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Using ribosome profiling to quantify differences in protein expression: a case study in Saccharomyces cerevisiae oxidative stress conditions

https://doi.org/10.1101/501478
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1007/978-1-4757-2711-1openalex-snapshot
Modern Multidimensional Scaling
inferredcites →https://doi.org/10.1016/j.cell.2011.10.002openalex-snapshot
Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity and Dynamics of Mammalian Proteomes
inferredcites →https://doi.org/10.1016/j.cell.2016.02.066openalex-snapshot
Ribosome Footprint Profiling of Translation throughout the Genome
inferredcites →https://doi.org/10.1016/j.celrep.2014.07.045openalex-snapshot
Ribosome Profiling Reveals Pervasive Translation Outside of Annotated Protein-Coding Genes
inferredcites →https://doi.org/10.1016/j.molcel.2017.10.015openalex-snapshot
The Stress Granule Transcriptome Reveals Principles of mRNA Accumulation in Stress Granules
inferredcites →https://doi.org/10.1016/j.tibs.2014.10.010openalex-snapshot
The utility of protein and mRNA correlation
inferredcites →https://doi.org/10.1016/j.ymeth.2015.07.003openalex-snapshot
Simple and inexpensive ribosome profiling analysis of mRNA translation
inferredcites →https://doi.org/10.1021/acs.biochem.7b01162openalex-snapshot
P-Bodies: Composition, Properties, and Functions
inferredcites →https://doi.org/10.1038/75556openalex-snapshot
Gene Ontology: tool for the unification of biology
inferredcites →https://doi.org/10.1038/msb.2011.48openalex-snapshot
A dynamic model of proteome changes reveals new roles for transcript alteration in yeast
inferredcites →https://doi.org/10.1038/nature10098openalex-snapshot
Global quantification of mammalian gene expression control
inferredcites →https://doi.org/10.1038/nature13578openalex-snapshot
Promoter sequences direct cytoplasmic localization and translation of mRNAs during starvation in yeast
inferredcites →https://doi.org/10.1038/nature25174openalex-snapshot
AMD1 mRNA employs ribosome stalling as a mechanism for molecular memory formation
inferredcites →https://doi.org/10.1038/nchembio.1120openalex-snapshot
Peptidomic discovery of short open reading frame–encoded peptides in human cells
inferredcites →https://doi.org/10.1038/nprot.2008.211openalex-snapshot
Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
inferredcites →https://doi.org/10.1038/nprot.2012.086openalex-snapshot
The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments
inferredcites →https://doi.org/10.1039/b908315dopenalex-snapshot
Global signatures of protein and mRNA expression levels
inferredcites →https://doi.org/10.1073/pnas.0832254100openalex-snapshot
Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS
inferredcites →https://doi.org/10.1073/pnas.1120799109openalex-snapshot
Genome-wide ribosome profiling reveals complex translational regulation in response to oxidative stress
inferredcites →https://doi.org/10.1074/jbc.m601545200openalex-snapshot
Global Translational Responses to Oxidative Stress Impact upon Multiple Levels of Protein Synthesis
inferredcites →https://doi.org/10.1093/bioinformatics/btp352openalex-snapshot
The Sequence Alignment/Map format and SAMtools
inferredcites →https://doi.org/10.1093/bioinformatics/btp616openalex-snapshot
edgeR : a Bioconductor package for differential expression analysis of digital gene expression data
inferredcites →https://doi.org/10.1093/bioinformatics/btu170openalex-snapshot
Trimmomatic: a flexible trimmer for Illumina sequence data
inferredcites →https://doi.org/10.1093/bioinformatics/btu638openalex-snapshot
HTSeq—a Python framework to work with high-throughput sequencing data
inferredcites →https://doi.org/10.1093/bioinformatics/btw585openalex-snapshot
RiboDiff: detecting changes of mRNA translation efficiency from ribosome footprints
inferredcites →https://doi.org/10.1093/nar/gkv972openalex-snapshot
RPFdb: a database for genome wide information of translated mRNA generated from ribosome profiling
inferredcites →https://doi.org/10.1093/nar/gkx1034openalex-snapshot
TranslatomeDB: a comprehensive database and cloud-based analysis platform for translatome sequencing data
inferredcites →https://doi.org/10.1093/nar/gkx790openalex-snapshot
GWIPS-viz: 2018 update
inferredcites →https://doi.org/10.1101/gr.133249.111openalex-snapshot
Observation of dually decoded regions of the human genome using ribosome profiling data
inferredcites →https://doi.org/10.1101/gr.209015.116openalex-snapshot
A novel translational control mechanism involving RNA structures within coding sequences
inferredcites →https://doi.org/10.1111/tpj.12482openalex-snapshot
Correlation of mRNA and protein abundance in the developing maize leaf
inferredcites →https://doi.org/10.1126/science.1168978openalex-snapshot
Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling
inferredcites →https://doi.org/10.1186/1471-2164-13-220openalex-snapshot
Widespread uncoupling between transcriptome and translatome variations after a stimulus in mammalian cells
inferredcites →https://doi.org/10.1186/gb-2009-10-3-r25openalex-snapshot
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
inferredcites →https://doi.org/10.1186/gb-2013-14-9-r95openalex-snapshot
Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data
inferredcites →https://doi.org/10.1186/gb-2014-15-2-r29openalex-snapshot
voom: precision weights unlock linear model analysis tools for RNA-seq read counts
inferredcites →https://doi.org/10.1371/journal.pbio.1000414openalex-snapshot
The Role of Nucleosome Positioning in the Evolution of Gene Regulation
inferredcites →https://doi.org/10.14806/ej.17.1.200openalex-snapshot
Cutadapt removes adapter sequences from high-throughput sequencing reads
inferredcites →https://doi.org/10.15252/msb.20167144openalex-snapshot
Gene‐specific correlation of RNA and protein levels in human cells and tissues
inferredcites →https://doi.org/10.1534/genetics.111.128033openalex-snapshot
The Response to Heat Shock and Oxidative Stress in Saccharomyces cerevisiae
inferredcites →https://doi.org/10.7554/elife.03523openalex-snapshot
Long non-coding RNAs as a source of new peptides
inferredcites →https://doi.org/10.7554/elife.03528openalex-snapshot
Extensive translation of small Open Reading Frames revealed by Poly-Ribo-Seq

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1016/j.ymben.2025.04.007openalex-snapshot
Ribo-seq guided design of enhanced protein secretion in Komagataella phaffii
inferred← citeshttps://doi.org/10.3389/fmicb.2021.626715openalex-snapshot
Gene Expression Profiling of Pseudomonas aeruginosa Upon Exposure to Colistin and Tobramycin
inferred← citeshttps://doi.org/10.3390/cells11192966openalex-snapshot
Tracing Translational Footprint by Ribo-Seq: Principle, Workflow, and Applications to Understand the Mechanism of Human Diseases
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