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

Pervasive functional translation of noncanonical human open reading frames

(2020) Jin Chen et al.   SCIENCE

The Translational Landscape of the Human Heart

(2019) Sebastiaan van Heesch et al.   CELL

Discovery of high-confidence human protein-coding genes and exons by whole-genome PhyloCSF helps elucidate 118 GWAS loci

(2019) Jonathan M. Mudge et al.   GENOME RESEARCH

Accurate annotation of human protein-coding small open reading frames

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

Distinct response to GDF15 knockdown in pediatric and adult glioblastoma cell lines

(2018) Mirella Baroni et al.   JOURNAL OF NEURO-ONCOLOGY

Uniting GDF15 and GFRAL: Therapeutic Opportunities in Obesity and Beyond

(2018) Shannon E. Mullican et al.   TRENDS IN ENDOCRINOLOGY AND METABOLISM

The GCTx format and cmap{Py, R, M, J} packages: resources for optimized storage and integrated traversal of annotated dense matrices

(2018) Oana M Enache et al.   BIOINFORMATICS

Progress on Identifying and Characterizing the Human Proteome: 2018 Metrics from the HUPO Human Proteome Project

(2018) Gilbert S. Omenn et al.   JOURNAL OF PROTEOME RESEARCH

MiPanda: A Resource for Analyzing and Visualizing Next-Generation Sequencing Transcriptomics Data

(2018) Yashar S. Niknafs et al.   NEOPLASIA

NF-κB regulates GDF-15 to suppress macrophage surveillance during early tumor development

(2017) Nivedita M. Ratnam et al.   JOURNAL OF CLINICAL INVESTIGATION

TimeTree: A Resource for Timelines, Timetrees, and Divergence Times

(2017) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

Computational correction of copy number effect improves specificity of CRISPR–Cas9 essentiality screens in cancer cells

(2017) Robin M Meyers et al.   NATURE GENETICS

Targeting Obesity and Cachexia: Identification of the GFRAL Receptor–MIC-1/GDF15 Pathway

(2017) Samuel N. Breit et al.   TRENDS IN MOLECULAR MEDICINE

Growth differentiation factor 15 mediates epithelial mesenchymal transition and invasion of breast cancers through IGF-1R-FoxM1 signaling

(2017) Bridgette F. Peake et al.   Oncotarget

Analyzing CRISPR genome-editing experiments with CRISPResso

(2016) Luca Pinello et al.   NATURE BIOTECHNOLOGY

High-throughput identification of genotype-specific cancer vulnerabilities in mixtures of barcoded tumor cell lines

(2016) Channing Yu et al.   NATURE BIOTECHNOLOGY

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

(2016) John G Doench et al.   NATURE BIOTECHNOLOGY

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

(2016) S. John Liu et al.   SCIENCE

The landscape of long noncoding RNAs in the human transcriptome

(2015) Matthew K Iyer et al.   NATURE GENETICS

Detecting actively translated open reading frames in ribosome profiling data

(2015) Lorenzo Calviello et al.   NATURE METHODS

The Phyre2 web portal for protein modeling, prediction and analysis

(2015) Lawrence A Kelley et al.   Nature Protocols

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

(2015) Zhe Ji et al.   eLife

DISOPRED3: precise disordered region predictions with annotated protein-binding activity

(2014) David T. Jones et al.   BIOINFORMATICS

Cas-OFFinder: a fast and versatile algorithm that searches for potential off-target sites of Cas9 RNA-guided endonucleases

(2014) S. Bae et al.   BIOINFORMATICS

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

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

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

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

Measuring error rates in genomic perturbation screens: gold standards for human functional genomics

(2014) T. Hart et al.   Molecular Systems Biology

A draft map of the human proteome

(2014) Min-Sik Kim et al.   NATURE

Mass-spectrometry-based draft of the human proteome

(2014) Mathias Wilhelm et al.   NATURE

Quantitative profiling of initiating ribosomes in vivo

(2014) Xiangwei Gao et al.   NATURE METHODS

Integration of mass spectrometry and RNA-Seq data to confirm human ab initio predicted genes and lncRNAs

(2014) Han Sun et al.   PROTEOMICS

A proteogenomics approach integrating proteomics and ribosome profiling increases the efficiency of protein identification and enables the discovery of alternative translation start sites

(2014) Alexander Koch et al.   PROTEOMICS

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

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

Long non-coding RNAs as a source of new peptides

(2014) Jorge Ruiz-Orera et al.   eLife

Epigenomic Analysis of Multilineage Differentiation of Human Embryonic Stem Cells

(2013) Wei Xie et al.   CELL

Systematic Analysis of Missing Proteins Provides Clues to Help Define All of the Protein-Coding Genes on Human Chromosome 1

(2013) Chengpu Zhang et al.   JOURNAL OF PROTEOME RESEARCH

Chemoproteomic Discovery of Cysteine-Containing Human Short Open Reading Frames

(2013) Adam G. Schwaid et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

HiRIEF LC-MS enables deep proteome coverage and unbiased proteogenomics

(2013) Rui M M Branca et al.   NATURE METHODS

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

(2013) Benoît Vanderperre et al.   PLoS One

Pinstripe: a suite of programs for integrating transcriptomic and proteomic datasets identifies novel proteins and improves differentiation of protein-coding and non-coding genes

(2012) Dennis K. Gascoigne et al.   BIOINFORMATICS

Bioactivity and Prognostic Significance of Growth Differentiation Factor GDF15 Secreted by Bone Marrow Mesenchymal Stem Cells in Multiple Myeloma

(2012) J. Corre et al.   CANCER RESEARCH

Long noncoding RNAs are rarely translated in two human cell lines

(2012) B. Banfai et al.   GENOME RESEARCH

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

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

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

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

A public genome-scale lentiviral expression library of human ORFs

(2011) Xiaoping Yang et al.   NATURE METHODS

SignalP 4.0: discriminating signal peptides from transmembrane regions

(2011) Thomas Nordahl Petersen et al.   NATURE METHODS

Differentiating Protein-Coding and Noncoding RNA: Challenges and Ambiguities

(2008) Marcel E. Dinger et al.   PLoS Computational Biology