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Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analyses
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Outgoing claims: the papers this work cites, builds on, or argues with.
inferredcites →https://doi.org/10.1002/j.1538-7305.1948.tb01338.xopenalex-snapshot
A Mathematical Theory of Communication
inferredcites →https://doi.org/10.1007/978-1-4899-7478-5_751openalex-snapshot
Taxonomic Classification of Metagenomic Shotgun Sequences with CARMA3
inferredcites →https://doi.org/10.1007/978-1-4939-2990-0_2openalex-snapshot
Bias in Whole Genome Amplification: Causes and Considerations
inferredcites →https://doi.org/10.1007/978-1-4939-3369-3_13openalex-snapshot
MG-RAST, a Metagenomics Service for Analysis of Microbial Community Structure and Function
inferredcites →https://doi.org/10.1007/978-1-4939-7015-5_3openalex-snapshot
From Gene Annotation to Function Prediction for Metagenomics
inferredcites →https://doi.org/10.1007/978-1-4939-9048-1_27openalex-snapshot
Analysis of the Pulmonary Microbiome Composition of Legionella pneumophila-Infected Patients
inferredcites →https://doi.org/10.1007/978-1-4939-9173-0_3openalex-snapshot
Structural and Functional Annotation of Eukaryotic Genomes with GenSAS
inferredcites →https://doi.org/10.1007/978-1-4939-9173-0_6openalex-snapshot
EuGene: An Automated Integrative Gene Finder for Eukaryotes and Prokaryotes
inferredcites →https://doi.org/10.1007/978-3-540-78839-3_3openalex-snapshot
CompostBin: A DNA Composition-Based Algorithm for Binning Environmental Shotgun Reads
inferredcites →https://doi.org/10.1007/978-3-642-12683-3_28openalex-snapshot
IDBA – A Practical Iterative de Bruijn Graph De Novo Assembler
inferredcites →https://doi.org/10.1016/0006-3207(92)91201-3openalex-snapshot
Conservation evaluation and phylogenetic diversity
inferredcites →https://doi.org/10.1016/j.bdq.2015.02.001openalex-snapshot
Assessing the performance of the Oxford Nanopore Technologies MinION
inferredcites →https://doi.org/10.1016/j.cell.2014.06.037openalex-snapshot
Conducting a Microbiome Study
inferredcites →https://doi.org/10.1016/j.cell.2019.01.001openalex-snapshot
Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle
inferredcites →https://doi.org/10.1016/j.cell.2019.07.010openalex-snapshot
Benchmarking Metagenomics Tools for Taxonomic Classification
inferredcites →https://doi.org/10.1016/j.celrep.2020.02.036openalex-snapshot
An Integrated Metagenome Catalog Reveals New Insights into the Murine Gut Microbiome
inferredcites →https://doi.org/10.1016/j.chom.2018.07.005openalex-snapshot
Effect of Antibiotic-Mediated Microbiome Modulation on Rotavirus Vaccine Immunogenicity: A Human, Randomized-Control Proof-of-Concept Trial
inferredcites →https://doi.org/10.1016/j.csbj.2016.11.005openalex-snapshot
Bioinformatics strategies for taxonomy independent binning and visualization of sequences in shotgun metagenomics
inferredcites →https://doi.org/10.1016/j.jhazmat.2019.120841openalex-snapshot
Metagenomic assembly provides a deep insight into the antibiotic resistome alteration induced by drinking water chlorination and its correlations with bacterial host changes
inferredcites →https://doi.org/10.1016/j.mimet.2018.06.007openalex-snapshot
Practical evaluation of 11 de novo assemblers in metagenome assembly
inferredcites →https://doi.org/10.1016/j.ygeno.2010.03.001openalex-snapshot
Assembly algorithms for next-generation sequencing data
inferredcites →https://doi.org/10.1016/s0022-2836(05)80360-2openalex-snapshot
Basic Local Alignment Search Tool
inferredcites →https://doi.org/10.1021/pr700864xopenalex-snapshot
Metabonomic and Microbiological Analysis of the Dynamic Effect of Vancomycin-Induced Gut Microbiota Modification in the Mouse
inferredcites →https://doi.org/10.1038/ismej.2011.116openalex-snapshot
Assessing the complex sponge microbiota: core, variable and species-specific bacterial communities in marine sponges
inferredcites →https://doi.org/10.1038/ismej.2011.119openalex-snapshot
Using network analysis to explore co-occurrence patterns in soil microbial communities
inferredcites →https://doi.org/10.1038/nature13421openalex-snapshot
Persistent gut microbiota immaturity in malnourished Bangladeshi children
inferredcites →https://doi.org/10.1038/nature24621openalex-snapshot
A communal catalogue reveals Earth’s multiscale microbial diversity
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/nbt.2939openalex-snapshot
Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes
inferredcites →https://doi.org/10.1038/nbt.3935openalex-snapshot
Shotgun metagenomics, from sampling to analysis
inferredcites →https://doi.org/10.1038/ncomms11257openalex-snapshot
Fast and sensitive taxonomic classification for metagenomics with Kaiju
inferredcites →https://doi.org/10.1038/ncomms2203openalex-snapshot
Virtual metagenome reconstruction from 16S rRNA gene sequences
inferredcites →https://doi.org/10.1038/nmeth.1358openalex-snapshot
Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models
inferredcites →https://doi.org/10.1038/nmeth.2066openalex-snapshot
Metagenomic microbial community profiling using unique clade-specific marker genes
