(2014) Luke A. Gilbert et al.   CELL

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

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

A Human Short Open Reading Frame (sORF)-encoded Polypeptide That Stimulates DNA End Joining

(2014) Sarah A. Slavoff et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Minimal, encapsulated proteomic-sample processing applied to copy-number estimation in eukaryotic cells

(2014) Nils A Kulak et al.   NATURE METHODS

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

(2014) A. Pauli et al.   SCIENCE

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

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

Distinct stages of the translation elongation cycle revealed by sequencing ribosome-protected mRNA fragments

(2014) Liana F Lareau et al.   eLife

A Systematic Mammalian Genetic Interaction Map Reveals Pathways Underlying Ricin Susceptibility

(2013) Michael C. Bassik et al.   CELL

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

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

(2013) E. G. Magny et al.   SCIENCE

Genetic Screens in Human Cells Using the CRISPR-Cas9 System

(2013) Tim Wang et al.   SCIENCE

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

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

Cozzarelli Prize Winner: Robust cardiomyocyte differentiation from human pluripotent stem cells via temporal modulation of canonical Wnt signaling

(2012) X. Lian et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ab initio protein structure assembly using continuous structure fragments and optimized knowledge-based force field

(2012) Dong Xu et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Decoding Human Cytomegalovirus

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

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

(2011) M. F. Lin 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

MiD49 and MiD51, new components of the mitochondrial fission machinery

(2011) Catherine S Palmer et al.   EMBO REPORTS

Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses

(2011) M. N. Cabili et al.   GENES & DEVELOPMENT

The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function

(2010) David Warde-Farley et al.   NUCLEIC ACIDS RESEARCH

Small Peptides Switch the Transcriptional Activity of Shavenbaby During Drosophila Embryogenesis

(2010) T. Kondo et al.   SCIENCE