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A review of methods and databases for metagenomic classification and assembly

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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/pmic.201500183openalex-snapshot

A decade of metaproteomics: Where we stand and what the future holds

inferredcites →https://doi.org/10.1007/11557067openalex-snapshot

Algorithms in Bioinformatics

inferredcites →https://doi.org/10.1007/978-3-319-46326-1_10openalex-snapshot

Beyond Metabolomics: A Review of Multi-Omics-Based Approaches

inferredcites →https://doi.org/10.1007/978-3-642-33122-0_18openalex-snapshot

Succinct de Bruijn Graphs

inferredcites →https://doi.org/10.1007/s00253-013-5457-xopenalex-snapshot

Microbial genomics, transcriptomics and proteomics: new discoveries in decomposition research using complementary methods

inferredcites →https://doi.org/10.1007/s10142-015-0433-4openalex-snapshot

Insights from 20 years of bacterial genome sequencing

inferredcites →https://doi.org/10.1016/0378-1097(92)90647-7openalex-snapshot

International code of nomenclature of bacteria bacteriological code, 1990 revision

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.mib.2014.11.014openalex-snapshot

One chromosome, one contig: complete microbial genomes from long-read sequencing and assembly

inferredcites →https://doi.org/10.1016/j.mib.2014.11.016openalex-snapshot

Ten years of pan-genome analyses

inferredcites →https://doi.org/10.1016/j.ram.2016.03.008openalex-snapshot

New virus discovered in blood supply: Human hepegivirus-1 (HHpgV-1)

inferredcites →https://doi.org/10.1016/j.syapm.2015.01.001openalex-snapshot

Classifying the uncultivated microbial majority: A place for metagenomic data in the Candidatus proposal

inferredcites →https://doi.org/10.1016/j.syapm.2015.02.001openalex-snapshot

Past and future species definitions for Bacteria and Archaea

inferredcites →https://doi.org/10.1016/s0022-2836(05)80360-2openalex-snapshot

Basic Local Alignment Search Tool

inferredcites →https://doi.org/10.1016/s1286-4579(02)01637-4openalex-snapshot

Escherichia coli in disguise: molecular origins of Shigella

inferredcites →https://doi.org/10.1038/ismej.2012.94openalex-snapshot

Sizing up metatranscriptomics

inferredcites →https://doi.org/10.1038/ismej.2014.256openalex-snapshot

Microbial dark matter ecogenomics reveals complex synergistic networks in a methanogenic bioreactor

inferredcites →https://doi.org/10.1038/ismej.2014.87openalex-snapshot

Re-analysis of omics data indicates Smithella may degrade alkanes by addition to fumarate under methanogenic conditions

inferredcites →https://doi.org/10.1038/nature01099openalex-snapshot

Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii

inferredcites →https://doi.org/10.1038/nature14486openalex-snapshot

Unusual biology across a group comprising more than 15% of domain Bacteria

inferredcites →https://doi.org/10.1038/nature19094openalex-snapshot

Uncovering Earth’s virome

inferredcites →https://doi.org/10.1038/nbt.2579openalex-snapshot

Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes

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.3519openalex-snapshot

Near-optimal probabilistic RNA-seq quantification

inferredcites →https://doi.org/10.1038/ncomms11257openalex-snapshot

Fast and sensitive taxonomic classification for metagenomics with Kaiju

inferredcites →https://doi.org/10.1038/ng.1028openalex-snapshot

De novo assembly and genotyping of variants using colored de Bruijn graphs

inferredcites →https://doi.org/10.1038/nmeth.1923openalex-snapshot

Fast gapped-read alignment with Bowtie 2

inferredcites →https://doi.org/10.1038/nmeth.2604openalex-snapshot

UPARSE: highly accurate OTU sequences from microbial amplicon reads

inferredcites →https://doi.org/10.1038/nmeth.2693openalex-snapshot

Metagenomic species profiling using universal phylogenetic marker genes

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/nmicrobiol.2015.32openalex-snapshot

Metagenomics uncovers gaps in amplicon-based detection of microbial diversity

inferredcites →https://doi.org/10.1038/npjbiofilms.2016.4openalex-snapshot

A perspective on 16S rRNA operational taxonomic unit clustering using sequence similarity

inferredcites →https://doi.org/10.1038/nrg3367openalex-snapshot

Sequence assembly demystified

inferredcites →https://doi.org/10.1038/nrmicro.2016.177openalex-snapshot

Virus taxonomy in the age of metagenomics

inferredcites →https://doi.org/10.1038/nrmicro3451openalex-snapshot

Sequencing and beyond: integrating molecular 'omics' for microbial community profiling

inferredcites →https://doi.org/10.1038/sdata.2017.35openalex-snapshot

A geographically-diverse collection of 418 human gut microbiome pathway genome databases

inferredcites →https://doi.org/10.1038/srep19233openalex-snapshot

An evaluation of the accuracy and speed of metagenome analysis tools

inferredcites →https://doi.org/10.1038/srep29681openalex-snapshot

Analysis of the mouse gut microbiome using full-length 16S rRNA amplicon sequencing

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/10.1089/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/10.1089/cmb.2014.0173openalex-snapshot

A Coverage Criterion for Spaced Seeds and Its Applications to Support Vector Machine String Kernels and k -Mer Distances

inferredcites →https://doi.org/10.1093/bib/bbs054openalex-snapshot

Classification of metagenomic sequences: methods and challenges

inferredcites →https://doi.org/10.1093/bib/bbx051openalex-snapshot

Bioinformatics tools for quantitative and functional metagenome and metatranscriptome data analysis in microbes

inferredcites →https://doi.org/10.1093/bib/bby012openalex-snapshot

Bioinformatics tools for quantitative and functional metagenome and metatranscriptome data analysis in microbes

inferredcites →https://doi.org/10.1093/bioinformatics/18.3.440openalex-snapshot

PatternHunter: faster and more sensitive homology search

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/btp324openalex-snapshot

Fast and accurate short read alignment with Burrows–Wheeler transform

inferredcites →https://doi.org/10.1093/bioinformatics/btp698openalex-snapshot

Fast and accurate long-read alignment with Burrows–Wheeler transform

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/bts397openalex-snapshot

MetaCluster 5.0: a two-round binning approach for metagenomic data for low-abundance species in a noisy sample

inferredcites →https://doi.org/10.1093/bioinformatics/btt389openalex-snapshot

Scalable metagenomic taxonomy classification using a reference genome database

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/btv351openalex-snapshot

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

inferredcites →https://doi.org/10.1093/bioinformatics/btv419openalex-snapshot

Spaced seeds improve k -mer-based metagenomic classification

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/btw150openalex-snapshot

DUDes: a top-down taxonomic profiler for metagenomics

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/btw354openalex-snapshot

MultiQC: summarize analysis results for multiple tools and samples in a single report

inferredcites →https://doi.org/10.1093/bioinformatics/btw542openalex-snapshot

Higher classification sensitivity of short metagenomic reads with CLARK- S

inferredcites →https://doi.org/10.1093/bioinformatics/btx106openalex-snapshot

Pseudoalignment for metagenomic read assignment

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/jpids/piw066openalex-snapshot