inferredcites →https://doi.org/10.1038/nmeth.2658openalex-snapshot
Differential abundance analysis for microbial marker-gene surveys
inferredcites →https://doi.org/10.1038/nmeth.3103openalex-snapshot
Binning metagenomic contigs by coverage and composition
inferredcites →https://doi.org/10.1038/nmeth.3176openalex-snapshot
Fast and sensitive protein alignment using DIAMOND
inferredcites →https://doi.org/10.1038/nmeth.3589openalex-snapshot
MetaPhlAn2 for enhanced metagenomic taxonomic profiling
inferredcites →https://doi.org/10.1038/nmeth.3802openalex-snapshot
Strain-level microbial epidemiology and population genomics from shotgun metagenomics
inferredcites →https://doi.org/10.1038/nmeth.3869openalex-snapshot
DADA2: High-resolution sample inference from Illumina amplicon data
inferredcites →https://doi.org/10.1038/nmeth.4458openalex-snapshot
Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software
inferredcites →https://doi.org/10.1038/nmeth.f.303openalex-snapshot
QIIME allows analysis of high-throughput community sequencing data
inferredcites →https://doi.org/10.1038/nrmicro.2016.177openalex-snapshot
Virus taxonomy in the age of metagenomics
inferredcites →https://doi.org/10.1038/s41467-018-03317-6openalex-snapshot
Assembly of 913 microbial genomes from metagenomic sequencing of the cow rumen
inferredcites →https://doi.org/10.1038/s41564-018-0171-1openalex-snapshot
Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy
inferredcites →https://doi.org/10.1038/s41579-018-0029-9openalex-snapshot
Best practices for analysing microbiomes
inferredcites →https://doi.org/10.1038/s41586-019-0965-1openalex-snapshot
A new genomic blueprint of the human gut microbiota
inferredcites →https://doi.org/10.1038/s41587-019-0191-2openalex-snapshot
Hybrid metagenomic assembly enables high-resolution analysis of resistance determinants and mobile elements in human microbiomes
inferredcites →https://doi.org/10.1038/s41587-019-0209-9openalex-snapshot
Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2
inferredcites →https://doi.org/10.1038/s41592-018-0176-yopenalex-snapshot
Species-level functional profiling of metagenomes and metatranscriptomes
inferredcites →https://doi.org/10.1038/s41598-018-37208-zopenalex-snapshot
Characterizing both bacteria and fungi improves understanding of the Arabidopsis root microbiome
inferredcites →https://doi.org/10.1038/s41598-019-39576-6openalex-snapshot
Metagenome-assembled genomes provide new insight into the microbial diversity of two thermal pools in Kamchatka, Russia
inferredcites →https://doi.org/10.1038/s41598-019-51284-9openalex-snapshot
Scalable Genome Assembly through Parallel de Bruijn Graph Construction for Multiple k-mers
inferredcites →https://doi.org/10.1038/srep06480openalex-snapshot
Improved Assemblies Using a Source-Agnostic Pipeline for MetaGenomic Assembly by Merging (MeGAMerge) of Contigs
inferredcites →https://doi.org/10.1038/srep24175openalex-snapshot
Accurate binning of metagenomic contigs via automated clustering sequences using information of genomic signatures and marker genes
inferredcites →https://doi.org/10.1073/pnas.1117018109openalex-snapshot
Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi
inferredcites →https://doi.org/10.1073/pnas.74.11.5088openalex-snapshot
Phylogenetic structure of the prokaryotic domain: The primary kingdoms
inferredcites →https://doi.org/10.1080/01621459.1952.10483441openalex-snapshot
Use of Ranks in One-Criterion Variance Analysis
inferredcites →https://doi.org/10.1089/cmb.2010.0245openalex-snapshot
A Novel Abundance-Based Algorithm for Binning Metagenomic Sequences Using l -tuples
inferredcites →https://doi.org/10.1089/cmb.2011.0276openalex-snapshot
MetaCluster 4.0: A Novel Binning Algorithm for NGS Reads and Huge Number of Species
inferredcites →https://doi.org/10.1089/cmb.2012.0021openalex-snapshot
SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing
inferredcites →https://doi.org/10.1093/bib/bbs031openalex-snapshot
Taxonomic binning of metagenome samples generated by next-generation sequencing technologies
inferredcites →https://doi.org/10.1093/bib/bbx105openalex-snapshot
MG-RAST version 4—lessons learned from a decade of low-budget ultra-high-throughput metagenome analysis
inferredcites →https://doi.org/10.1093/bib/bbx120openalex-snapshot
A review of methods and databases for metagenomic classification and assembly
inferredcites →https://doi.org/10.1093/bib/bbz025openalex-snapshot
Assessment of metagenomic assemblers based on hybrid reads of real and simulated metagenomic sequences
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/btq455openalex-snapshot
METAREP: JCVI metagenomics reports—an open source tool for high-performance comparative metagenomics
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/btq608openalex-snapshot
SPHINX—an algorithm for taxonomic binning of metagenomic sequences
inferredcites →https://doi.org/10.1093/bioinformatics/btr026openalex-snapshot
Quality control and preprocessing of metagenomic datasets
inferredcites →https://doi.org/10.1093/bioinformatics/btr595openalex-snapshot
RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data
