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Metagenome-wide measurement of protein synthesis in the human fecal microbiota using MetaRibo-Seq

https://doi.org/10.1101/482430
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What this work says

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

inferredcites →https://doi.org/10.1002/0471250953.bi1320s40openalex-snapshot
Byonic: Advanced Peptide and Protein Identification Software
inferredcites →https://doi.org/10.1002/pmic.201500183openalex-snapshot
A decade of metaproteomics: Where we stand and what the future holds
inferredcites →https://doi.org/10.1002/wrna.1370openalex-snapshot
The role of mRNA structure in bacterial translational regulation
inferredcites →https://doi.org/10.1007/978-3-642-37195-0_13openalex-snapshot
Assembling Genomes and Mini-metagenomes from Highly Chimeric Reads
inferredcites →https://doi.org/10.1016/j.cell.2011.10.044openalex-snapshot
Selective Ribosome Profiling Reveals the Cotranslational Chaperone Action of Trigger Factor In Vivo
inferredcites →https://doi.org/10.1016/j.cell.2014.02.033openalex-snapshot
Quantifying Absolute Protein Synthesis Rates Reveals Principles Underlying Allocation of Cellular Resources
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.cell.2018.03.007openalex-snapshot
Evolutionary Convergence of Pathway-Specific Enzyme Expression Stoichiometry
inferredcites →https://doi.org/10.1016/j.celrep.2015.03.014openalex-snapshot
High-Precision Analysis of Translational Pausing by Ribosome Profiling in Bacteria Lacking EFP
inferredcites →https://doi.org/10.1016/j.celrep.2015.12.073openalex-snapshot
Clarifying the Translational Pausing Landscape in Bacteria by Ribosome Profiling
inferredcites →https://doi.org/10.1016/j.celrep.2016.09.001openalex-snapshot
Discovery and Function of a General Core Hormetic Stress Response in E. coli Induced by Sublethal Concentrations of Antibiotics
inferredcites →https://doi.org/10.1016/j.febslet.2009.10.036openalex-snapshot
Correlation of mRNA and protein in complex biological samples
inferredcites →https://doi.org/10.1016/s0079-6603(08)60256-1openalex-snapshot
Diverse Mechanisms for Regulating Ribosomal Protein Synthesis in Escherichia coli
inferredcites →https://doi.org/10.1037/1082-989x.12.4.399openalex-snapshot
Toward using confidence intervals to compare correlations.
inferredcites →https://doi.org/10.1038/ismej.2015.93openalex-snapshot
Monitoring host responses to the gut microbiota
inferredcites →https://doi.org/10.1038/nature10965openalex-snapshot
The anti-Shine–Dalgarno sequence drives translational pausing and codon choice in bacteria
inferredcites →https://doi.org/10.1038/nbt.1754openalex-snapshot
Integrative genomics viewer
inferredcites →https://doi.org/10.1038/ncomms11605openalex-snapshot
The dynamic transcriptional and translational landscape of the model antibiotic producer Streptomyces coelicolor A3(2)
inferredcites →https://doi.org/10.1038/nmeth.1322openalex-snapshot
Universal sample preparation method for proteome analysis
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/s41564-017-0084-4openalex-snapshot
Metatranscriptome of human faecal microbial communities in a cohort of adult men
inferredcites →https://doi.org/10.1038/s41564-017-0089-zopenalex-snapshot
Dynamics of metatranscription in the inflammatory bowel disease gut microbiome
inferredcites →https://doi.org/10.1038/s41564-017-0096-0openalex-snapshot
Stability of the human faecal microbiome in a cohort of adult men
inferredcites →https://doi.org/10.1038/s41564-018-0189-4openalex-snapshot
Defining microbiome function
inferredcites →https://doi.org/10.1038/s41591-018-0202-8openalex-snapshot
Precision identification of diverse bloodstream pathogens in the gut microbiome
inferredcites →https://doi.org/10.1038/srep26775openalex-snapshot
An Improved Method for High Quality Metagenomics DNA Extraction from Human and Environmental Samples
inferredcites →https://doi.org/10.1039/c3ib40120kopenalex-snapshot
Changes in translational efficiency is a dominant regulatory mechanism in the environmental response of bacteria
inferredcites →https://doi.org/10.1073/pnas.1319284111openalex-snapshot
Relating the metatranscriptome and metagenome of the human gut
inferredcites →https://doi.org/10.1073/pnas.1525206113openalex-snapshot
Translation quality control is critical for bacterial responses to amino acid stress
inferredcites →https://doi.org/10.1073/pnas.72.7.2743openalex-snapshot
Cluster of genes in Escherichia coli for ribosomal proteins, ribosomal RNA, and RNA polymerase subunits.