Neurobrucellosis: Unexpected Answer From Metagenomic Next-Generation Sequencing

inferredcites →https://doi.org/10.1093/nar/30.11.2478openalex-snapshot

Fast algorithms for large-scale genome alignment and comparison

inferredcites →https://doi.org/10.1093/nar/gki038openalex-snapshot

The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis

inferredcites →https://doi.org/10.1093/nar/gkr1006openalex-snapshot

The International Nucleotide Sequence Database Collaboration

inferredcites →https://doi.org/10.1093/nar/gkr1178openalex-snapshot

The NCBI Taxonomy database

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/gku1062openalex-snapshot

Update on RefSeq microbial genomes resources

inferredcites →https://doi.org/10.1093/nar/gku1127openalex-snapshot

Type material in the NCBI Taxonomy Database

inferredcites →https://doi.org/10.1093/nar/gku1207openalex-snapshot

NCBI Viral Genomes Resource

inferredcites →https://doi.org/10.1093/nar/gkv1323openalex-snapshot

The International Nucleotide Sequence Database Collaboration

inferredcites →https://doi.org/10.1093/nar/gkv180openalex-snapshot

Accurate read-based metagenome characterization using a hierarchical suite of unique signatures

inferredcites →https://doi.org/10.1093/nar/gkw1070openalex-snapshot

GenBank

inferredcites →https://doi.org/10.1093/nar/gkw1248openalex-snapshot

k-SLAM: accurate and ultra-fast taxonomic classification and gene identification for large metagenomic data sets

inferredcites →https://doi.org/10.1098/rstb.2011.0065openalex-snapshot

Old and new challenges in using species diversity for assessing biodiversity

inferredcites →https://doi.org/10.1099/00207713-45-1-186openalex-snapshot

Taxonomic Note: Implementation of the Provisional Status Candidatus for Incompletely Described Procaryotes

inferredcites →https://doi.org/10.1099/ijsem.0.000778openalex-snapshot

International Code of Nomenclature of Prokaryotes

inferredcites →https://doi.org/10.1099/ijsem.0.001369openalex-snapshot

Rule 27 of the International Code of Nomenclature of prokaryotes: the basonym is not enough

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/10.1099/vir.0.000016openalex-snapshot

Methods for virus classification and the challenge of incorporating metagenomic sequence data

inferredcites →https://doi.org/10.1101/036681openalex-snapshot

Searching more genomic sequence with less memory for fast and accurate metagenomic profiling

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.113985.110openalex-snapshot

Adaptive seeds tame genomic sequence comparison

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.5969107openalex-snapshot

MEGAN analysis of metagenomic data

inferredcites →https://doi.org/10.1109/sequen.1997.666900openalex-snapshot

On the resemblance and containment of documents

inferredcites →https://doi.org/10.1111/1462-2920.13374openalex-snapshot

Methanogenic paraffin degradation proceeds via alkane addition to fumarate by ‘Smithella’ spp. mediated by a syntrophic coupling with hydrogenotrophic methanogens

inferredcites →https://doi.org/10.1111/j.1574-6968.1992.tb05316.xopenalex-snapshot

International Code of Nomenclature of Bacteria Bacteriological Code, 1990 Revision

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.03006-05openalex-snapshot

Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB

inferredcites →https://doi.org/10.1128/genomea.01085-14openalex-snapshot

Draft Genome Sequences of Three Smithella spp. Obtained from a Methanogenic Alkane-Degrading Culture and Oil Field Produced Water

inferredcites →https://doi.org/10.1128/msystems.00003-15openalex-snapshot

Open-Source Sequence Clustering Methods Improve the State Of the Art

inferredcites →https://doi.org/10.1164/rccm.201706-1097leopenalex-snapshot

Metagenomic Sequencing Detects Respiratory Pathogens in Hematopoietic Cellular Transplant Patients

inferredcites →https://doi.org/10.1186/1471-2105-10-421openalex-snapshot

BLAST+: architecture and applications

inferredcites →https://doi.org/10.1186/1471-2105-11-544openalex-snapshot

Clustering metagenomic sequences with interpolated Markov models

inferredcites →https://doi.org/10.1186/gb-2009-10-8-r85openalex-snapshot

Community-wide analysis of microbial genome sequence signatures

inferredcites →https://doi.org/10.1186/gb-2012-13-12-r122openalex-snapshot

Ray Meta: scalable de novo metagenome assembly and profiling

inferredcites →https://doi.org/10.1186/gb-2013-14-1-r2openalex-snapshot

MetAMOS: a modular and open source metagenomic assembly and analysis pipeline

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/s12864-015-1419-2openalex-snapshot

CLARK: fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers

inferredcites →https://doi.org/10.1186/s12864-015-2194-9openalex-snapshot

A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling

inferredcites →https://doi.org/10.1186/s12864-017-3501-4openalex-snapshot

SILVA, RDP, Greengenes, NCBI and OTT — how do these taxonomies compare?

inferredcites →https://doi.org/10.1186/s12866-015-0351-6openalex-snapshot

The truth about metagenomics: quantifying and counteracting bias in 16S rRNA studies

inferredcites →https://doi.org/10.1186/s12915-014-0087-zopenalex-snapshot

Reagent and laboratory contamination can critically impact sequence-based microbiome analyses

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/s13059-016-0997-xopenalex-snapshot

Mash: fast genome and metagenome distance estimation using MinHash

inferredcites →https://doi.org/10.1186/s13073-015-0235-2openalex-snapshot

Clinical metagenomic identification of Balamuthia mandrillaris encephalitis and assembly of the draft genome: the continuing case for reference genome sequencing

inferredcites →https://doi.org/10.1186/s40168-014-0066-1openalex-snapshot

VizBin - an application for reference-independent visualization and human-augmented binning of metagenomic data

inferredcites →https://doi.org/10.1186/s40168-015-0094-5openalex-snapshot

The vocabulary of microbiome research: a proposal

inferredcites →https://doi.org/10.1186/s40168-016-0154-5openalex-snapshot

Recovering complete and draft population genomes from metagenome datasets

inferredcites →https://doi.org/10.1186/s40793-017-0224-8openalex-snapshot

Towards long-read metagenomics: complete assembly of three novel genomes from bacteria dependent on a diazotrophic cyanobacterium in a freshwater lake co-culture

inferredcites →https://doi.org/10.1212/nxi.0000000000000251openalex-snapshot

Next-generation sequencing in neuropathologic diagnosis of infections of the nervous system