inferredcites →https://doi.org/10.1093/bioinformatics/bts174openalex-snapshot
IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth
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/btt310openalex-snapshot
Informed and automated k -mer size selection for genome assembly
inferredcites →https://doi.org/10.1093/bioinformatics/btt476openalex-snapshot
The MaSuRCA genome assembler
inferredcites →https://doi.org/10.1093/bioinformatics/btt593openalex-snapshot
PEAR: a fast and accurate Illumina Paired-End reAd mergeR
inferredcites →https://doi.org/10.1093/bioinformatics/btu153openalex-snapshot
Prokka: rapid prokaryotic genome annotation
inferredcites →https://doi.org/10.1093/bioinformatics/btu170openalex-snapshot
Trimmomatic: a flexible trimmer for Illumina sequence data
inferredcites →https://doi.org/10.1093/bioinformatics/btu745openalex-snapshot
Taxator-tk: precise taxonomic assignment of metagenomes by fast approximation of evolutionary neighborhoods
inferredcites →https://doi.org/10.1093/bioinformatics/btv033openalex-snapshot
MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph
inferredcites →https://doi.org/10.1093/bioinformatics/btv287openalex-snapshot
Tax4Fun: predicting functional profiles from metagenomic 16S rRNA data
inferredcites →https://doi.org/10.1093/bioinformatics/btv638openalex-snapshot
MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets
inferredcites →https://doi.org/10.1093/bioinformatics/btv697openalex-snapshot
MetaQUAST: evaluation of metagenome assemblies
inferredcites →https://doi.org/10.1093/bioinformatics/btw183openalex-snapshot
MOCAT2: a metagenomic assembly, annotation and profiling framework
inferredcites →https://doi.org/10.1093/bioinformatics/btw290openalex-snapshot
COCACOLA: binning metagenomic contigs using sequence COmposition, read CoverAge, CO-alignment and paired-end read LinkAge
inferredcites →https://doi.org/10.1093/bioinformatics/btx021openalex-snapshot
PALADIN: protein alignment for functional profiling whole metagenome shotgun data
inferredcites →https://doi.org/10.1093/bioinformatics/btx086openalex-snapshot
Binning_refiner: improving genome bins through the combination of different binning programs
inferredcites →https://doi.org/10.1093/bioinformatics/btx153openalex-snapshot
GenomeScope: fast reference-free genome profiling from short reads
inferredcites →https://doi.org/10.1093/bioinformatics/btx637openalex-snapshot
findGSE : estimating genome size variation within human and Arabidopsis using k -mer frequencies
inferredcites →https://doi.org/10.1093/bioinformatics/btx713openalex-snapshot
DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication
inferredcites →https://doi.org/10.1093/bioinformatics/bty519openalex-snapshot
BMC3C: binning metagenomic contigs using codon usage, sequence composition and read coverage
inferredcites →https://doi.org/10.1093/bioinformatics/bty905openalex-snapshot
MAGpy: a reproducible pipeline for the downstream analysis of metagenome-assembled genomes (MAGs)
inferredcites →https://doi.org/10.1093/bioinformatics/btz253openalex-snapshot
SolidBin: improving metagenome binning with semi-supervised normalized cut
inferredcites →https://doi.org/10.1093/bioinformatics/btz577openalex-snapshot
MetaBMF: a scalable binning algorithm for large-scale reference-free metagenomic studies
inferredcites →https://doi.org/10.1093/dnares/dsn027openalex-snapshot
MetaGeneAnnotator: Detecting Species-Specific Patterns of Ribosomal Binding Site for Precise Gene Prediction in Anonymous Prokaryotic and Phage Genomes
inferredcites →https://doi.org/10.1093/dnares/dsu041openalex-snapshot
MetaVelvet-SL: an extension of the Velvet assembler to a de novo metagenomic assembler utilizing supervised learning
inferredcites →https://doi.org/10.1093/gigascience/giy069openalex-snapshot
AMBER: Assessment of Metagenome BinnERs
inferredcites →https://doi.org/10.1093/gigascience/giz020openalex-snapshot
MGS-Fast: Metagenomic shotgun data fast annotation using microbial gene catalogs
inferredcites →https://doi.org/10.1093/nar/27.23.4636openalex-snapshot
Improved microbial gene identification with GLIMMER
inferredcites →https://doi.org/10.1093/nar/gkg847openalex-snapshot
Enzyme-specific profiles for genome annotation: PRIAM
inferredcites →https://doi.org/10.1093/nar/gki458openalex-snapshot
AUGUSTUS: a web server for gene prediction in eukaryotes that allows user-defined constraints
inferredcites →https://doi.org/10.1093/nar/gki937openalex-snapshot
Gene identification in novel eukaryotic genomes by self-training algorithm
inferredcites →https://doi.org/10.1093/nar/gkl723openalex-snapshot
MetaGene: prokaryotic gene finding from environmental genome shotgun sequences
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/gkn785openalex-snapshot
InterPro: the integrative protein signature database
inferredcites →https://doi.org/10.1093/nar/gkq275openalex-snapshot
Ab initio gene identification in metagenomic sequences
inferredcites →https://doi.org/10.1093/nar/gkq747openalex-snapshot
FragGeneScan: predicting genes in short and error-prone reads
inferredcites →https://doi.org/10.1093/nar/gkr1067openalex-snapshot