inferredcites →https://doi.org/10.1073/pnas.76.7.3411openalex-snapshot
Regulation of ribosomal protein synthesis in Escherichia coli by selective mRNA inactivation.
inferredcites →https://doi.org/10.1073/pnas.77.6.3590openalex-snapshot
Feedback regulation of ribosomal protein gene expression in Escherichia coli.
inferredcites →https://doi.org/10.1093/bioinformatics/btl158openalex-snapshot
Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences
inferredcites →https://doi.org/10.1093/bioinformatics/btq033openalex-snapshot
BEDTools: a flexible suite of utilities for comparing genomic features
inferredcites →https://doi.org/10.1093/bioinformatics/bts429openalex-snapshot
Gene and translation initiation site prediction in metagenomic sequences
inferredcites →https://doi.org/10.1093/bioinformatics/btu153openalex-snapshot
Prokka: rapid prokaryotic genome annotation
inferredcites →https://doi.org/10.1093/nar/gkh131openalex-snapshot
UniProt: the Universal Protein knowledgebase
inferredcites →https://doi.org/10.1093/nar/gkh152openalex-snapshot
ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences
inferredcites →https://doi.org/10.1093/nar/gkn176openalex-snapshot
High-throughput functional annotation and data mining with the Blast2GO suite
inferredcites →https://doi.org/10.1093/nar/gkn923openalex-snapshot
Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists
inferredcites →https://doi.org/10.1093/nar/gkr367openalex-snapshot
HMMER web server: interactive sequence similarity searching
inferredcites →https://doi.org/10.1093/nar/gkx295openalex-snapshot
MicrobiomeAnalyst: a web-based tool for comprehensive statistical, visual and meta-analysis of microbiome data
inferredcites →https://doi.org/10.1093/nar/gkx758openalex-snapshot
REPARATION: ribosome profiling assisted (re-)annotation of bacterial genomes
inferredcites →https://doi.org/10.1093/nar/gky335openalex-snapshot
Translational control plays an important role in the adaptive heat-shock response of Streptomyces coelicolor
inferredcites →https://doi.org/10.1093/nar/gky574openalex-snapshot
Translational regulation in mycobacteria and its implications for pathogenicity
inferredcites →https://doi.org/10.1101/027607openalex-snapshot
One Codex: A Sensitive and Accurate Data Platform for Genomic Microbial Identification
inferredcites →https://doi.org/10.1101/gr.193342.115openalex-snapshot
Integrative analysis of RNA, translation, and protein levels reveals distinct regulatory variation across humans
inferredcites →https://doi.org/10.1111/1574-6976.12083openalex-snapshot
The bacterial translation stress response
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/10.1128/jb.00073-09openalex-snapshot
Translational Control of the Antibiotic Inducibility of the PA5471 Gene Required for mexXY Multidrug Efflux Gene Expression in Pseudomonas aeruginosa
inferredcites →https://doi.org/10.1186/1471-2105-11-119openalex-snapshot
Prodigal: prokaryotic gene recognition and translation initiation site identification
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/preaccept-1406008234136429openalex-snapshot
A straightforward and efficient analytical pipeline for metaproteome characterization
inferredcites →https://doi.org/10.1186/s12864-015-1694-yopenalex-snapshot
Stool metatranscriptomics: A technical guideline for mRNA stabilisation and isolation
inferredcites →https://doi.org/10.1186/s13059-014-0550-8openalex-snapshot
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
inferredcites →https://doi.org/10.1261/rna.2536111openalex-snapshot
RNAcode: Robust discrimination of coding and noncoding regions in comparative sequence data
inferredcites →https://doi.org/10.14806/ej.17.1.200openalex-snapshot
Cutadapt removes adapter sequences from high-throughput sequencing reads
inferredcites →https://doi.org/10.2144/000114302openalex-snapshot
A Streamlined Ribosome Profiling Protocol for the Characterization of Microorganisms
inferredcites →https://doi.org/10.3389/fchem.2017.00004openalex-snapshot
Metaproteomics as a Complementary Approach to Gut Microbiota in Health and Disease

What points at this work

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

inferred← citeshttps://doi.org/10.1101/2020.05.18.103374openalex-snapshot
Repurposing Ribo-Seq to provide insights into structured RNAs
inferred← citeshttps://doi.org/10.1186/s13059-021-02319-wopenalex-snapshot
Comparative genomics identifies thousands of candidate structured RNAs in human microbiomes
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