inferredcites →https://doi.org/10.12688/f1000research.6743.1openalex-snapshot

Re-analysis of metagenomic sequences from acute flaccid myelitis patients reveals alternatives to enterovirus D68 infection

inferredcites →https://doi.org/10.12688/f1000research.6924.1openalex-snapshot

The khmer software package: enabling efficient nucleotide sequence analysis

inferredcites →https://doi.org/10.12688/f1000research.8986.1openalex-snapshot

Bioconductor Workflow for Microbiome Data Analysis: from raw reads to community analyses

inferredcites →https://doi.org/10.1371/journal.pcbi.1002195openalex-snapshot

Accelerated Profile HMM Searches

inferredcites →https://doi.org/10.1371/journal.pcbi.1004957openalex-snapshot

MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data

inferredcites →https://doi.org/10.1371/journal.pone.0031386openalex-snapshot

Assessment of Metagenomic Assembly Using Simulated Next Generation Sequencing Data

inferredcites →https://doi.org/10.1371/journal.pone.0038581openalex-snapshot

The PhyloPythiaS Web Server for Taxonomic Assignment of Metagenome Sequences

inferredcites →https://doi.org/10.1371/journal.pone.0061217openalex-snapshot

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

inferredcites →https://doi.org/10.1371/journal.pone.0148028openalex-snapshot

Comparing Apples and Oranges?: Next Generation Sequencing and Its Impact on Microbiome Analysis

inferredcites →https://doi.org/10.1371/journal.pone.0169563openalex-snapshot

Assessment of Common and Emerging Bioinformatics Pipelines for Targeted Metagenomics

inferredcites →https://doi.org/10.1371/journal.pone.0169662openalex-snapshot

Comparing and Evaluating Metagenome Assembly Tools from a Microbiologist’s Perspective - Not Only Size Matters!

inferredcites →https://doi.org/10.1371/journal.ppat.1005325openalex-snapshot

Discovery of a Novel Human Pegivirus in Blood Associated with Hepatitis C Virus Co-Infection

inferredcites →https://doi.org/10.14806/ej.17.1.200openalex-snapshot

Cutadapt removes adapter sequences from high-throughput sequencing reads

inferredcites →https://doi.org/10.21105/joss.00027openalex-snapshot

sourmash: a library for MinHash sketching of DNA

inferredcites →https://doi.org/10.3389/fmicb.2015.00771openalex-snapshot

Primer and platform effects on 16S rRNA tag sequencing

inferredcites →https://doi.org/10.4056/sigs.4851102openalex-snapshot

Toward richer metadata for microbial sequences: replacing strain-level NCBI taxonomy taxids with BioProject, BioSample and Assembly records

inferredcites →https://doi.org/10.4137/bbi.s12462openalex-snapshot

Metagenomics: Tools and Insights for Analyzing Next-Generation Sequencing Data Derived from Biodiversity Studies

inferredcites →https://doi.org/10.48550/arxiv.1203.4802openalex-snapshot

A Reference-Free Algorithm for Computational Normalization of Shotgun Sequencing Data

inferredcites →https://doi.org/10.5598/imafungus.2011.02.02.01openalex-snapshot

One Fungus = One Name: DNA and fungal nomenclature twenty years after PCR

inferredcites →https://doi.org/10.5858/arpa.2016-0539-raopenalex-snapshot

Validation of Metagenomic Next-Generation Sequencing Tests for Universal Pathogen Detection

inferredcites →https://doi.org/10.7326/m17-0085openalex-snapshot

Presence of Human Hepegivirus-1 in a Cohort of People Who Inject Drugs

inferredcites →https://doi.org/10.7554/elife.08490openalex-snapshot

Viral dark matter and virus–host interactions resolved from publicly available microbial genomes

inferredcites →https://doi.org/10.7717/peerj-cs.104openalex-snapshot

Bracken: estimating species abundance in metagenomics data

inferredcites →https://doi.org/10.7717/peerj.1165openalex-snapshot

MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities

inferredcites →https://doi.org/10.7717/peerj.1319openalex-snapshot

Anvi’o: an advanced analysis and visualization platform for ‘omics data

inferredcites →https://doi.org/10.7717/peerj.1603openalex-snapshot

PhyloPythiaS+: a self-training method for the rapid reconstruction of low-ranking taxonomic bins from metagenomes

inferredcites →https://doi.org/10.7717/peerj.243openalex-snapshot

PhyloSift: phylogenetic analysis of genomes and metagenomes

inferredcites →https://doi.org/10.7717/peerj.593openalex-snapshot

Swarm: robust and fast clustering method for amplicon-based studies

inferredcites →https://doi.org/10.7717/peerj.603openalex-snapshot

GroopM: an automated tool for the recovery of population genomes from related metagenomes

inferredcites →https://doi.org/10.7717/peerj.675openalex-snapshot

Unexpected cross-species contamination in genome sequencing projects

What points at this work

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

inferred← citeshttps://doi.org/10.1007/s13127-019-00391-6zenodo-depositor-declared

In defence of taxonomic governance

inferred← citeshttps://doi.org/10.1002/2688-8319.12027openalex-snapshot

Preparing for the worst: Utilizing stress‐tolerant soil microbial communities to aid ecological restoration in the Anthropocene

inferred← citeshttps://doi.org/10.1002/9781394313785.ch10openalex-snapshot

The Microbiome Connection

inferred← citeshttps://doi.org/10.1002/9781683670438.mcm0008openalex-snapshot

Molecular Techniques

inferred← citeshttps://doi.org/10.1002/9781683674849.mcm0008openalex-snapshot

Molecular Techniques

inferred← citeshttps://doi.org/10.1002/alz.13076openalex-snapshot

Establishment of a consensus protocol to explore the brain pathobiome in patients with mild cognitive impairment and Alzheimer's disease

inferred← citeshttps://doi.org/10.1002/aps3.1034openalex-snapshot

Algorithms and strategies in short‐read shotgun metagenomic reconstruction of plant communities

inferred← citeshttps://doi.org/10.1002/aps3.70013openalex-snapshot

From WGS to gels: Development and testing of PCR primers targeting toxic Digitalis in support of food safety

inferred← citeshttps://doi.org/10.1002/asia.202200774openalex-snapshot

Nanopore Electrochemistry for Pathogen Detection

inferred← citeshttps://doi.org/10.1002/edn3.336openalex-snapshot

Pleistocene glacial and interglacial ecosystems inferred from ancient DNA analyses of permafrost sediments from Batagay megaslump, East Siberia

inferred← citeshttps://doi.org/10.1002/edn3.70172openalex-snapshot

Towards Comprehensive Metagenomic Recovery and Data Mining of Complex Environmental DNA Viromes

inferred← citeshttps://doi.org/10.1002/fsn3.70772openalex-snapshot

Can Metagenomic Analyses Be Used Effectively in Safe Food Production?

