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Taxator-tk: precise taxonomic assignment of metagenomes by fast approximation of evolutionary neighborhoods

https://doi.org/10.1093/bioinformatics/btu745

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What this work says

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

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Short- and long-run determinants of sovereign debt credit ratings

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Genomic variation landscape of the human gut microbiome

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

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Metagenomic microbial community profiling using unique clade-specific marker genes

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Metagenomic species profiling using universal phylogenetic marker genes

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Binning metagenomic contigs by coverage and composition

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Taxonomic metagenome sequence assignment with structured output models

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PhymmBL expanded: confidence scores, custom databases, parallelization and more

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Use of simulated data sets to evaluate the fidelity of metagenomic processing methods

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Accurate phylogenetic classification of variable-length DNA fragments

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The Costs of Sovereign Default

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Are Government Bonds Net Wealth?

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A Unified Framework for Monetary Theory and Policy Analysis

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Taxonomic binning of metagenome samples generated by next-generation sequencing technologies

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SOrt-ITEMS: Sequence orthology based approach for improved taxonomic estimation of metagenomic sequences

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pIRS: Profile-based Illumina pair-end reads simulator

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Taxonomic classification of metagenomic shotgun sequences with CARMA3

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Metagenomic abundance estimation and diagnostic testing on species level

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Integrative analysis of environmental sequences using MEGAN4

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A RECONSIDERATION OF THE MICROFOUNDATIONS OF MONETARY THEORY

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BLAST+: architecture and applications

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pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree

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Parameters for accurate genome alignment

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MLTreeMap--accurate Maximum Likelihood placement of environmental DNA sequences into taxonomic and functional reference phylogenies.

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Reconciling taxonomy and phylogenetic inference: formalism and algorithms for describing discord and inferring taxonomic roots

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SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

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Kraken: ultrafast metagenomic sequence classification using exact alignments

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Erratum: SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

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Reconstructing the Genomic Content of Microbiome Taxa through Shotgun Metagenomic Deconvolution

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Conventional and Unconventional Monetary Policy

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Great Depressions of the Twentieth Century

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Financial Factors in Economic Fluctuations

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Models of Monetary Economies.

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Inflation and Economic Growth

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Next generation sequencing technologies and the changing landscape of phage genomics

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PhyloSift: phylogenetic analysis of genomes and metagenomes

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FOCUS: an alignment-free model to identify organisms in metagenomes using non-negative least squares

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

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inferred← citeshttps://doi.org/10.1128/mbio.01176-18openalex-snapshot

Antagonistic Pleiotropy in the Bifunctional Surface Protein FadL (OmpP1) during Adaptation of Haemophilus influenzae to Chronic Lung Infection Associated with Chronic Obstructive Pulmonary Disease

inferred← citeshttps://doi.org/10.1128/mra.01042-21openalex-snapshot

Complete Genome Sequence of Aggregatibacter actinomycetemcomitans Strain CU1000N

inferred← citeshttps://doi.org/10.1128/mra.01336-18openalex-snapshot

Complete Genome Sequences of Bacteriocin-Producing Streptococcus thermophilus Strains ST106 and ST109

inferred← citeshttps://doi.org/10.1128/mra.01641-18openalex-snapshot

Draft Genome Sequence of Porphyromonas gingivalis Strain 381 Okayama (381OKJP) Stock Culture

inferred← citeshttps://doi.org/10.1128/msphere.00300-17openalex-snapshot

Lignocellulose-Degrading Microbial Communities in Landfill Sites Represent a Repository of Unexplored Biomass-Degrading Diversity

inferred← citeshttps://doi.org/10.1128/msystems.00020-16openalex-snapshot

MetaPalette: a k -mer Painting Approach for Metagenomic Taxonomic Profiling and Quantification of Novel Strain Variation

inferred← citeshttps://doi.org/10.1128/msystems.00810-23openalex-snapshot

Fecal microbial gene transfer contributes to the high-grain diet-induced augmentation of aminoglycoside resistance in dairy cattle