Gene prediction with Glimmer for metagenomic sequences augmented by classification and clustering
inferredcites →https://doi.org/10.1093/nar/gkr225openalex-snapshot
Taxonomic classification of metagenomic shotgun sequences with CARMA3
inferredcites →https://doi.org/10.1093/nar/gks1160openalex-snapshot
The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy
inferredcites →https://doi.org/10.1093/nar/gks678openalex-snapshot
MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads
inferredcites →https://doi.org/10.1093/nar/gkt1223openalex-snapshot
Pfam: the protein families database
inferredcites →https://doi.org/10.1093/nar/gkt1244openalex-snapshot
Ribosomal Database Project: data and tools for high throughput rRNA analysis
inferredcites →https://doi.org/10.1093/nar/gkt1252openalex-snapshot
BacMet: antibacterial biocide and metal resistance genes database
inferredcites →https://doi.org/10.1093/nar/gku1201openalex-snapshot
rrnDB: improved tools for interpreting rRNA gene abundance in bacteria and archaea and a new foundation for future development
inferredcites →https://doi.org/10.1093/nar/gkw569openalex-snapshot
NCBI prokaryotic genome annotation pipeline
inferredcites →https://doi.org/10.1093/nar/gkw837openalex-snapshot
MetaMLST: multi-locus strain-level bacterial typing from metagenomic samples
inferredcites →https://doi.org/10.1093/nar/gky1022openalex-snapshot
The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications
inferredcites →https://doi.org/10.1093/nar/gky901openalex-snapshot
IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes
inferredcites →https://doi.org/10.1093/nar/gkz148openalex-snapshot
Autometa: automated extraction of microbial genomes from individual shotgun metagenomes
inferredcites →https://doi.org/10.1093/nar/gkz485openalex-snapshot
APERO: a genome-wide approach for identifying bacterial small RNAs from RNA-Seq data
inferredcites →https://doi.org/10.1093/nar/gkz926openalex-snapshot
MicroScope: an integrated platform for the annotation and exploration of microbial gene functions through genomic, pangenomic and metabolic comparative analysis
inferredcites →https://doi.org/10.1093/nar/gkz935openalex-snapshot
CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database
inferredcites →https://doi.org/10.1093/sysbio/45.3.380openalex-snapshot
The Probabilistic Basis of Jaccard's Index of Similarity
inferredcites →https://doi.org/10.1097/mjt.0b013e31817c941fopenalex-snapshot
Methods in Molecular Biology
inferredcites →https://doi.org/10.1099/jgv.0.000016openalex-snapshot
Methods for virus classification and the challenge of incorporating metagenomic sequence data
inferredcites →https://doi.org/10.1101/074252openalex-snapshot
UCHIME2: improved chimera prediction for amplicon sequencing
inferredcites →https://doi.org/10.1101/672295openalex-snapshot
PICRUSt2: An improved and customizable approach for metagenome inference
inferredcites →https://doi.org/10.1101/gr.074492.107openalex-snapshot
Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
inferredcites →https://doi.org/10.1101/gr.081612.108openalex-snapshot
Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training
inferredcites →https://doi.org/10.1101/gr.186072.114openalex-snapshot
CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes
inferredcites →https://doi.org/10.1101/gr.210641.116openalex-snapshot
Centrifuge: rapid and sensitive classification of metagenomic sequences
inferredcites →https://doi.org/10.1101/gr.213959.116openalex-snapshot
metaSPAdes: a new versatile metagenomic assembler
inferredcites →https://doi.org/10.1101/gr.216242.116openalex-snapshot
Microbial strain-level population structure and genetic diversity from metagenomes
inferredcites →https://doi.org/10.1101/gr.225276.117openalex-snapshot
taxMaps: comprehensive and highly accurate taxonomic classification of short-read data in reasonable time
inferredcites →https://doi.org/10.1101/gr.229202openalex-snapshot
BLAT —The BLAST -Like Alignment Tool
inferredcites →https://doi.org/10.1101/gr.230615.117openalex-snapshot
Modeling leaderless transcription and atypical genes results in more accurate gene prediction in prokaryotes
inferredcites →https://doi.org/10.1109/bibm.2010.5706544openalex-snapshot
MetaPhyler: Taxonomic profiling for metagenomic sequences
inferredcites →https://doi.org/10.1111/1755-0998.12410openalex-snapshot
PFR 2 : a curated database of planktonic foraminifera 18S ribosomal DNA as a resource for studies of plankton ecology, biogeography and evolution
inferredcites →https://doi.org/10.1111/1755-0998.12726openalex-snapshot
Impact of sequence processing and taxonomic classification approaches on eukaryotic community structure from environmental samples with emphasis on diatoms
inferredcites →https://doi.org/10.1111/j.1442-9993.1993.tb00438.xopenalex-snapshot
Non‐parametric multivariate analyses of changes in community structure
inferredcites →https://doi.org/10.1111/j.1442-9993.2001.01070.pp.xopenalex-snapshot
A new method for non‐parametric multivariate analysis of variance
inferredcites →https://doi.org/10.1111/jbi.14281openalex-snapshot
The detection of disease clustering and a generalized regression approach.