inferred← citeshttps://doi.org/10.1002/imt2.46openalex-snapshot

MetaTrass: A high‐quality metagenome assembler of the human gut microbiome by cobarcoding sequencing reads

inferred← citeshttps://doi.org/10.1002/mbo3.1142openalex-snapshot

Epipelagic microbiome of the Small Aral Sea: Metagenomic structure and ecological diversity

inferred← citeshttps://doi.org/10.1002/smll.202307963openalex-snapshot

High‐Throughput Screening of pH‐Dependent β‐sheet Self‐Assembling Peptide

inferred← citeshttps://doi.org/10.1002/wer.10810openalex-snapshot

Toxicity determination, pollution source delineation, and microbial diversity evaluation of PAHs‐contaminated sediments for an urban river

inferred← citeshttps://doi.org/10.1007/978-1-0716-1518-8_11openalex-snapshot

Usage of Metatranscriptomics to Understand Oral Disease

inferred← citeshttps://doi.org/10.1007/978-1-0716-2445-6_33openalex-snapshot

Reconstruction of Archaeal Genomes from Short-Read Metagenomes

inferred← citeshttps://doi.org/10.1007/978-1-0716-4180-4_32openalex-snapshot

Multivariate Analysis of Plant Microbiome Diversity Using Paleontological Statistics (PAST)

inferred← citeshttps://doi.org/10.1007/978-1-4939-8561-6_1openalex-snapshot

Identifying Bacterial Strains from Sequencing Data

inferred← citeshttps://doi.org/10.1007/978-1-4939-9721-3_12openalex-snapshot

Profiling of Active Microorganisms by Stable Isotope Probing—Metagenomics

inferred← citeshttps://doi.org/10.1007/978-3-030-38281-0_9openalex-snapshot

Meta-Pangenome: At the Crossroad of Pangenomics and Metagenomics

inferred← citeshttps://doi.org/10.1007/978-3-030-45885-0_8openalex-snapshot

Microbial Communication Networks: Sketching a Method for Analyzing the Communication of Bacteriophages Inside Environmental Communities

inferred← citeshttps://doi.org/10.1007/978-3-030-62155-1_7openalex-snapshot

Metagenomic Applications for Infectious Disease Testing in Clinical Laboratories

inferred← citeshttps://doi.org/10.1007/978-3-030-73351-3_2openalex-snapshot

Statistical and Computational Methods for Analysis of Shotgun Metagenomics Sequencing Data

inferred← citeshttps://doi.org/10.1007/978-3-030-73351-3_3openalex-snapshot

Bioinformatics Pre-Processing of Microbiome Data with An Application to Metagenomic Forensics

inferred← citeshttps://doi.org/10.1007/978-3-030-98415-1_2openalex-snapshot

Novel Methods for Studying the Structure and Function of Hot Desert Microorganisms and Their Communities

inferred← citeshttps://doi.org/10.1007/978-3-031-04881-4_25openalex-snapshot

Feature-Based Classification of Archaeal Sequences Using Compression-Based Methods

inferred← citeshttps://doi.org/10.1007/978-3-031-07179-9_4openalex-snapshot

The Use of Big Data in the Field of Food Mycology and Mycotoxins

inferred← citeshttps://doi.org/10.1007/978-3-031-75845-4_23openalex-snapshot

Deciphering the Rhizosphere Microbiome Through Metagenomics

inferred← citeshttps://doi.org/10.1007/978-3-032-14971-8_7openalex-snapshot

Metagenomic Insights into Gut Microbiota and Fish Health for Improved Food Security

inferred← citeshttps://doi.org/10.1007/978-3-319-99429-1_22openalex-snapshot

Systems Metagenomics: Applying Systems Biology Thinking to Human Microbiome Analysis

inferred← citeshttps://doi.org/10.1007/978-981-16-0889-6_1openalex-snapshot

Rhizosphere Metagenomics: Methods and Challenges

inferred← citeshttps://doi.org/10.1007/978-981-16-6005-4_8openalex-snapshot

Soil Microbial Metagenomics in Agroforestry System: Tools and Techniques

inferred← citeshttps://doi.org/10.1007/978-981-19-3696-8_12openalex-snapshot

Metagenomic Approaches for Studying Plant–Microbe Interactions

inferred← citeshttps://doi.org/10.1007/978-981-19-8210-1_7openalex-snapshot

Microbiome Data Analysis and Interpretation: Correlation Inference and Dynamic Pattern Discovery

inferred← citeshttps://doi.org/10.1007/978-981-95-8840-4_11openalex-snapshot

Synthesis and Outlook: Advancing Microbial Research

inferred← citeshttps://doi.org/10.1007/978-981-97-1844-3_1openalex-snapshot

Overview on Multi-omics Research in Microbiome Analysis

inferred← citeshttps://doi.org/10.1007/978-981-99-2981-8_12openalex-snapshot

Identifying Novel Antibiotic Resistance Genes (ARGs): Important Aspect of Metagenomic Research

inferred← citeshttps://doi.org/10.1007/s00203-023-03813-4openalex-snapshot

Tips and tools to obtain and assess mosquito viromes

inferred← citeshttps://doi.org/10.1007/s00203-026-04825-6openalex-snapshot

Genetically engineered lipases: advances in expression and upscaling for industrial applications

inferred← citeshttps://doi.org/10.1007/s00216-026-06459-5openalex-snapshot

Potential of SERS and proteomics for biomarker detection in cancer cells

inferred← citeshttps://doi.org/10.1007/s00248-021-01801-zopenalex-snapshot

Characterization of Grapevine Wood Microbiome Through a Metatranscriptomic Approach

inferred← citeshttps://doi.org/10.1007/s00248-022-02168-5openalex-snapshot

An Environmental DNA Primer for Microbial and Restoration Ecology

inferred← citeshttps://doi.org/10.1007/s00248-025-02598-xopenalex-snapshot

Land-use legacies shape soil microbial communities and nutrient cycling functions in rotational shifting cultivation fields of Northern Thailand

inferred← citeshttps://doi.org/10.1007/s00284-023-03451-5openalex-snapshot

Recent Advances in Metagenomic Approaches, Applications, and Challenges

inferred← citeshttps://doi.org/10.1007/s10453-025-09871-zopenalex-snapshot

Investigating the interplay of indoor microbial diversity with pollutant variables and human health profile in Indian slums: a metagenomic approach

inferred← citeshttps://doi.org/10.1007/s10815-024-03292-6openalex-snapshot

Methodological approaches in 16S sequencing of female reproductive tract in fertility patients: a review

inferred← citeshttps://doi.org/10.1007/s11157-019-09513-0openalex-snapshot

Next-generation sequencing and waste/wastewater treatment: a comprehensive overview

inferred← citeshttps://doi.org/10.1007/s11274-021-03168-2openalex-snapshot

The endophytome (plant-associated microbiome): methodological approaches, biological aspects, and biotech applications