inferred← citeshttps://doi.org/10.1128/spectrum.04035-23openalex-snapshot

Rich microbial and depolymerising diversity in Antarctic krill gut

inferred← citeshttps://doi.org/10.1155/2015/292950openalex-snapshot

Challenges of the Unknown: Clinical Application of Microbial Metagenomics

inferred← citeshttps://doi.org/10.1186/s12859-019-2896-0openalex-snapshot

Taxonomy based performance metrics for evaluating taxonomic assignment methods

inferred← citeshttps://doi.org/10.1186/s12864-017-4168-6openalex-snapshot

TaxMapper: an analysis tool, reference database and workflow for metatranscriptome analysis of eukaryotic microorganisms

inferred← citeshttps://doi.org/10.1186/s12866-025-03823-wopenalex-snapshot

Eradication of Helicobacter pylori reshapes gut microbiota and facilitates the evolution of antimicrobial resistance through gene transfer and genomic mutations in the gut

inferred← citeshttps://doi.org/10.1186/s12866-026-04799-xopenalex-snapshot

Metagenomic sequencing and binning reveal carbon cycling microorganisms and gene functions in park environments

inferred← citeshttps://doi.org/10.1186/s12915-015-0195-4openalex-snapshot

MetAnnotate: function-specific taxonomic profiling and comparison of metagenomes

inferred← citeshttps://doi.org/10.1186/s13059-019-1817-xopenalex-snapshot

Robust taxonomic classification of uncharted microbial sequences and bins with CAT and BAT

inferred← citeshttps://doi.org/10.1186/s13059-019-1834-9openalex-snapshot

Optimizing sequencing protocols for leaderboard metagenomics by combining long and short reads

inferred← citeshttps://doi.org/10.1186/s13059-020-01964-xopenalex-snapshot

Longitudinal survey of microbiome associated with particulate matter in a megacity

inferred← citeshttps://doi.org/10.1186/s13068-016-0565-3openalex-snapshot

Identification and genome reconstruction of abundant distinct taxa in microbiomes from one thermophilic and three mesophilic production-scale biogas plants

inferred← citeshttps://doi.org/10.1186/s13073-025-01446-4openalex-snapshot

Metronidazole response profiles of Gardnerella species are congruent with phylogenetic and comparative genomic analyses

inferred← citeshttps://doi.org/10.1186/s40168-018-0541-1openalex-snapshot

MetaWRAP—a flexible pipeline for genome-resolved metagenomic data analysis

inferred← citeshttps://doi.org/10.1186/s40168-018-0556-7openalex-snapshot

Dynamics of microbial populations mediating biogeochemical cycling in a freshwater lake

inferred← citeshttps://doi.org/10.1186/s40168-020-00861-6openalex-snapshot

Reservoirs of antimicrobial resistance genes in retail raw milk

inferred← citeshttps://doi.org/10.1186/s40168-022-01234-xopenalex-snapshot

The phyllosphere microbiome shifts toward combating melanose pathogen

inferred← citeshttps://doi.org/10.1186/s40168-024-01860-7openalex-snapshot

Genomic and induction evidence for bacteriophage contributions to sargassum-bacteria symbioses

inferred← citeshttps://doi.org/10.13023/etd.2018.121openalex-snapshot

Novel Computational Methods for Sequencing Data Analysis

inferred← citeshttps://doi.org/10.1371/journal.pntd.0010815openalex-snapshot

Shotgun metagenomics of fecal samples from children in Peru reveals frequent complex co-infections with multiple Campylobacter species

inferred← citeshttps://doi.org/10.1371/journal.pone.0140644openalex-snapshot

ARK: Aggregation of Reads by K-Means for Estimation of Bacterial Community Composition

inferred← citeshttps://doi.org/10.1371/journal.ppat.1014649openalex-snapshot

A bacterial pangenome association study identifies a role for polyamine metabolism and alkaline tolerance in middle ear infections

inferred← citeshttps://doi.org/10.14264/uql.2020.723openalex-snapshot

Enrichment and characterisation of novel microorganisms involved in the nitrogen cycle

inferred← citeshttps://doi.org/10.21203/rs.3.rs-3010645/v1openalex-snapshot

Infant age negatively correlates with the overall load of gut resistome reflecting modifications of carbohydrate metabolism during early life

inferred← citeshttps://doi.org/10.3389/fcimb.2021.744742openalex-snapshot

Transition of Serotype 35B Pneumococci From Commensal to Prevalent Virulent Strain in Children

