Profiling mouse brown and white adipocytes to identify metabolically relevant small ORFs and functional microproteins

Limited Evidence for Protein Products of Noncoding Transcripts in the HEK293T Cellular Cytosol

(2022) Annelies Bogaert et al.   MOLECULAR & CELLULAR PROTEOMICS

An Upstream Open Reading Frame in Phosphatase and Tensin Homolog Encodes a Circuit Breaker of Lactate Metabolism

(2021) Nunu Huang et al.   Cell Metabolism

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

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

ORFLine: a bioinformatic pipeline to prioritise small open reading frames identifies candidate secreted small proteins from lymphocytes

(2021) Martin Turner et al.   BIOINFORMATICS

Coding and non-coding roles of MOCCI (C15ORF48) coordinate to regulate host inflammation and immunity

(2021) Cheryl Q. E. Lee et al.   Nature Communications

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

(2021) Igor Fesenko et al.   NUCLEIC ACIDS RESEARCH

Unraveling the hidden role of a uORF-encoded peptide as a kinase inhibitor of PKCs

(2021) Divya Ram Jayaram et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Novel Hypothalamic Factor, Neurosecretory Protein GM, Causes Fat Deposition in Chicks

(2021) Masaki Kato et al.   Frontiers in Physiology

Pervasive functional translation of noncanonical human open reading frames

(2020) Jin Chen et al.   SCIENCE

Acquiring and Analyzing Data Independent Acquisition Proteomics Experiments without Spectrum Libraries

(2020) Lindsay K Pino et al.   MOLECULAR & CELLULAR PROTEOMICS

Generating high quality libraries for DIA MS with empirically corrected peptide predictions

(2020) Brian C. Searle et al.   Nature Communications

Mitoregulin Controls β-Oxidation in Human and Mouse Adipocytes

(2020) Max Friesen et al.   Stem Cell Reports

A micropeptide encoded by lncRNA MIR155HG suppresses autoimmune inflammation via modulating antigen presentation

(2020) Liman Niu et al.   Science Advances

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

(2020) Qiushuang Wu et al.   EMBO JOURNAL

Long Noncoding RNA AW112010 Promotes the Differentiation of Inflammatory T Cells by Suppressing IL-10 Expression through Histone Demethylation

(2020) Xiaoming Yang et al.   JOURNAL OF IMMUNOLOGY

A Pilot Screen of a Novel Peptide Hormone Library Identified Candidate GPR83 Ligands

(2020) Nathan A. Sallee et al.   SLAS Discovery

Evaluation of VGF peptides as potential anti-obesity candidates in pre-clinical animal models

(2020) Louise S. Dalbøge et al.   PEPTIDES

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

SignalP 5.0 improves signal peptide predictions using deep neural networks

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

Plasma proteome profiling discovers novel proteins associated with non‐alcoholic fatty liver disease

(2019) Lili Niu et al.   Molecular Systems Biology

Improving Precursor Selectivity in Data-Independent Acquisition Using Overlapping Windows

(2019) Dario Amodei et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

The central fibroblast growth factor receptor/beta klotho system: Comprehensive mapping in Mus musculus and comparisons to nonhuman primate and human samples using an automated in situ hybridization platform

(2019) Karin Hultman et al.   JOURNAL OF COMPARATIVE NEUROLOGY

An Evolutionarily Conserved uORF Regulates PGC1α and Oxidative Metabolism in Mice, Flies, and Bluefin Tuna

(2019) Phillip A. Dumesic et al.   Cell Metabolism

Prosit: proteome-wide prediction of peptide tandem mass spectra by deep learning

(2019) Siegfried Gessulat et al.   NATURE METHODS

WebGestalt 2019: gene set analysis toolkit with revamped UIs and APIs

(2019) Yuxing Liao et al.   NUCLEIC ACIDS RESEARCH

Mapping the transcriptional diversity of genetically and anatomically defined cell populations in the mouse brain

(2019) Ken Sugino et al.   eLife

The Translational Landscape of the Human Heart

(2019) Sebastiaan van Heesch et al.   CELL

A novel mitochondrial micropeptide MPM enhances mitochondrial respiratory activity and promotes myogenic differentiation

(2019) Yi-Fang Lin et al.   Cell Death & Disease

Emerging Role of Lymphocyte Antigen-6 Family of Genes in Cancer and Immune Cells

(2019) Geeta Upadhyay   Frontiers in Immunology

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

Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 3.0

(2019) Eric W. Deutsch et al.   JOURNAL OF PROTEOME RESEARCH

Regulation of the ER stress response by a mitochondrial microprotein

(2019) Qian Chu et al.   Nature Communications

Accurate annotation of human protein-coding small open reading frames

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

Adipose PTEN regulates adult adipose tissue homeostasis and redistribution via a PTEN-leptin-sympathetic loop

(2019) Wei Huang et al.   Molecular Metabolism

The influence of transcript assembly on the proteogenomics discovery of microproteins

(2018) Jiao Ma et al.   PLoS One

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

Data‐independent acquisition‐based SWATH‐MS for quantitative proteomics: a tutorial