inferred← citeshttps://doi.org/10.1007/s11274-026-04905-1openalex-snapshot

Fungal diversity associated with coffee leaf rust (Hemileia vastatrix) pustules based on ITS1 amplicon sequencing

inferred← citeshttps://doi.org/10.1007/s11912-024-01520-xopenalex-snapshot

Current Trends and Challenges of Microbiome Research in Prostate Cancer

inferred← citeshttps://doi.org/10.1007/s12275-020-9525-5openalex-snapshot

Microbial community analysis using high-throughput sequencing technology: a beginner’s guide for microbiologists

inferred← citeshttps://doi.org/10.1007/s12551-018-0491-7openalex-snapshot

Host and microbiome multi-omics integration: applications and methodologies

inferred← citeshttps://doi.org/10.1007/s12551-023-01124-yopenalex-snapshot

Tools for microbial single-cell genomics for obtaining uncultured microbial genomes

inferred← citeshttps://doi.org/10.1007/s12601-022-00064-0openalex-snapshot

Optimized Metavirome Analysis of Marine DNA Virus Communities for Taxonomic Profiling

inferred← citeshttps://doi.org/10.1007/s13205-025-04382-7openalex-snapshot

Adaptations, diversity, and biotechnological potential of thermophilic microorganisms: exploring culture-dependent and culture-independent approaches in extreme environments

inferred← citeshttps://doi.org/10.1007/s13258-019-00839-1openalex-snapshot

Comparison of de-novo assembly tools for plasmid metagenome analysis

inferred← citeshttps://doi.org/10.1007/s13562-025-01013-3openalex-snapshot

Advancement in rhizospheric microbial diversity analysis: an updated perspective

inferred← citeshttps://doi.org/10.1007/s13580-023-00516-zopenalex-snapshot

Effects of rhizosphere microbiome on the fruit of Cinnamomum migao H. W. Li: culture, amplicon sequencing, and metagenomic sequencing

inferred← citeshttps://doi.org/10.1007/s40291-024-00727-9openalex-snapshot

Clinical Metagenomic Next-Generation Sequencing for Diagnosis of Central Nervous System Infections: Advances and Challenges

inferred← citeshttps://doi.org/10.1007/s42770-025-01737-3openalex-snapshot

Microbial profiling of swine-waste digestates: implications for biofertilizer application

inferred← citeshttps://doi.org/10.1007/s42994-024-00178-0openalex-snapshot

Impact of database choice and confidence score on the performance of taxonomic classification using Kraken2

inferred← citeshttps://doi.org/10.1007/s43538-025-00658-xopenalex-snapshot

Progresses in microbial taxonomy research methods

inferred← citeshttps://doi.org/10.1016/b978-0-08-100596-5.21792-7openalex-snapshot

Next-Generation Sequencing

inferred← citeshttps://doi.org/10.1016/b978-0-08-100596-5.22922-3openalex-snapshot

The Role of Omic Technologies in the Study of the Human Gut Microbiome

inferred← citeshttps://doi.org/10.1016/b978-0-12-801496-7.00004-6openalex-snapshot

Clinical metagenomics for infection diagnosis

inferred← citeshttps://doi.org/10.1016/b978-0-12-816413-6.00012-5openalex-snapshot

The wound microbiome

inferred← citeshttps://doi.org/10.1016/b978-0-12-817495-1.00005-0openalex-snapshot

Metagenomic insights into the diversity and functions of microbial assemblages in lakes

inferred← citeshttps://doi.org/10.1016/b978-0-12-819265-8.00016-4openalex-snapshot

Skin Microbiome

inferred← citeshttps://doi.org/10.1016/b978-0-12-819715-8.00009-4openalex-snapshot

Maize microbiome: current insights for the sustainable agriculture

inferred← citeshttps://doi.org/10.1016/b978-0-12-819715-8.00011-2openalex-snapshot

Modern era of microbial biotechnology: opportunities and future prospects

inferred← citeshttps://doi.org/10.1016/b978-0-12-822824-1.00002-xopenalex-snapshot

Artificial intelligence and deep learning in molecular testing

inferred← citeshttps://doi.org/10.1016/b978-0-12-823991-9.00007-1openalex-snapshot

Metagenomics: a powerful lens viewing the microbial world

inferred← citeshttps://doi.org/10.1016/b978-0-323-91631-8.00001-9openalex-snapshot

Computational and statistical considerations in the analysis of metagenomic data

inferred← citeshttps://doi.org/10.1016/b978-0-323-91631-8.00016-0openalex-snapshot

Understanding the resistome of the human microbiome: A metagenomic approach

inferred← citeshttps://doi.org/10.1016/b978-0-323-96113-4.00003-2openalex-snapshot

Metagenomic approaches for understanding microbial communities in contaminated environments: Bioinformatic tools, case studies and future outlook

inferred← citeshttps://doi.org/10.1016/b978-0-323-98372-3.00001-0openalex-snapshot

Gene prediction through metagenomics

inferred← citeshttps://doi.org/10.1016/b978-0-323-99920-5.00003-2openalex-snapshot

Microbial biotechnology for wastewater treatment into circular economy

inferred← citeshttps://doi.org/10.1016/b978-0-323-99931-1.00156-2openalex-snapshot

Ancient human microbiomes

inferred← citeshttps://doi.org/10.1016/b978-0-443-13320-6.00008-1openalex-snapshot

Microbial Community Structure of the Sundarbans Mangrove Ecosystem

inferred← citeshttps://doi.org/10.1016/b978-0-443-13531-6.00002-1openalex-snapshot

Analysis of complex microbial communities in soil and wastewater treatment processes

inferred← citeshttps://doi.org/10.1016/b978-0-443-16092-9.00020-5openalex-snapshot

Current trends and approaches in clinical metagenomics

inferred← citeshttps://doi.org/10.1016/b978-0-443-21980-1.00004-8openalex-snapshot

Metagenomics: Concepts and scope

inferred← citeshttps://doi.org/10.1016/b978-0-443-22376-1.00006-4openalex-snapshot

Highly accurate long-read PacBio HiFi sequencing for microbiome and metagenomic applications

inferred← citeshttps://doi.org/10.1016/b978-0-443-23691-4.00017-8openalex-snapshot

Applications and importance of metagenomic studies for exploring rhizomicrobiome dynamics

inferred← citeshttps://doi.org/10.1016/b978-0-443-31402-5.00003-7openalex-snapshot

Technical challenges and innovations in moving HMMs forward

inferred← citeshttps://doi.org/10.1016/b978-0-443-40634-8.00026-xopenalex-snapshot