inferred← citeshttps://doi.org/10.3389/fevo.2020.00142openalex-snapshot

Complete Mitochondrial Genomes and Bacterial Metagenomic Data From Two Species of Parasitic Avian Nasal-Mites (Rhinonyssidae: Mesostigmata)

inferred← citeshttps://doi.org/10.3389/fevo.2023.1126149openalex-snapshot

DNA virome composition of two sympatric wild felids, bobcat (Lynx rufus) and puma (Puma concolor) in Sonora, Mexico

inferred← citeshttps://doi.org/10.3389/fmars.2017.00107openalex-snapshot

DNA Sequencing as a Tool to Monitor Marine Ecological Status

inferred← citeshttps://doi.org/10.3389/fmars.2023.1177401openalex-snapshot

Exploring the plankton bacteria diversity and distribution patterns in the surface water of northwest pacific ocean by metagenomic methods

inferred← citeshttps://doi.org/10.3389/fmicb.2015.01069openalex-snapshot

Recovering full-length viral genomes from metagenomes

inferred← citeshttps://doi.org/10.3389/fmicb.2017.00809openalex-snapshot

A Metagenomic Approach to Cyanobacterial Genomics

inferred← citeshttps://doi.org/10.3389/fmicb.2019.01779openalex-snapshot

Genome Sequences of a Plant Beneficial Synthetic Bacterial Community Reveal Genetic Features for Successful Plant Colonization

inferred← citeshttps://doi.org/10.3389/fmicb.2021.642543openalex-snapshot

Patterns of Microbiome Variation Among Infrapopulations of Permanent Bloodsucking Parasites

inferred← citeshttps://doi.org/10.3389/fmicb.2022.708335openalex-snapshot

Potential Use of Microbial Community Genomes in Various Dimensions of Agriculture Productivity and Its Management: A Review

inferred← citeshttps://doi.org/10.3389/fmicb.2023.1125709openalex-snapshot

Monthly dynamics of microbial communities and variation of nitrogen-cycling genes in an industrial-scale expanded granular sludge bed reactor

inferred← citeshttps://doi.org/10.3389/fmicb.2025.1516033openalex-snapshot

Riverine antibiotic resistome along an anthropogenic gradient

inferred← citeshttps://doi.org/10.3389/fmicb.2025.1652652openalex-snapshot

The hidden nitrogen nexus: stochastic assembly and linear gene synergies drive urban park microbial networks

inferred← citeshttps://doi.org/10.3389/fphys.2022.1072893openalex-snapshot

Gut microbiota contributes to lignocellulose deconstruction and nitrogen fixation of the larva of Apriona swainsoni

inferred← citeshttps://doi.org/10.3389/fsufs.2022.886987openalex-snapshot

Metagenomics: A Tool for Exploring Key Microbiome With the Potentials for Improving Sustainable Agriculture

inferred← citeshttps://doi.org/10.3389/fsufs.2024.1499973openalex-snapshot

Synergistic integration of remote sensing and soil metagenomics data: advancing precision agriculture through interdisciplinary approaches

inferred← citeshttps://doi.org/10.3390/jmse12101796openalex-snapshot

Seasonal Surges in Bacterial Diversity along the Coastal Waters of the Eastern Arabian Sea

inferred← citeshttps://doi.org/10.3390/microorganisms11071702openalex-snapshot

Potential of Microbial Communities to Perform Dehalogenation Processes in Natural and Anthropogenically Modified Environments—A Metagenomic Study

inferred← citeshttps://doi.org/10.3390/microorganisms9081734openalex-snapshot

Genome-Resolved Metagenomic Analyses Reveal the Presence of a Putative Bacterial Endosymbiont in an Avian Nasal Mite (Rhinonyssidae; Mesostigmata)

inferred← citeshttps://doi.org/10.37501/soilsa/163080openalex-snapshot

Metagenomics approaches to understanding soil health in environmental research - a review

inferred← citeshttps://doi.org/10.53846/goediss-8565openalex-snapshot

Metagenomic approaches to discover lipolytic enzymes

inferred← citeshttps://doi.org/10.5772/intechopen.1012591openalex-snapshot

Advanced Bioinformatics Explores Mycological Composition and Function from Metatranscriptomic Sequencing

