Mapping subcellular localizations of unannotated microproteins and alternative proteins with MicroID

A high-throughput assay for directly monitoring nucleolar rRNA biogenesis

(2022) Carson J. Bryant et al.   Open Biology

Nascent alt-protein chemoproteomics reveals a pre-60S assembly checkpoint inhibitor

(2022) Xiongwen Cao et al.   Nature Chemical Biology

Potentiation of B2 receptor signaling by AltB2R, a newly identified alternative protein encoded in the human bradykinin B2 receptor gene

(2021) Maxime Gagnon et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Deciphering molecular interactions by proximity labeling

(2021) Wei Qin et al.   NATURE METHODS

A short ORF-encoded transcriptional regulator

(2021) Minseob Koh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Alt-RPL36 downregulates the PI3K-AKT-mTOR signaling pathway by interacting with TMEM24

(2021) Xiongwen Cao et al.   Nature Communications

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

(2021) Nunu Huang et al.   Cell Metabolism

Increased numbers of nucleoli in a genome-wide RNAi screen reveal proteins that link the cell cycle to RNA polymerase I transcription

(2021) Lisa M. Ogawa et al.   MOLECULAR BIOLOGY OF THE CELL

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

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

Multi-protease Approach for the Improved Identification and Molecular Characterization of Small Proteins and Short Open Reading Frame-Encoded Peptides

(2021) Philipp T. Kaulich et al.   JOURNAL OF PROTEOME RESEARCH

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

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

Proteomics of protein trafficking by in vivo tissue-specific labeling

(2021) Ilia A. Droujinine et al.   Nature Communications

An atlas of protein-protein interactions across mouse tissues

(2021) Michael A. Skinnider et al.   CELL

A proximity-dependent biotinylation map of a human cell

(2021) Christopher D. Go et al.   NATURE

Cytoplasmic long noncoding RNAs are differentially regulated and translated during human neuronal differentiation

(2021) Katerina Douka et al.   RNA

Cell-Surface Proteomic Profiling in the Fly Brain Uncovers Wiring Regulators

(2020) Jiefu Li et al.   CELL

Pervasive functional translation of noncanonical human open reading frames

(2020) Jin Chen et al.   SCIENCE

Comparative proteomic profiling of unannotated microproteins and alternative proteins in human cell lines

(2020) Xiongwen Cao et al.   JOURNAL OF PROTEOME RESEARCH

Mitochondrial peptide BRAWNIN is essential for vertebrate respiratory complex III assembly

(2020) Shan Zhang et al.   Nature Communications

The NBDY Microprotein Regulates Cellular RNA Decapping

(2020) Zhenkun Na et al.   BIOCHEMISTRY

The FUS gene is dual‐coding with both proteins contributing to FUS ‐mediated toxicity

(2020) Marie A Brunet et al.   EMBO REPORTS

Cell type-selective secretome profiling in vivo

(2020) Wei Wei et al.   Nature Chemical Biology

Fanconi anemia protein FANCI functions in ribosome biogenesis

(2019) Samuel B. Sondalle et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

One-step generation of modular CAR-T cells with AAV–Cpf1

(2019) Xiaoyun Dai et al.   NATURE METHODS

Function and Evolution of Upstream ORFs in Eukaryotes

(2019) Hong Zhang et al.   TRENDS IN BIOCHEMICAL SCIENCES

Atlas of Subcellular RNA Localization Revealed by APEX-Seq

(2019) Furqan M. Fazal et al.   CELL

Nuclear Actin and Actin-Binding Proteins in DNA Repair

(2019) Verena Hurst et al.   TRENDS IN CELL BIOLOGY

DNA translocation mechanism of the MCM complex and implications for replication initiation

(2019) Martin Meagher et al.   Nature Communications

SRSF3-Regulated RNA Alternative Splicing Promotes Glioblastoma Tumorigenicity by Affecting Multiple Cellular Processes

(2019) Xiao Song et al.   CANCER RESEARCH

Alternative ORFs and small ORFs: shedding light on the dark proteome

(2019) Mona Wu Orr et al.   NUCLEIC ACIDS RESEARCH

Multiplexed activation of endogenous genes by CRISPRa elicits potent antitumor immunity

(2019) Guangchuan Wang et al.   NATURE IMMUNOLOGY

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

Context-Dependent and Disease-Specific Diversity in Protein Interactions within Stress Granules

(2018) Sebastian Markmiller et al.   CELL

Recognition of the polycistronic nature of human genes is critical to understanding the genotype-phenotype relationship

(2018) Marie A. Brunet et al.   GENOME RESEARCH

Discovery of proteins associated with a predefined genomic locus via dCas9–APEX-mediated proximity labeling