Thanatomicrobiome analysis to estimate postmortem time interval (PMI)

inferred← citeshttps://doi.org/10.1016/bs.aambs.2023.05.001openalex-snapshot

Metagenomic next generation sequencing for studying antibiotic resistance genes in the environment

inferred← citeshttps://doi.org/10.1016/bs.afnr.2024.09.007openalex-snapshot

The application of omics tools in food mycology

inferred← citeshttps://doi.org/10.1016/bs.pmbts.2022.06.027openalex-snapshot

Emerging tools for understanding the human microbiome

inferred← citeshttps://doi.org/10.1016/j.advnut.2023.09.002openalex-snapshot

Carotenoids in Health as Studied by Omics-Related Endpoints

inferred← citeshttps://doi.org/10.1016/j.bcp.2021.114590openalex-snapshot

A comprehensive time course and correlation analysis of indomethacin-induced inflammation, bile acid alterations and dysbiosis in the rat small intestine

inferred← citeshttps://doi.org/10.1016/j.biortech.2021.126455openalex-snapshot

Bioprospecting lipid-producing microorganisms: From metagenomic-assisted isolation techniques to industrial application and innovations

inferred← citeshttps://doi.org/10.1016/j.compbiolchem.2026.109015openalex-snapshot

Prediction of gene expression levels in Saccharomyces cerevisiae based on chromatin accessibility using multiple machine learning models

inferred← citeshttps://doi.org/10.1016/j.crmicr.2024.100289openalex-snapshot

Transdisciplinary approaches for the study of cyanobacteria and cyanotoxins

inferred← citeshttps://doi.org/10.1016/j.crmicr.2025.100438openalex-snapshot

Polyphasic taxonomy and genome mining of Desertivibrio insolitus gen. nov., sp. nov., a novel psychrotolerant pectin-degrading actinobacterium isolated from desert soil

inferred← citeshttps://doi.org/10.1016/j.csbj.2020.06.028openalex-snapshot

From bag-of-genes to bag-of-genomes: metabolic modelling of communities in the era of metagenome-assembled genomes

inferred← citeshttps://doi.org/10.1016/j.csbj.2021.12.035openalex-snapshot

Exploring the universal healthy human gut microbiota around the World

inferred← citeshttps://doi.org/10.1016/j.csbj.2022.09.024openalex-snapshot

NanoRTax, a real-time pipeline for taxonomic and diversity analysis of nanopore 16S rRNA amplicon sequencing data

inferred← citeshttps://doi.org/10.1016/j.csbj.2023.09.010openalex-snapshot

Uncultured prokaryotic genomes in the spotlight: An examination of publicly available data from metagenomics and single-cell genomics

inferred← citeshttps://doi.org/10.1016/j.csbj.2023.10.034openalex-snapshot

Exercise and microbiome: From big data to therapy

inferred← citeshttps://doi.org/10.1016/j.csbj.2024.04.060openalex-snapshot

Visualizing metagenomic and metatranscriptomic data: A comprehensive review

inferred← citeshttps://doi.org/10.1016/j.csbj.2024.05.025openalex-snapshot

A survey of k-mer methods and applications in bioinformatics

inferred← citeshttps://doi.org/10.1016/j.earscirev.2020.103196openalex-snapshot

The what, how and why of archaeological coprolite analysis

inferred← citeshttps://doi.org/10.1016/j.ejar.2021.02.003openalex-snapshot

Applications and challenges of DNA barcoding and metabarcoding in African fisheries

inferred← citeshttps://doi.org/10.1016/j.envint.2020.105667openalex-snapshot

Platforms for elucidating antibiotic resistance in single genomes and complex metagenomes

inferred← citeshttps://doi.org/10.1016/j.envint.2024.108869openalex-snapshot

Beyond water and soil: Air emerges as a major reservoir of human pathogens

inferred← citeshttps://doi.org/10.1016/j.envres.2024.119514openalex-snapshot

Diversity, abundance, and expression of proteorhodopsin genes in the northern South China Sea

inferred← citeshttps://doi.org/10.1016/j.envres.2026.125050openalex-snapshot

Use of metagenomics for the detection of pathogens in the environment: A scoping review

inferred← citeshttps://doi.org/10.1016/j.fawpar.2025.e00265openalex-snapshot

Detection of parasites in food and water matrices by shotgun metagenomics: A narrative review

inferred← citeshttps://doi.org/10.1016/j.fbio.2024.104541openalex-snapshot

Integrating artificial intelligence in exploring multiscale gut microbiota and diet relations for health promotion: A comprehensive review

inferred← citeshttps://doi.org/10.1016/j.fochms.2025.100309openalex-snapshot

Detection of Bacillus production strains and contaminants in food enzyme products

inferred← citeshttps://doi.org/10.1016/j.forsciint.2022.111462openalex-snapshot

Microbiome analysis: An emerging forensic investigative tool

inferred← citeshttps://doi.org/10.1016/j.fsigen.2021.102627openalex-snapshot

Integrating the human microbiome in the forensic toolkit: Current bottlenecks and future solutions

inferred← citeshttps://doi.org/10.1016/j.genrep.2026.102506openalex-snapshot

The convergence of synthetic biology and metagenomics: Current advances and future perspectives

inferred← citeshttps://doi.org/10.1016/j.hazadv.2026.101115openalex-snapshot

Environmental microbiome, resistome and plasmidome in agricultural areas with intensive poultry litter use: A metagenomic multicompartmental analysis of antimicrobial resistance gene dissemination

inferred← citeshttps://doi.org/10.1016/j.idairyj.2020.104714openalex-snapshot

The microbiota of dairy milk: A review

inferred← citeshttps://doi.org/10.1016/j.isci.2023.108538openalex-snapshot

An accurate aging clock developed from large-scale gut microbiome and human gene expression data

inferred← citeshttps://doi.org/10.1016/j.jare.2021.09.012openalex-snapshot

Metagenomics next-generation sequencing tests take the stage in the diagnosis of lower respiratory tract infections

inferred← citeshttps://doi.org/10.1016/j.jcv.2025.105877openalex-snapshot

Some assembly required: Comparison of bioinformatic pipelines for analysis of viral metagenomic sequencing from nosocomial respiratory virus outbreaks

inferred← citeshttps://doi.org/10.1016/j.jece.2025.119246openalex-snapshot

Sea cucumbers as bioindicators of pollution and sea cucumber microbiomes as markers of environmental stress: A review

inferred← citeshttps://doi.org/10.1016/j.jmb.2026.170027openalex-snapshot

PrimerBac: A Searchable Database of Taxon-specific Primers for Rapid Microbial Identification

inferred← citeshttps://doi.org/10.1016/j.jwpe.2024.105642openalex-snapshot

Microbial succession and enrichment of antibiotic resistance genes during algal-bacterial biofilm purification of aquaculture wastewater

inferred← citeshttps://doi.org/10.1016/j.lfs.2025.124114openalex-snapshot

Oral indomethacin modifies small intestine biofilms and host-microbe interaction mediators