inferred← citeshttps://doi.org/10.6084/m9.figshare.26756839openalex-snapshot

Additional file 1 of Genomic and induction evidence for bacteriophage contributions to sargassum-bacteria symbioses

inferred← citeshttps://doi.org/10.6084/m9.figshare.26756842openalex-snapshot

Additional file 2 of Genomic and induction evidence for bacteriophage contributions to sargassum-bacteria symbioses

inferred← citeshttps://doi.org/10.6084/m9.figshare.26756845openalex-snapshot

Additional file 3 of Genomic and induction evidence for bacteriophage contributions to sargassum-bacteria symbioses

inferred← citeshttps://doi.org/10.6084/m9.figshare.26756848openalex-snapshot

Additional file 4 of Genomic and induction evidence for bacteriophage contributions to sargassum-bacteria symbioses

inferred← citeshttps://doi.org/10.6084/m9.figshare.26756851openalex-snapshot

Additional file 5 of Genomic and induction evidence for bacteriophage contributions to sargassum-bacteria symbioses

inferred← citeshttps://doi.org/10.6084/m9.figshare.26756854openalex-snapshot

Additional file 6 of Genomic and induction evidence for bacteriophage contributions to sargassum-bacteria symbioses

inferred← citeshttps://doi.org/10.6084/m9.figshare.26756857openalex-snapshot

Additional file 7 of Genomic and induction evidence for bacteriophage contributions to sargassum-bacteria symbioses

inferred← citeshttps://doi.org/10.6084/m9.figshare.26756860openalex-snapshot

Additional file 8 of Genomic and induction evidence for bacteriophage contributions to sargassum-bacteria symbioses

inferred← citeshttps://doi.org/10.6084/m9.figshare.26756863openalex-snapshot

Additional file 9 of Genomic and induction evidence for bacteriophage contributions to sargassum-bacteria symbioses

inferred← citeshttps://doi.org/10.71548/21081openalex-snapshot

Methodology and Application of Metagenomics for the Characterization of Bacterial Populations in Aquatic Environments

inferred← citeshttps://doi.org/10.7287/peerj-cs.117v0.1/reviews/1openalex-snapshot

Peer Review #1 of "A probabilistic model to recover individual genomes from metagenomes (v0.1)"

inferred← citeshttps://doi.org/10.7287/peerj-cs.117v0.1/reviews/2openalex-snapshot

Peer Review #2 of "A probabilistic model to recover individual genomes from metagenomes (v0.1)"

inferred← citeshttps://doi.org/10.7287/peerj-cs.117v0.1/reviews/3openalex-snapshot

Peer Review #3 of "A probabilistic model to recover individual genomes from metagenomes (v0.1)"

inferred← citeshttps://doi.org/10.7287/peerj-cs.117v0.2/reviews/1openalex-snapshot

Peer Review #1 of "A probabilistic model to recover individual genomes from metagenomes (v0.2)"

inferred← citeshttps://doi.org/10.7287/peerj-cs.117v0.2/reviews/2openalex-snapshot

Peer Review #2 of "A probabilistic model to recover individual genomes from metagenomes (v0.2)"

inferred← citeshttps://doi.org/10.7287/peerj-cs.117v0.2/reviews/3openalex-snapshot

Peer Review #3 of "A probabilistic model to recover individual genomes from metagenomes (v0.2)"

inferred← citeshttps://doi.org/10.7287/peerj.preprints.2626v1openalex-snapshot

A probabilistic model to recover genomes in shotgun metagenomics

inferred← citeshttps://doi.org/10.7717/peerj-cs.117openalex-snapshot

A probabilistic model to recover individual genomes from metagenomes

inferred← citeshttps://doi.org/10.7717/peerj.1603openalex-snapshot

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

inferred← citeshttps://doi.org/10.7717/peerj.6160openalex-snapshot

Identifying accurate metagenome and amplicon software via a meta-analysis of sequence to taxonomy benchmarking studies

inferred← citeshttps://doi.org/10.7717/peerj.9688openalex-snapshot

Evaluation of computational methods for human microbiome analysis using simulated data

Editorial review for independent work. ICSAC — the Institute for Complexity Science and Advanced Computing — runs a structured editorial panel for researchers publishing outside journals, and publishes on CiteStamp rails. Submission is free and goes through ORCID: icsacinstitute.org/submit.