(2018) Christina Ludwig et al.   Molecular Systems Biology

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

(2018) Ruaidhrí Jackson et al.   NATURE

Chromatogram libraries improve peptide detection and quantification by data independent acquisition mass spectrometry

(2018) Brian C. Searle et al.   Nature Communications

Neurosecretory Protein GL, a Hypothalamic Small Secretory Protein, Participates in Energy Homeostasis in Male Mice

(2017) Daichi Matsuura et al.   ENDOCRINOLOGY

Transcriptome-wide measurement of translation by ribosome profiling

(2017) Nicholas J. McGlincy et al.   METHODS

A molecular census of arcuate hypothalamus and median eminence cell types

(2017) John N Campbell et al.   NATURE NEUROSCIENCE

Adapting to obesity with adipose tissue inflammation

(2017) Shannon M. Reilly et al.   Nature Reviews Endocrinology

Health Effects of Overweight and Obesity in 195 Countries over 25 Years

(2017)   NEW ENGLAND JOURNAL OF MEDICINE

Control of muscle formation by the fusogenic micropeptide myomixer

(2017) Pengpeng Bi et al.   SCIENCE

The microprotein Minion controls cell fusion and muscle formation

(2017) Qiao Zhang et al.   Nature Communications

Thermogenic adipocytes promote HDL turnover and reverse cholesterol transport

(2017) Alexander Bartelt et al.   Nature Communications

Neurosecretory protein GL stimulates food intake, de novo lipogenesis, and onset of obesity

(2017) Eiko Iwakoshi-Ukena et al.   eLife

Improved Identification and Analysis of Small Open Reading Frame Encoded Polypeptides

(2016) Jiao Ma et al.   ANALYTICAL CHEMISTRY

Complex heatmaps reveal patterns and correlations in multidimensional genomic data

(2016) Zuguang Gu et al.   BIOINFORMATICS

Adipose tissue regulates insulin sensitivity: role of adipogenesis,de novolipogenesis and novel lipids

(2016) U. Smith et al.   JOURNAL OF INTERNAL MEDICINE

Fast and Accurate Protein False Discovery Rates on Large-Scale Proteomics Data Sets with Percolator 3.0

(2016) Matthew The et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

A multicenter study benchmarks software tools for label-free proteome quantification

(2016) Pedro Navarro et al.   NATURE BIOTECHNOLOGY

Targeting adipose tissue in the treatment of obesity-associated diabetes

(2016) Christine M. Kusminski et al.   NATURE REVIEWS DRUG DISCOVERY

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

(2016) B. R. Nelson et al.   SCIENCE

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

(2015) Douglas M. Anderson et al.   CELL

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

(2015) Changhan Lee et al.   Cell Metabolism

De Novo Reconstruction of Adipose Tissue Transcriptomes Reveals Long Non-coding RNA Regulators of Brown Adipocyte Development

(2015) Juan R. Alvarez-Dominguez et al.   Cell Metabolism

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

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

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

(2015) Hélène Mouilleron 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

Tissue-based map of the human proteome

(2015) M. Uhlen et al.   SCIENCE

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

(2015) Zhe Ji et al.   eLife

Identification of a cDNA encoding a novel small secretory protein, neurosecretory protein GL, in the chicken hypothalamic infundibulum

(2014) Kazuyoshi Ukena et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

What We Talk About When We Talk About Fat

(2014) Evan D. Rosen et al.   CELL

β-Aminoisobutyric Acid Induces Browning of White Fat and Hepatic β-Oxidation and Is Inversely Correlated with Cardiometabolic Risk Factors

(2014) Lee D. Roberts et al.   Cell Metabolism

A comparative encyclopedia of DNA elements in the mouse genome

(2014) Feng Yue et al.   NATURE

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Targeted Data Extraction of the MS/MS Spectra Generated by Data-independent Acquisition: A New Concept for Consistent and Accurate Proteome Analysis

(2012) Ludovic C. Gillet et al.   MOLECULAR & CELLULAR PROTEOMICS

A cross-platform toolkit for mass spectrometry and proteomics

(2012) Matthew C Chambers et al.   NATURE BIOTECHNOLOGY

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

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

EvolView, an online tool for visualizing, annotating and managing phylogenetic trees

(2012) Huangkai Zhang et al.   NUCLEIC ACIDS RESEARCH

Comet: An open-source MS/MS sequence database search tool

(2012) Jimmy K. Eng et al.   PROTEOMICS

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

Different Metabolic Responses of Human Brown Adipose Tissue to Activation by Cold and Insulin

(2011) Janne Orava et al.   Cell Metabolism

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

(2010) Brendan MacLean et al.   BIOINFORMATICS

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

An Upstream Open Reading Frame Regulates Translation of GADD34 during Cellular Stresses That Induce eIF2α Phosphorylation

(2009) Yun-Young Lee et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Differential regulation of CHOP translation by phosphorylated eIF4E under stress conditions

(2009) Yi-Jiun Chen et al.   NUCLEIC ACIDS RESEARCH

Upstream open reading frames cause widespread reduction of protein expression and are polymorphic among humans

(2009) S. E. Calvo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2009) N. T. Ingolia et al.   SCIENCE