inferredcites →https://doi.org/10.1111/nph.12243openalex-snapshot
Fungal community analysis by high‐throughput sequencing of amplified markers – a user's guide
inferredcites →https://doi.org/10.1126/science.1058040openalex-snapshot
The Sequence of the Human Genome
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.01177-06openalex-snapshot
Use of 16S rRNA and rpoB Genes as Molecular Markers for Microbial Ecology Studies
inferredcites →https://doi.org/10.1128/aem.01541-09openalex-snapshot
Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities
inferredcites →https://doi.org/10.1128/aem.01996-06openalex-snapshot
Quantitative and Qualitative β Diversity Measures Lead to Different Insights into Factors That Structure Microbial Communities
inferredcites →https://doi.org/10.1128/aem.02627-17openalex-snapshot
The Madness of Microbiome: Attempting To Find Consensus “Best Practice” for 16S Microbiome Studies
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/10.1128/aem.61.7.2798-2801.1995openalex-snapshot
Effect of genome size and rrn gene copy number on PCR amplification of 16S rRNA genes from a mixture of bacterial species
inferredcites →https://doi.org/10.1128/jb.186.9.2629-2635.2004openalex-snapshot
Divergence and Redundancy of 16S rRNA Sequences in Genomes with Multiple rrn Operons
inferredcites →https://doi.org/10.1128/msphere.00163-19openalex-snapshot
The Impact of DNA Polymerase and Number of Rounds of Amplification in PCR on 16S rRNA Gene Sequence Data
inferredcites →https://doi.org/10.1128/msystems.00190-17openalex-snapshot
On the Road to Strain-Resolved Comparative Metagenomics
inferredcites →https://doi.org/10.1128/msystems.00191-16openalex-snapshot
Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns
inferredcites →https://doi.org/10.1128/msystems.00271-18openalex-snapshot
Impact of Preservation Method and 16S rRNA Hypervariable Region on Gut Microbiota Profiling
inferredcites →https://doi.org/10.1146/annurev-marine-120709-142802openalex-snapshot
Marine Protistan Diversity
inferredcites →https://doi.org/10.1186/1471-2105-10-316openalex-snapshot
Unsupervised statistical clustering of environmental shotgun sequences
inferredcites →https://doi.org/10.1186/1471-2105-10-421openalex-snapshot
BLAST+: architecture and applications
inferredcites →https://doi.org/10.1186/1471-2105-10-56openalex-snapshot
TACOA – Taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach
inferredcites →https://doi.org/10.1186/1471-2105-11-119openalex-snapshot
Prodigal: prokaryotic gene recognition and translation initiation site identification
inferredcites →https://doi.org/10.1186/1471-2105-11-538openalex-snapshot
pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree
inferredcites →https://doi.org/10.1186/1471-2105-11-544openalex-snapshot
Clustering metagenomic sequences with interpolated Markov models
inferredcites →https://doi.org/10.1186/1471-2105-11-94openalex-snapshot
Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments
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MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects
inferredcites →https://doi.org/10.1186/1471-2105-13-183openalex-snapshot
Short-read reading-frame predictors are not created equal: sequence error causes loss of signal
inferredcites →https://doi.org/10.1186/1471-2105-13-283openalex-snapshot
Denoising PCR-amplified metagenome data
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GAM-NGS: genomic assemblies merger for next generation sequencing
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The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes
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Space-efficient and exact de Bruijn graph representation based on a Bloom filter
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A review of software for analyzing molecular sequences
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SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler
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CopyRighter: a rapid tool for improving the accuracy of microbial community profiles through lineage-specific gene copy number correction
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Community-wide analysis of microbial genome sequence signatures
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Differential expression analysis for sequence count data
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Metagenomic biomarker discovery and explanation
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Ray Meta: scalable de novo metagenome assembly and profiling
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MetAMOS: a modular and open source metagenomic assembly and analysis pipeline
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Characterizing and measuring bias in sequence data
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voom: precision weights unlock linear model analysis tools for RNA-seq read counts
