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SINAPS: Prediction of microbial traits from marker gene sequences

https://doi.org/10.1101/124156
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What this work says

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

inferredcites →https://doi.org/10.1038/ismej.2011.139openalex-snapshot
An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea
inferredcites →https://doi.org/10.1038/ismej.2013.141openalex-snapshot
Resistance and resilience of the forest soil microbiome to logging-associated compaction
inferredcites →https://doi.org/10.1038/nbt.2676openalex-snapshot
Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences
inferredcites →https://doi.org/10.1038/nrg3182openalex-snapshot
The human microbiome: at the interface of health and disease
inferredcites →https://doi.org/10.1038/nrmicro3330openalex-snapshot
Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences
inferredcites →https://doi.org/10.1093/nar/27.1.29openalex-snapshot
KEGG: Kyoto Encyclopedia of Genes and Genomes
inferredcites →https://doi.org/10.1093/nar/gkm864openalex-snapshot
SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB
inferredcites →https://doi.org/10.1093/nar/gkt1209openalex-snapshot
The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks
inferredcites →https://doi.org/10.1093/nar/gkw964openalex-snapshot
The landscape of microbial phenotypic traits and associated genes
inferredcites →https://doi.org/10.1093/protein/12.2.85openalex-snapshot
Twilight zone of protein sequence alignments
inferredcites →https://doi.org/10.1101/074161openalex-snapshot
SINTAX: a simple non-Bayesian taxonomy classifier for 16S and ITS sequences
inferredcites →https://doi.org/10.1101/124149openalex-snapshot
UNBIAS: An attempt to correct abundance bias in 16S sequencing, with limited success
inferredcites →https://doi.org/10.1111/j.1574-6941.2007.00283.xopenalex-snapshot
Effect of primer mismatch, annealing temperature and PCR cycle number on 16S rRNA gene-targetting bacterial community analysis
inferredcites →https://doi.org/10.1126/science.278.5338.631openalex-snapshot
A Genomic Perspective on Protein Families
inferredcites →https://doi.org/10.1126/science.aac8455openalex-snapshot
The global ocean microbiome
inferredcites →https://doi.org/10.1128/aem.00062-07openalex-snapshot
Naive Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy
inferredcites →https://doi.org/10.1128/aem.01043-13openalex-snapshot
Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform
inferredcites →https://doi.org/10.1128/aem.02953-09openalex-snapshot
Diversity of 16S rRNA Genes within Individual Prokaryotic Genomes
inferredcites →https://doi.org/10.1128/aem.03006-05openalex-snapshot
Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB
inferredcites →https://doi.org/10.1146/annurev-pathol-011811-132421openalex-snapshot
Human Microbiome in Health and Disease
inferredcites →https://doi.org/10.1371/journal.pcbi.1002743openalex-snapshot
Incorporating 16S Gene Copy Number Information Improves Estimates of Microbial Diversity and Abundance

What points at this work

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

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High-level classification of the Fungi and a tool for evolutionary ecological analyses
inferred← citeshttps://doi.org/10.1016/j.ecoinf.2024.102817openalex-snapshot
Modelling soil prokaryotic traits across environments with the trait sequence database ampliconTraits and the R package MicEnvMod
inferred← citeshttps://doi.org/10.1016/j.geoderma.2026.118044openalex-snapshot
Prokaryotic traits and microbial activities predict litter decomposition and greenhouse gas fluxes across Greenlandic soils
inferred← citeshttps://doi.org/10.1038/s43247-025-03028-zopenalex-snapshot
Cross-continental soil prokaryotic traits driven by precipitation regime and land cover
inferred← citeshttps://doi.org/10.1101/124149openalex-snapshot
UNBIAS: An attempt to correct abundance bias in 16S sequencing, with limited success
inferred← citeshttps://doi.org/10.1101/2020.08.20.260398openalex-snapshot
Phenotypic reconstruction of the last universal common ancestor reveals a complex cell
inferred← citeshttps://doi.org/10.1111/1755-0998.12959openalex-snapshot
High‐throughput identification and diagnostics of pathogens and pests: Overview and practical recommendations
inferred← citeshttps://doi.org/10.1111/1755-0998.13398openalex-snapshot
Bioinformatic pipelines combining denoising and clustering tools allow for more comprehensive prokaryotic and eukaryotic metabarcoding
inferred← citeshttps://doi.org/10.1111/2041-210x.13060openalex-snapshot
Functional exploration of natural networks and ecological communities
inferred← citeshttps://doi.org/10.1186/s12864-019-6427-1openalex-snapshot
Piphillin predicts metagenomic composition and dynamics from DADA2-corrected 16S rDNA sequences
inferred← citeshttps://doi.org/10.1371/journal.pone.0219235openalex-snapshot
Exploring thematic structure and predicted functionality of 16S rRNA amplicon data
inferred← citeshttps://doi.org/10.70675/0d2d4921z2c39z4b84zb3a5za8f479f89d14openalex-snapshot
Metabarcoding in the abyss : uncovering deep-sea biodiversity through environmental DNA
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