(2018) Samuel A. Myers et al.   NATURE METHODS

The cancer-associated microprotein CASIMO1 controls cell proliferation and interacts with squalene epoxidase modulating lipid droplet formation

(2018) Maria Polycarpou-Schwarz et al.   ONCOGENE

KPNB1 inhibition disrupts proteostasis and triggers unfolded protein response-mediated apoptosis in glioblastoma cells

(2018) Zhi-Chuan Zhu et al.   ONCOGENE

An AP-MS- and BioID-compatible MAC-tag enables comprehensive mapping of protein interactions and subcellular localizations

(2018) Xiaonan Liu et al.   Nature Communications

qSR: a quantitative super-resolution analysis tool reveals the cell-cycle dependent organization of RNA Polymerase I in live human cells

(2018) J. O. Andrews et al.   Scientific Reports

Diverse Regulators of Human Ribosome Biogenesis Discovered by Changes in Nucleolar Number

(2018) Katherine I. Farley-Barnes et al.   Cell Reports

CellProfiler 3.0: Next-generation image processing for biology

(2018) Claire McQuin et al.   PLOS BIOLOGY

Nucleolar integrity during interphase supports faithful Cdk1 activation and mitotic entry

(2018) Yuki Hayashi et al.   Science Advances

Nuclear ARP2/3 drives DNA break clustering for homology-directed repair

(2018) Benjamin R. Schrank et al.   NATURE

Efficient proximity labeling in living cells and organisms with TurboID

(2018) Tess C Branon et al.   NATURE BIOTECHNOLOGY

Use of the iNo score to discriminate normal from altered nucleolar morphology, with applications in basic cell biology and potential in human disease diagnostics

(2018) Vassiliki Stamatopoulou et al.   Nature Protocols

Integrative proteomics and bioinformatic prediction enable a high-confidence apicoplast proteome in malaria parasites

(2018) Michael J. Boucher et al.   PLOS BIOLOGY

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

(2018) Ruaidhrí Jackson et al.   NATURE

Regulation of DNA repair pathway choice in S and G2 phases by the NHEJ inhibitor CYREN

(2017) Nausica Arnoult et al.   NATURE

AAV-mediated direct in vivo CRISPR screen identifies functional suppressors in glioblastoma

(2017) Ryan D Chow et al.   NATURE NEUROSCIENCE

Classification and function of small open reading frames

(2017) Juan-Pablo Couso et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

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

(2017) Sondos Samandi et al.   eLife

Proteomic mapping of cytosol-facing outer mitochondrial and ER membranes in living human cells by proximity biotinylation

(2017) Victoria Hung et al.   eLife

Proteomic Analysis of Unbounded Cellular Compartments: Synaptic Clefts

(2016) Ken H. Loh et al.   CELL

A Dynamic Protein Interaction Landscape of the Human Centrosome-Cilium Interface

(2015) Gagan D. Gupta et al.   CELL

Primate-Specific ORF0 Contributes to Retrotransposon-Mediated Diversity

(2015) Ahmet M. Denli et al.   CELL

Proteomic mapping of ER–PM junctions identifies STIMATE as a regulator of Ca2+ influx

(2015) Ji Jing et al.   NATURE CELL BIOLOGY

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

Genome engineering using the CRISPR-Cas9 system

(2013) F Ann Ran et al.   Nature Protocols

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

(2013) Benoît Vanderperre et al.   PLoS One

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

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

NIH Image to ImageJ: 25 years of image analysis

(2012) Caroline A Schneider et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Function of homo- and hetero-oligomers of human nucleoplasmin/nucleophosmin family proteins NPM1, NPM2 and NPM3 during sperm chromatin remodeling

(2012) M. Okuwaki et al.   NUCLEIC ACIDS RESEARCH

Nuclear Import of Exogenous FGF1 Requires the ER-Protein LRRC59 and the Importins Kpnα1 and Kpnβ1

(2012) Yan Zhen et al.   TRAFFIC

NOL11, Implicated in the Pathogenesis of North American Indian Childhood Cirrhosis, Is Required for Pre-rRNA Transcription and Processing

(2012) Emily F. Freed et al.   PLoS Genetics

The RNA-binding landscapes of two SR proteins reveal unique functions and binding to diverse RNA classes

(2012) Minna-Liisa Änkö et al.   GENOME BIOLOGY

Assembly and disassembly of the nucleolus during the cell cycle

(2011) Danièle Hernandez-Verdun   Nucleus

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

SUnSET, a nonradioactive method to monitor protein synthesis

(2009) Enrico K Schmidt et al.   NATURE METHODS

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

(2009) N. T. Ingolia et al.   SCIENCE

Exploring RNA transcription and turnover in vivo by using click chemistry

(2008) C. Y. Jao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA