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

Quantitative Proteomics of the Cancer Cell Line Encyclopedia

(2020) David P. Nusinow et al.   CELL

Ribosome profiling analysis identified a KRAS-interacting microprotein that represses oncogenic signaling in hepatocellular carcinoma cells

(2019) Wenli Xu et al.   Science China-Life Sciences

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

(2019) Daehwan Kim et al.   NATURE BIOTECHNOLOGY

Co-regulation map of the human proteome enables identification of protein functions

(2019) Georg Kustatscher et al.   NATURE BIOTECHNOLOGY

Regulation of the ER stress response by a mitochondrial microprotein

(2019) Qian Chu et al.   Nature Communications

A Mitochondrial Micropeptide Is Required for Activation of the Nlrp3 Inflammasome

(2019) Ankit Bhatta et al.   JOURNAL OF IMMUNOLOGY

Accurate annotation of human protein-coding small open reading frames

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

OUP accepted manuscript

(2018)   BIOINFORMATICS

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

(2018) Maria Polycarpou-Schwarz et al.   ONCOGENE

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

FSPP: A Tool for Genome-Wide Prediction of smORF-Encoded Peptides and Their Functions

(2018) Hui Li et al.   Frontiers in Genetics

MIEF1 Microprotein Regulates Mitochondrial Translation

(2018) Annie Rathore et al.   BIOCHEMISTRY

Computational models for lncRNA function prediction and functional similarity calculation

(2018) Xing Chen et al.   Briefings in Functional Genomics

Protein Function Prediction from Protein-Protein Interaction Network Using Gene Ontology Based Neighborhood Analysis and Physico-Chemical Features

(2018) Sovan Saha et al.   Journal of Bioinformatics and Computational Biology

UniProt: a worldwide hub of protein knowledge

(2018)   NUCLEIC ACIDS RESEARCH

STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets

(2018) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

GENCODE reference annotation for the human and mouse genomes

(2018) Adam Frankish et al.   NUCLEIC ACIDS RESEARCH

The Gene Ontology Resource: 20 years and still GOing strong

(2018)   NUCLEIC ACIDS RESEARCH

An atlas of human long non-coding RNAs with accurate 5′ ends

(2017) Chung-Chau Hon et al.   NATURE

Classification and function of small open reading frames

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

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

(2017) Volodimir Olexiouk et al.   NUCLEIC ACIDS RESEARCH

The Reactome Pathway Knowledgebase

(2017) Antonio Fabregat et al.   NUCLEIC ACIDS RESEARCH

The microprotein Minion controls cell fusion and muscle formation

(2017) Qiao Zhang et al.   Nature Communications

Gene‐specific correlation of RNA and protein levels in human cells and tissues

(2016) Fredrik Edfors et al.   Molecular Systems Biology

A human microprotein that interacts with the mRNA decapping complex

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

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

(2016) B. R. Nelson et al.   SCIENCE

Discovery and characterization of smORF-encoded bioactive polypeptides

(2015) Alan Saghatelian et al.   Nature Chemical Biology

DIANA-miRPath v3.0: deciphering microRNA function with experimental support

(2015) Ioannis S. Vlachos et al.   NUCLEIC ACIDS RESEARCH

Multiple evidence strands suggest that there may be as few as 19 000 human protein-coding genes

(2014) Iakes Ezkurdia et al.   HUMAN MOLECULAR GENETICS

Comparison of RNA-Seq and Microarray in Transcriptome Profiling of Activated T Cells

(2014) Shanrong Zhao et al.   PLoS One

A bioinformatics method for predicting long noncoding RNAs associated with vascular disease

(2014) JianWei Li et al.   Science China-Life Sciences

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

CrossMap: a versatile tool for coordinate conversion between genome assemblies

(2013) Hao Zhao et al.   BIOINFORMATICS

An upstream interacting context based framework for the computational inference of microRNA functions

(2012) Chengxiang Qiu et al.   Molecular BioSystems

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

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

ncFANs: a web server for functional annotation of long non-coding RNAs

(2011) Q. Liao et al.   NUCLEIC ACIDS RESEARCH

Phenobarbital Mediates an Epigenetic Switch at the Constitutive Androstane Receptor (CAR) Target Gene Cyp2b10 in the Liver of B6C3F1 Mice

(2011) Harri Lempiäinen et al.   PLoS One

Evaluating Gene Expression in C57BL/6J and DBA/2J Mouse Striatum Using RNA-Seq and Microarrays

(2011) Daniel Bottomly et al.   PLoS One

A framework for oligonucleotide microarray preprocessing

(2010) Benilton S. Carvalho et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

SeqMap: mapping massive amount of oligonucleotides to the genome

(2008) H. Jiang et al.   BIOINFORMATICS

An international standardization programme towards the application of gene expression profiling in routine leukaemia diagnostics: the Microarray Innovations in LEukemia study prephase

(2008) Alexander Kohlmann et al.   BRITISH JOURNAL OF HAEMATOLOGY