inferred← citeshttps://doi.org/10.1016/j.lwt.2022.113787openalex-snapshot

Optimisation of working parameters for lactic acid bacteria and yeast recovery from table olive biofilms, preserving fruit integrity and reducing chloroplast recovery

inferred← citeshttps://doi.org/10.1016/j.meegid.2018.11.017openalex-snapshot

WITHDRAWN: Indel-informed bayesian analysis suggests cryptic divisions between Plasmodium knowlesi of humans and long-tailed macaques (Macaca fascicularis) in Malaysian Borneo

inferred← citeshttps://doi.org/10.1016/j.meegid.2019.103994openalex-snapshot

Indel-informed Bayesian analysis suggests cryptic population structure between Plasmodium knowlesi of humans and long-tailed macaques (Macaca fascicularis) in Malaysian Borneo

inferred← citeshttps://doi.org/10.1016/j.mimet.2025.107231openalex-snapshot

Performance of shotgun metagenomics on whole blood from patients with suspected bloodstream infection: Challenges remain

inferred← citeshttps://doi.org/10.1016/j.neo.2022.100868openalex-snapshot

A systematic review of microbiome-derived biomarkers for early colorectal cancer detection

inferred← citeshttps://doi.org/10.1016/j.neubiorev.2023.105105openalex-snapshot

A snapshot of gut microbiota data from murine models of Autism Spectrum Disorder: Still a blurred picture

inferred← citeshttps://doi.org/10.1016/j.pnpbp.2025.111276openalex-snapshot

Dysbiosis is associated with the behavioral phenotype observed in the triple-hit Wisket rat model of schizophrenia

inferred← citeshttps://doi.org/10.1016/j.sajb.2025.05.057openalex-snapshot

Optimization of a method for fermenting bee pollen: breaking down the grain wall and maximizing the release of phenolic compounds

inferred← citeshttps://doi.org/10.1016/j.scitotenv.2018.08.119openalex-snapshot

Metagenomic assessment of the microbial community and methanogenic pathways in biosolids from a municipal wastewater treatment plant in Medellín, Colombia

inferred← citeshttps://doi.org/10.1016/j.synbio.2025.07.006openalex-snapshot

Gene Surfing: An efficient and versatile tool for targeted enzyme mining in metagenomics

inferred← citeshttps://doi.org/10.1016/j.tig.2021.09.013openalex-snapshot

Advances in integrative African genomics

inferred← citeshttps://doi.org/10.1016/j.tig.2023.05.004openalex-snapshot

Current concepts, advances, and challenges in deciphering the human microbiota with metatranscriptomics

inferred← citeshttps://doi.org/10.1016/j.tma.2020.07.004openalex-snapshot

The microbiome: An emerging key player in aging and longevity

inferred← citeshttps://doi.org/10.1016/j.virusres.2023.199110openalex-snapshot

Metaviromic analyses of DNA virus community from sediments of the N-Choe stream, North India

inferred← citeshttps://doi.org/10.1016/j.watres.2020.116160openalex-snapshot

Identification of multiple potential viral diseases in a large urban center using wastewater surveillance

inferred← citeshttps://doi.org/10.1016/j.watres.2022.118363openalex-snapshot

Abundance, diversity, and host assignment of total, intracellular, and extracellular antibiotic resistance genes in riverbed sediments

inferred← citeshttps://doi.org/10.1016/j.yamp.2023.01.002openalex-snapshot

Artificial Intelligence, Bioinformatics, and Pathology

inferred← citeshttps://doi.org/10.1016/s2666-5247(22)00328-7openalex-snapshot

A case for investment in clinical metagenomics in low-income and middle-income countries

inferred← citeshttps://doi.org/10.1017/s0031182022001688openalex-snapshot

Revisiting fecal metatranscriptomics analyses of macaques with idiopathic chronic diarrhoea with a focus on trichomonad parasites

inferred← citeshttps://doi.org/10.1038/s41390-025-03942-0openalex-snapshot

Upper and lower airway microbiota across infancy and childhood

inferred← citeshttps://doi.org/10.1038/s41396-020-0665-8openalex-snapshot

Combining whole-genome shotgun sequencing and rRNA gene amplicon analyses to improve detection of microbe–microbe interaction networks in plant leaves

inferred← citeshttps://doi.org/10.1038/s41467-019-12111-xopenalex-snapshot

The fecal resistome of dairy cattle is associated with diet during nursing

inferred← citeshttps://doi.org/10.1038/s41467-022-34409-zopenalex-snapshot

De novo identification of microbial contaminants in low microbial biomass microbiomes with Squeegee

inferred← citeshttps://doi.org/10.1038/s41467-024-51957-8openalex-snapshot

Time-series sewage metagenomics distinguishes seasonal, human-derived and environmental microbial communities potentially allowing source-attributed surveillance

inferred← citeshttps://doi.org/10.1038/s41467-024-55542-xopenalex-snapshot

Potential plant extinctions with the loss of the Pleistocene mammoth steppe

inferred← citeshttps://doi.org/10.1038/s41538-023-00199-xopenalex-snapshot

‘Multi-omics’ data integration: applications in probiotics studies

inferred← citeshttps://doi.org/10.1038/s41564-022-01089-wopenalex-snapshot

Metagenomics-enabled microbial surveillance

inferred← citeshttps://doi.org/10.1038/s41592-018-0182-0openalex-snapshot

Quantifying and comparing bacterial growth dynamics in multiple metagenomic samples

inferred← citeshttps://doi.org/10.1038/s41592-021-01141-3openalex-snapshot

Challenges in benchmarking metagenomic profilers

inferred← citeshttps://doi.org/10.1038/s41592-022-01419-0openalex-snapshot

CAMI II: identifying best practices and issues for metagenomics software

inferred← citeshttps://doi.org/10.1038/s41592-022-01431-4openalex-snapshot

Critical Assessment of Metagenome Interpretation: the second round of challenges

inferred← citeshttps://doi.org/10.1038/s41592-024-02273-yopenalex-snapshot

Metabuli: sensitive and specific metagenomic classification via joint analysis of amino acid and DNA

inferred← citeshttps://doi.org/10.1038/s41592-025-02625-2openalex-snapshot

Efficient and robust search of microbial genomes via phylogenetic compression

inferred← citeshttps://doi.org/10.1038/s41596-022-00738-yopenalex-snapshot

Metagenome analysis using the Kraken software suite

inferred← citeshttps://doi.org/10.1038/s41597-020-0427-5openalex-snapshot

Gut microbiome diversity detected by high-coverage 16S and shotgun sequencing of paired stool and colon sample

inferred← citeshttps://doi.org/10.1038/s41597-024-03672-8openalex-snapshot

Benchmarking bacterial taxonomic classification using nanopore metagenomics data of several mock communities

inferred← citeshttps://doi.org/10.1038/s41597-025-06166-3openalex-snapshot

A high-resolution diel survey of surface ocean metagenomes, metatranscriptomes, and transfer RNA transcripts

