Exploring microproteins from various model organisms using the mip-mining database

Investigating CENPW as a Novel Biomarker Correlated With the Development and Poor Prognosis of Breast Carcinoma

(2022) Luyang Wang et al.   Frontiers in Genetics

MicroProteins: expanding functions and novel modes of regulation

(2021) Kaushal Kumar Bhati et al.   Molecular Plant

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

(2021) Xiongwen Cao et al.   Nature Communications

Revisiting sORFs: overcoming challenges to identify and characterize functional microproteins

(2021) Dörte Schlesinger et al.   FEBS Journal

Transcriptional coregualtor NUPR1 maintains tamoxifen resistance in breast cancer cells

(2021) Lingling Wang et al.   Cell Death & Disease

Acetic acid stress in budding yeast: from molecular mechanisms to applications

(2021) Nicoletta Guaragnella et al.   YEAST

Physiological limitations and opportunities in microbial metabolic engineering

(2021) José Montaño López et al.   NATURE REVIEWS MICROBIOLOGY

Developing climate‐resilient crops: improving plant tolerance to stress combination

(2021) Rosa M. Rivero et al.   PLANT JOURNAL

The evolution of the antimicrobial peptide database ( APD ) over 18 years: Milestones and new features

(2021) Guangshun Wang et al.   PROTEIN SCIENCE

Acyl-CoA synthetase-4 mediates radioresistance of breast cancer cells by regulating FOXM1

(2021) Yun-Suk Kwon et al.   BIOCHEMICAL PHARMACOLOGY

Molecular Regulation of Plant Responses to Environmental Temperatures

(2020) Yanglin Ding et al.   Molecular Plant

Stress-tolerant non-conventional microbes enable next-generation chemical biosynthesis

(2020) Sarah Thorwall et al.   Nature Chemical Biology

Plasma membrane aquaporins PIPs act in concert to regulate cold acclimation and freezing tolerance responses in Arabidopsis thaliana

(2020) Arifa Rahman et al.   PLANT AND CELL PHYSIOLOGY

The exposome and health: Where chemistry meets biology

(2020) Roel Vermeulen et al.   SCIENCE

Effects of Oxidative Stress on Protein Translation: Implications for Cardiovascular Diseases

(2020) Arnab Ghosh et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

PsORF: a database of small ORFs in plants

(2020) Yanjun Chen et al.   PLANT BIOTECHNOLOGY JOURNAL

Allosteric deactivation of PIFs and EIN3 by microproteins in light control of plant development

(2020) Qingqing Wu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2020) Xiangwen Ji et al.   BMC BIOINFORMATICS

Identification of miPEP133 as a novel tumor-suppressor microprotein encoded by miR-34a pri-miRNA

(2020) Min Kang et al.   Molecular Cancer

Innovative Tools and Strategies for Optimizing Yeast Cell Factories

(2020) Gregory Guirimand et al.   TRENDS IN BIOTECHNOLOGY

Automated Prediction and Annotation of Small Open Reading Frames in Microbial Genomes

(2020) Matthew G. Durrant et al.   Cell Host & Microbe

Computational discovery and annotation of conserved small open reading frames in fungal genomes

(2019) Shuhaila Mat-Sharani et al.   BMC BIOINFORMATICS

MiTPeptideDB: a proteogenomic resource for the discovery of novel peptides

(2019) Elizabeth Guruceaga et al.   BIOINFORMATICS

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

(2019) Daehwan Kim et al.   NATURE BIOTECHNOLOGY

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

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

SNHG12: An LncRNA as a Potential Therapeutic Target and Biomarker for Human Cancer

(2019) Suraksha Tamang et al.   Frontiers in Oncology

Accurate annotation of human protein-coding small open reading frames

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

OUP accepted manuscript

(2018)   BIOINFORMATICS

Approaches to identify and characterize microProteins and their potential uses in biotechnology

(2018) Kaushal Kumar Bhati et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

High-throughput creation and functional profiling of DNA sequence variant libraries using CRISPR–Cas9 in yeast

(2018) Xiaoge Guo et al.   NATURE BIOTECHNOLOGY

GENCODE reference annotation for the human and mouse genomes

(2018) Adam Frankish et al.   NUCLEIC ACIDS RESEARCH

Ribosomal protein S27-like regulates autophagy via the β-TrCP-DEPTOR-mTORC1 axis

(2018) Xiufang Xiong et al.   Cell Death & Disease

Classification and function of small open reading frames

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

Ensembl 2018

(2017) Daniel R Zerbino et al.   NUCLEIC ACIDS RESEARCH

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

(2017) Volodimir Olexiouk et al.   NUCLEIC ACIDS RESEARCH

YEASTRACT: an upgraded database for the analysis of transcription regulatory networks in Saccharomyces cerevisiae

(2017) Miguel C Teixeira et al.   NUCLEIC ACIDS RESEARCH

N-terminomics identifies Prli42 as a membrane miniprotein conserved in Firmicutes and critical for stressosome activation in Listeria monocytogenes

(2017) Francis Impens et al.   Nature Microbiology

MultiQC: summarize analysis results for multiple tools and samples in a single report

(2016) Philip Ewels et al.   BIOINFORMATICS

Yeast toxicogenomics: lessons from a eukaryotic cell model and cell factory

(2015) Sandra C dos Santos et al.   CURRENT OPINION IN BIOTECHNOLOGY

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

Ballgown bridges the gap between transcriptome assembly and expression analysis

(2015) Alyssa C Frazee et al.   NATURE BIOTECHNOLOGY

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

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

(2015) Volodimir Olexiouk et al.   NUCLEIC ACIDS RESEARCH

The LYR Factors SDHAF1 and SDHAF3 Mediate Maturation of the Iron-Sulfur Subunit of Succinate Dehydrogenase

(2014) Un Na et al.   Cell Metabolism

Engineering alcohol tolerance in yeast

(2014) F. H. Lam et al.   SCIENCE

TISdb: a database for alternative translation initiation in mammalian cells

(2013) Ji Wan et al.   NUCLEIC ACIDS RESEARCH

An efficient xylose-fermenting recombinant Saccharomyces cerevisiae strain obtained through adaptive evolution and its global transcription profile

(2012) Yu Shen et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

ProtTest 3: fast selection of best-fit models of protein evolution

(2011) Diego Darriba et al.   BIOINFORMATICS

tsORFdb: Theoretical Small Open Reading Frames (ORFs) database and massProphet: Peptide Mass Fingerprinting (PMF) tool for unknown small functional ORFs

(2010) Hyoung-Sam Heo et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

The Sequence Read Archive

(2010) R. Leinonen et al.   NUCLEIC ACIDS RESEARCH

The RIM101 pathway has a role inSaccharomyces cerevisiaeadaptive response and resistance to propionic acid and other weak acids

(2008) Nuno P. Mira et al.   FEMS YEAST RESEARCH