inferredcites →https://doi.org/10.1186/gb-2014-15-3-r46openalex-snapshot
Kraken: ultrafast metagenomic sequence classification using exact alignments
inferredcites →https://doi.org/10.1186/s12859-015-0473-8openalex-snapshot
MBBC: an efficient approach for metagenomic binning based on clustering
inferredcites →https://doi.org/10.1186/s12859-017-1653-5openalex-snapshot
ICoVeR – an interactive visualization tool for verification and refinement of metagenomic bins
inferredcites →https://doi.org/10.1186/s12859-018-2205-3openalex-snapshot
Taxonomy-aware feature engineering for microbiome classification
inferredcites →https://doi.org/10.1186/s12859-019-2818-1openalex-snapshot
GRASP2: fast and memory-efficient gene-centric assembly and homolog search for metagenomic sequencing data
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CLARK: fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers
inferredcites →https://doi.org/10.1186/s12864-015-2265-yopenalex-snapshot
Improved taxonomic assignment of human intestinal 16S rRNA sequences by a dedicated reference database
inferredcites →https://doi.org/10.1186/s12864-017-3918-9openalex-snapshot
Assembling metagenomes, one community at a time
inferredcites →https://doi.org/10.1186/s12864-018-4637-6openalex-snapshot
Comparison of normalization methods for the analysis of metagenomic gene abundance data
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/s13059-015-0834-7openalex-snapshot
Metagenome-assembled genomes uncover a global brackish microbiome
inferredcites →https://doi.org/10.1186/s13059-016-0969-1openalex-snapshot
Taxonomer: an interactive metagenomics analysis portal for universal pathogen detection and host mRNA expression profiling
inferredcites →https://doi.org/10.1186/s13059-017-1309-9openalex-snapshot
DESMAN: a new tool for de novo extraction of strains from metagenomes
inferredcites →https://doi.org/10.1186/s13059-019-1891-0openalex-snapshot
Improved metagenomic analysis with Kraken 2
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What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
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inferred← citeshttps://doi.org/10.1016/j.watres.2025.124057openalex-snapshot
Hydroperiodic dynamics of microbial-mediated nitrogen cycling and its multi-element coupling effect in the Weihe River
inferred← citeshttps://doi.org/10.1016/j.xcrm.2023.101167openalex-snapshot
The respiratory tract microbiome, the pathogen load, and clinical interventions define severity of bacterial pneumonia
inferred← citeshttps://doi.org/10.1038/s41597-024-03748-5openalex-snapshot
Datasets of fungal diversity and pseudo-chromosomal genomes of mangrove rhizosphere soil in China
inferred← citeshttps://doi.org/10.1038/s41597-025-05050-4openalex-snapshot
A curated bacterial and archaeal 16S rRNA Gene Oral Sequences dataset
inferred← citeshttps://doi.org/10.1038/s41598-024-80660-3openalex-snapshot
Evaluation of DNA extraction kits for long-read shotgun metagenomics using Oxford Nanopore sequencing for rapid taxonomic and antimicrobial resistance detection
inferred← citeshttps://doi.org/10.1038/s44185-025-00076-8openalex-snapshot
Advocating microbial diversity conservation in Antarctica
inferred← citeshttps://doi.org/10.1039/d3en00130jopenalex-snapshot
Reshaping fish intestinal microbiota and facilitating barrier function by ZnO nanoparticles
inferred← citeshttps://doi.org/10.1079/9781800627307.0023openalex-snapshot
Metagenomic Insights Into Plant–probiotic Bacterial Interactions Boosting Crop Growth and Yield
inferred← citeshttps://doi.org/10.1079/9781836990475.0003openalex-snapshot
Exploration of Microbial Diversity in the Internal Tissues of Plants, and Their Interactions with the Plant
inferred← citeshttps://doi.org/10.1079/9781836990475.0010openalex-snapshot
Exploration of the Unique Microbiomes of Medicinal Plants, Driven by Their Bioactive Secondary Metabolites
inferred← citeshttps://doi.org/10.1079/cabireviews.2024.0011openalex-snapshot
Multiple approaches in the study of ancient human microbiome
inferred← citeshttps://doi.org/10.1080/0269249x.2025.2576677openalex-snapshot
An ecologist's views on genetic barcodes and the future of diatom identification
inferred← citeshttps://doi.org/10.1080/07352689.2025.2494872openalex-snapshot
Combating Phytopathogens by Integration of Metagenomics and Phototrophic Biotechnologies: Toward Sustainable Agricultural Practices
inferred← citeshttps://doi.org/10.1080/1040841x.2023.2282447openalex-snapshot
Exploring microbial worlds: a review of whole genome sequencing and its application in characterizing the microbial communities
inferred← citeshttps://doi.org/10.1093/bib/bbad381openalex-snapshot
ACR: metagenome-assembled prokaryotic and eukaryotic genome refinement tool
inferred← citeshttps://doi.org/10.1093/bib/bbaf065openalex-snapshot
A review of neural networks for metagenomic binning
inferred← citeshttps://doi.org/10.1093/femsec/fiae117openalex-snapshot
