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AQMM: Enabling Absolute Quantification of Metagenome and Metatranscriptome

https://doi.org/10.1101/218347
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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/s12064-012-0162-3openalex-snapshot
Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples
inferredcites →https://doi.org/10.1016/j.anaerobe.2013.09.007openalex-snapshot
Efficiency of RNA extraction from selected bacteria in the context of biogas production and metatranscriptomics
inferredcites →https://doi.org/10.1016/j.mimet.2004.01.013openalex-snapshot
Convenient determination of DNA extraction efficiency using an external DNA recovery standard and quantitative-competitive PCR
inferredcites →https://doi.org/10.1016/j.watres.2010.04.027openalex-snapshot
Direct quantification of bacterial biomass in influent, effluent and activated sludge of wastewater treatment plants by using flow cytometry
inferredcites →https://doi.org/10.1016/s0022-1759(03)00223-0openalex-snapshot
A method for the absolute quantification of cDNA using real-time PCR
inferredcites →https://doi.org/10.1038/ismej.2010.141openalex-snapshot
Quantitative analysis of a deeply sequenced marine microbial metatranscriptome
inferredcites →https://doi.org/10.1038/ismej.2012.59openalex-snapshot
Metagenome, metatranscriptome and single-cell sequencing reveal microbial response to Deepwater Horizon oil spill
inferredcites →https://doi.org/10.1038/ismej.2012.94openalex-snapshot
Sizing up metatranscriptomics
inferredcites →https://doi.org/10.1038/ismej.2013.119openalex-snapshot
Comparative metatranscriptomics reveals kingdom level changes in the rhizosphere microbiome of plants
inferredcites →https://doi.org/10.1038/ismej.2015.155openalex-snapshot
Metatranscriptomic insights on gene expression and regulatory controls in Candidatus Accumulibacter phosphatis
inferredcites →https://doi.org/10.1038/ismej.2016.155openalex-snapshot
Co-occurrence of antibiotic and metal resistance genes revealed in complete genome collection
inferredcites →https://doi.org/10.1038/nature08055openalex-snapshot
Metatranscriptomics reveals unique microbial small RNAs in the ocean’s water column
inferredcites →https://doi.org/10.1038/nmeth.1226openalex-snapshot
Mapping and quantifying mammalian transcriptomes by RNA-Seq
inferredcites →https://doi.org/10.1038/nmeth.3176openalex-snapshot
Fast and sensitive protein alignment using DIAMOND
inferredcites →https://doi.org/10.1038/srep26447openalex-snapshot
MetaTrans: an open-source pipeline for metatranscriptomics
inferredcites →https://doi.org/10.1073/pnas.1421993112openalex-snapshot
Metatranscriptome analyses indicate resource partitioning between diatoms in the field
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/btq461openalex-snapshot
Search and clustering orders of magnitude faster than BLAST
inferredcites →https://doi.org/10.1093/bioinformatics/bts611openalex-snapshot
SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic 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/btw136openalex-snapshot
ARGs-OAP: online analysis pipeline for antibiotic resistance genes detection from metagenomic data using an integrated structured ARG-database
inferredcites →https://doi.org/10.1093/nar/17.22.9437openalex-snapshot
Absolute mRNA quantification using the polymerase chain reaction (PCR). A novel approach by aPCR aidedtranscipttitration assay (PATTY)
inferredcites →https://doi.org/10.1093/nar/gkh073openalex-snapshot
Database resources of the National Center for Biotechnology Information: update
inferredcites →https://doi.org/10.1093/nar/gkt1146openalex-snapshot
Database resources of the National Center for Biotechnology Information
inferredcites →https://doi.org/10.1128/mbio.01012-14openalex-snapshot
Metatranscriptomics of the Human Oral Microbiome during Health and Disease
inferredcites →https://doi.org/10.1186/1471-2105-11-119openalex-snapshot
Prodigal: prokaryotic gene recognition and translation initiation site identification
inferredcites →https://doi.org/10.1186/1471-2164-7-64openalex-snapshot
"Per cell" normalization method for mRNA measurement by quantitative PCR and microarrays
inferredcites →https://doi.org/10.1186/gb-2010-11-3-r25openalex-snapshot
A scaling normalization method for differential expression analysis of RNA-seq data
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/s12859-016-1270-8openalex-snapshot
SAMSA: a comprehensive metatranscriptome analysis pipeline
inferredcites →https://doi.org/10.1186/s12864-016-2964-zopenalex-snapshot
COMAN: a web server for comprehensive metatranscriptomics analysis
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/10.1186/s13059-015-0611-7openalex-snapshot
Average genome size estimation improves comparative metagenomics and sheds light on the functional ecology of the human microbiome
inferredcites →https://doi.org/10.1186/s13059-016-0881-8openalex-snapshot
A survey of best practices for RNA-seq data analysis
inferredcites →https://doi.org/10.1186/s13059-016-1116-8openalex-snapshot
IMP: a pipeline for reproducible reference-independent integrated metagenomic and metatranscriptomic analyses
inferredcites →https://doi.org/10.1371/journal.pone.0038183openalex-snapshot
Metagenomic and Metatranscriptomic Analysis of Microbial Community Structure and Gene Expression of Activated Sludge
inferredcites →https://doi.org/10.2175/106143007x221418openalex-snapshot
Bacterial Cell Monitoring in Wastewater Treatment Plants by Flow Cytometry
inferredcites →https://doi.org/10.7717/peerj.3859openalex-snapshot
How to normalize metatranscriptomic count data for differential expression analysis

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.watres.2021.117885openalex-snapshot
An assessment of resistome and mobilome in wastewater treatment plants through temporal and spatial metagenomic analysis
inferred← citeshttps://doi.org/10.64898/2026.02.26.708180openalex-snapshot
Calibrating for absolute microbiome abundances without spike-ins
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