inferred← citeshttps://doi.org/10.1038/s41598-020-66127-1openalex-snapshot

Shotgun sequencing of honey DNA can describe honey bee derived environmental signatures and the honey bee hologenome complexity

inferred← citeshttps://doi.org/10.1038/s41598-020-67443-2openalex-snapshot

Bladder cancer-related microbiota: examining differences in urine and tissue samples

inferred← citeshttps://doi.org/10.1038/s41598-021-00383-7openalex-snapshot

Shotgun-metagenomics based prediction of antibiotic resistance and virulence determinants in Staphylococcus aureus from periprosthetic tissue on blood culture bottles

inferred← citeshttps://doi.org/10.1038/s41598-021-82043-4openalex-snapshot

PACIFIC: a lightweight deep-learning classifier of SARS-CoV-2 and co-infecting RNA viruses

inferred← citeshttps://doi.org/10.1038/s41598-021-82726-yopenalex-snapshot

Comparison between 16S rRNA and shotgun sequencing data for the taxonomic characterization of the gut microbiota

inferred← citeshttps://doi.org/10.1038/s41598-022-07260-xopenalex-snapshot

Optimization of cerebrospinal fluid microbial DNA metagenomic sequencing diagnostics

inferred← citeshttps://doi.org/10.1038/s41598-023-33959-6openalex-snapshot

Comparison of DNA extraction methods for 16S rRNA gene sequencing in the analysis of the human gut microbiome

inferred← citeshttps://doi.org/10.1038/s41698-024-00617-7openalex-snapshot

A review of machine learning methods for cancer characterization from microbiome data

inferred← citeshttps://doi.org/10.1038/s42003-022-03114-4openalex-snapshot

BugSplit enables genome-resolved metagenomics through highly accurate taxonomic binning of metagenomic assemblies

inferred← citeshttps://doi.org/10.1038/s42003-026-09820-7openalex-snapshot

Multiple hypervariable markers improve mycobiome classification in metatranscriptome and metagenome data

inferred← citeshttps://doi.org/10.1038/s43586-024-00376-6openalex-snapshot

Analysis of metagenomic data

inferred← citeshttps://doi.org/10.1038/s43588-025-00855-0openalex-snapshot

MetaKSSD: boosting the scalability of the reference taxonomic marker database and the performance of metagenomic profiling using sketch operations

inferred← citeshttps://doi.org/10.1038/s43705-023-00338-1openalex-snapshot

Microbial gene expression analysis of healthy and cancerous esophagus uncovers bacterial biomarkers of clinical outcomes

inferred← citeshttps://doi.org/10.1042/etls20210257openalex-snapshot

Translational multi-omics microbiome research for strategies to improve cattle production and health

inferred← citeshttps://doi.org/10.1055/a-1336-1685openalex-snapshot

HPLC-UV, Metabarcoding and Genome Skims of Botanical Dietary Supplements: A Case Study in Echinacea

inferred← citeshttps://doi.org/10.1071/mf23042openalex-snapshot

Detection of RNA presence of different coronaviruses in aquatic environmental samples

inferred← citeshttps://doi.org/10.1080/1040841x.2021.1975642openalex-snapshot

Building up a clinical microbiota profiling: a quality framework proposal

inferred← citeshttps://doi.org/10.1080/1040841x.2021.2011833openalex-snapshot

Small investments with big returns: environmental genomic bioprospecting of microbial life

inferred← citeshttps://doi.org/10.1080/14737159.2025.2500655openalex-snapshot

The use of metagenomics to enhance diagnosis of encephalitis

inferred← citeshttps://doi.org/10.1080/19490976.2022.2029673openalex-snapshot

Single-cell genomics for resolution of conserved bacterial genes and mobile genetic elements of the human intestinal microbiota using flow cytometry

inferred← citeshttps://doi.org/10.1089/omi.2023.0232openalex-snapshot

Bridging the Gaps in Meta-Omic Analysis: Workflows and Reproducibility

inferred← citeshttps://doi.org/10.1093/bib/bbaa082openalex-snapshot

gutMEGA: a database of the human gut MEtaGenome Atlas

inferred← citeshttps://doi.org/10.1093/bib/bbaa105openalex-snapshot

MetaFS: Performance assessment of biomarker discovery in metaproteomics

inferred← citeshttps://doi.org/10.1093/bib/bbaa121openalex-snapshot

Comparison of microbiome samples: methods and computational challenges

inferred← citeshttps://doi.org/10.1093/bib/bbab477openalex-snapshot

iProbiotics: a machine learning platform for rapid identification of probiotic properties from whole-genome primary sequences

inferred← citeshttps://doi.org/10.1093/bib/bbac013openalex-snapshot

Computational analyses of bacterial strains from shotgun reads

inferred← citeshttps://doi.org/10.1093/bib/bbac069openalex-snapshot

A survey on the algorithm and development of multiple sequence alignment

inferred← citeshttps://doi.org/10.1093/bib/bbac216openalex-snapshot

Evaluating hierarchical machine learning approaches to classify biological databases

inferred← citeshttps://doi.org/10.1093/bib/bbac443openalex-snapshot

High-resolution shotgun metagenomics: the more data, the better?

inferred← citeshttps://doi.org/10.1093/bib/bbac594openalex-snapshot

To assemble or not to assemble: metagenomic profiling of microbially mediated biogeochemical pathways in complex communities

inferred← citeshttps://doi.org/10.1093/bib/bbaf065openalex-snapshot

A review of neural networks for metagenomic binning

inferred← citeshttps://doi.org/10.1093/bib/bbaf176openalex-snapshot

Bioinformatic approaches to blood and tissue microbiome analyses: challenges and perspectives

inferred← citeshttps://doi.org/10.1093/bib/bby012openalex-snapshot

Bioinformatics tools for quantitative and functional metagenome and metatranscriptome data analysis in microbes

inferred← citeshttps://doi.org/10.1093/bib/bby013openalex-snapshot

Recent developments of software and database in microbial genomics and functional genomics

inferred← citeshttps://doi.org/10.1093/bioadv/vbag166openalex-snapshot

DeepTaxa: a hybrid CNN-BERT framework for 16S rRNA taxonomic classification

inferred← citeshttps://doi.org/10.1093/bioinformatics/btaa458openalex-snapshot

ganon: precise metagenomics classification against large and up-to-date sets of reference sequences

inferred← citeshttps://doi.org/10.1093/bioinformatics/btac389openalex-snapshot

SNIKT: sequence-independent adapter identification and removal in long-read shotgun sequencing data

inferred← citeshttps://doi.org/10.1093/bioinformatics/btac495openalex-snapshot

Detecting DNA of novel fungal pathogens using ResNets and a curated fungi-hosts data collection

showing the first 200 of 574

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