Taxonomic and functional metagenomic assessment of a Dolichospermum bloom in a large and deep lake south of the Alps
inferred← citeshttps://doi.org/10.1093/femsmc/xtad016openalex-snapshot
Legionella relative abundance in shower hose biofilms is associated with specific microbiome members
inferred← citeshttps://doi.org/10.1093/ismejo/wraf107openalex-snapshot
Distinguishing among evolutionary and ecological processes shaping microbiome dynamics
inferred← citeshttps://doi.org/10.1093/jambio/lxag043openalex-snapshot
Microbes: the invisible codes of forensic science
inferred← citeshttps://doi.org/10.1093/nargab/lqab018openalex-snapshot
ResistoXplorer: a web-based tool for visual, statistical and exploratory data analysis of resistome data
inferred← citeshttps://doi.org/10.1093/nargab/lqag080openalex-snapshot
metaWEPP: leveraging biobank-scale intra-species phylogenies for near-haplotype resolution in metagenomic analysis
inferred← citeshttps://doi.org/10.1098/rsob.240231openalex-snapshot
Deciphering respiratory viral infections by harnessing organ-on-chip technology to explore the gut–lung axis
inferred← citeshttps://doi.org/10.1099/mgen.0.000654openalex-snapshot
Identification of isolated or mixed strains from long reads: a challenge met on Streptococcus thermophilus using a MinION sequencer
inferred← citeshttps://doi.org/10.1099/mgen.0.000899openalex-snapshot
A novel approach for combining the metagenome, metaresistome, metareplicome and causal inference to determine the microbes and their antibiotic resistance gene repertoire that contribute to dysbiosis
inferred← citeshttps://doi.org/10.1099/mgen.0.001231openalex-snapshot
Deep learning methods in metagenomics: a review
inferred← citeshttps://doi.org/10.1101/2021.10.15.464554openalex-snapshot
How low can you go? Driving down the DNA input requirements for nanopore sequencing
inferred← citeshttps://doi.org/10.1101/2023.10.09.561583openalex-snapshot
On the relationship between protist metabarcoding and protist metagenome-assembled genomes
inferred← citeshttps://doi.org/10.1101/2023.12.13.571510openalex-snapshot
MAGqual: A standalone pipeline to assess the quality of metagenome-assembled genomes
inferred← citeshttps://doi.org/10.1101/2024.01.26.577441openalex-snapshot
Decoding the Microbiome-Metabolome Nexus: A Systematic Benchmark of Integrative Strategies
inferred← citeshttps://doi.org/10.1101/2024.06.21.600076openalex-snapshot
RecA is a reliable marker for bacterial taxonomy, even in the Candidate Phyla Radiation
inferred← citeshttps://doi.org/10.1101/2024.09.17.613203openalex-snapshot
PANOMIQ: A Unified Approach to Whole-Genome, Exome, and Microbiome Data Analysis
inferred← citeshttps://doi.org/10.1101/2024.11.20.624313openalex-snapshot
Assessing the performance of current strain resolution tools on long-read metagenomes
inferred← citeshttps://doi.org/10.1101/2025.06.04.656517openalex-snapshot
Gener anno : A Genomic Foundation Model for Metagenomic Annotation
inferred← citeshttps://doi.org/10.1101/2025.07.29.25332408openalex-snapshot
Harmonizing the oral-brain axis: Music-induced microbiota shifts in age-related cognitive disorders and healthy aging
inferred← citeshttps://doi.org/10.1101/2025.11.25.689180openalex-snapshot
Biological insights and methodological challenges learned from working with a diverse heterotrophic marine bacterial library
inferred← citeshttps://doi.org/10.1109/access.2022.3195878openalex-snapshot
Demeter: A Fast and Energy-Efficient Food Profiler Using Hyperdimensional Computing in Memory
inferred← citeshttps://doi.org/10.1109/iisa62523.2024.10786654openalex-snapshot
A Web-Based Network Analysis Tool for the Metaganomic Analysis of Resistomes
inferred← citeshttps://doi.org/10.1111/1365-2656.70127openalex-snapshot
Harnessing 50 years of tick population genetics: Choosing the right molecular tool for contemporary research
inferred← citeshttps://doi.org/10.1111/1462-2920.16530openalex-snapshot
Simultaneous analysis of seven 16S rRNA hypervariable gene regions increases efficiency in marine bacterial diversity detection
inferred← citeshttps://doi.org/10.1111/1750-3841.17178openalex-snapshot
Impact of microorganisms on key processes of organic acid metabolism during the occurrence and disappearance of paocai pellicle
inferred← citeshttps://doi.org/10.1111/1751-7915.14396openalex-snapshot
Community‐scale models of microbiomes: Articulating metabolic modelling and metagenome sequencing
inferred← citeshttps://doi.org/10.1111/1751-7915.70147openalex-snapshot
The Respiratory Tract Microbiome and Human Health
inferred← citeshttps://doi.org/10.1111/2041-210x.13876openalex-snapshot
Soil bacterial biodiversity characterization by flow cytometry: The bottleneck of cell extraction from soil
inferred← citeshttps://doi.org/10.1111/bjd.21245openalex-snapshot
Patients with psoriasis have a dysbiotic taxonomic and functional gut microbiota*
inferred← citeshttps://doi.org/10.1111/cbdd.14505openalex-snapshot
Understanding gut microbiome‐based machine learning platforms: A review on therapeutic approaches using deep learning
inferred← citeshttps://doi.org/10.1111/ene.15819openalex-snapshot
Molecular systems biology approaches to investigate mechanisms of gut−brain communication in neurological diseases
inferred← citeshttps://doi.org/10.1111/imcb.12798openalex-snapshot
Integrating functional metagenomics to decipher microbiome–immune interactions
inferred← citeshttps://doi.org/10.1111/mec.16958openalex-snapshot
Inferring the ecological and evolutionary determinants of community genetic diversity
inferred← citeshttps://doi.org/10.1111/omi.12434openalex-snapshot
Critical review of 16S rRNA gene sequencing workflow in microbiome studies: From primer selection to advanced data analysis
inferred← citeshttps://doi.org/10.1111/prd.12393openalex-snapshot
The oral microbiome: Role of key organisms and complex networks in oral health and disease
inferred← citeshttps://doi.org/10.1128/aem.01723-25openalex-snapshot
How sequencing technology shapes our understanding of river water microbiomes and resistomes: a comparative study
inferred← citeshttps://doi.org/10.1128/msystems.01213-20openalex-snapshot
Interkingdom Gut Microbiome and Resistome of the Cockroach Blattella germanica
inferred← citeshttps://doi.org/10.1128/spectrum.01108-26openalex-snapshot
Impacts of flooding on agricultural soil microbiome
inferred← citeshttps://doi.org/10.1128/spectrum.01321-24openalex-snapshot
Integrating microbial profiling and machine learning for inference of drowning sites: a forensic investigation in the Northwest River
inferred← citeshttps://doi.org/10.1134/s0026261725604816openalex-snapshot
Taxonomic and Functional Diversity of Microbial Communities in Saline Lakes of Barguzin Depression (Russia) Assessed Using Shotgun Sequencing
inferred← citeshttps://doi.org/10.1139/cjss-2026-0052openalex-snapshot
Canada’s forest soils: the establishment of a nationwide network of long-term sites to examine soil carbon persistence and soil indicators
inferred← citeshttps://doi.org/10.1155/ijm/6677609openalex-snapshot
Brukina in Focus: A Narrative Review on Metagenomic Approaches to Fermentation and Food Safety
inferred← citeshttps://doi.org/10.11606/d.95.2021.tde-16092021-090947openalex-snapshot
MAGset: uma ferramenta para comparação de genomas recuperados de dados metagenômicos e sua aplicação para melhoria de suas montagens
inferred← citeshttps://doi.org/10.11606/d.95.2023.tde-09102023-164409openalex-snapshot
Recuperação e caracterização de genomas de bacteriófagos a partir de metagenomas de compostagem
inferred← citeshttps://doi.org/10.11606/t.95.2023.tde-04122023-211130openalex-snapshot
Recuperação de elementos genéticos móveis e prospecção de genes de resistência a antibióticos em dados metagenômicos de compostagem termofílica
inferred← citeshttps://doi.org/10.1177/15578666251401600openalex-snapshot
Elucidating Transitions of k -mer-Based Objects Across k -mer Sizes
inferred← citeshttps://doi.org/10.1177/24755303241242357openalex-snapshot
Whole-Genome Shotgun Metagenomic Sequencing Reveals Shifts in the Skin Microbiome and Bacteriophages of Psoriasis: An Extended Analysis of Published Data
inferred← citeshttps://doi.org/10.1186/s12859-024-05803-9openalex-snapshot
OMD Curation Toolkit: a workflow for in-house curation of public omics datasets
inferred← citeshttps://doi.org/10.1186/s12866-023-02798-wopenalex-snapshot
Composition, structure, and functional shifts of prokaryotic communities in response to co-composting of various nitrogenous green feedstocks
inferred← citeshttps://doi.org/10.1186/s12931-025-03404-5openalex-snapshot
Whole genome sequencing of the pulmonary microbiome in interstitial lung disease subtypes
inferred← citeshttps://doi.org/10.1186/s40168-023-01481-6openalex-snapshot
In silico evaluation and selection of the best 16S rRNA gene primers for use in next-generation sequencing to detect oral bacteria and archaea
inferred← citeshttps://doi.org/10.1186/s40168-024-01949-zopenalex-snapshot
MAGqual: a stand-alone pipeline to assess the quality of metagenome-assembled genomes
inferred← citeshttps://doi.org/10.1186/s40168-025-02276-7openalex-snapshot
Metagenomic profiling of airborne microbial communities from aircraft filters and face masks
inferred← citeshttps://doi.org/10.1186/s44330-025-00027-6openalex-snapshot
Assessment of rhizosphere microbial activity using optimized RNA extraction coupled with universal ribosomal RNA depletion techniques
inferred← citeshttps://doi.org/10.1242/jcs.263780openalex-snapshot
Origin and evolution of mitochondrial inner membrane composition
inferred← citeshttps://doi.org/10.12688/f1000research.51494.1openalex-snapshot
The National Ecological Observatory Network’s soil metagenomes: assembly and basic analysis
inferred← citeshttps://doi.org/10.12688/openreseurope.21147.1openalex-snapshot
Molecular tools for the study of microbiomes associated with marine animal forests
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