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2025
Machine Learning Enables Alignment‐Free Distance Calculation and Phylogenetic Placement Using k‐Mer Frequencies
Molecular Ecology Resources
2025
CoverM: read alignment statistics for metagenomics
Bioinformatics
2025
Methane filtration and metabolic cooperation of microbial communities in cold seep water columns from South China Sea
Communications Biology
2025
PCVR: a pre-trained contextualized visual representation for DNA sequence classification
BMC Bioinformatics
2025
Chemoautotrophy in subzero environments and the potential for cold-adapted Rubisco
Applied and Environmental Microbiology
2024
Taxometer: Improving taxonomic classification of metagenomics contigs
Nature Communications
2024
A genome-centric view of the role of the Acropora kenti microbiome in coral health and resilience
Nature Communications
2024
Modern Taxonomy of Bacteria and Archaea
2024
Step-by-Step Metagenomics for Food Microbiome Analysis: A Detailed Review
Foods
2024
Recent toolset of metagenomics for taxonomical and functional annotation of marine associated viruses: A review
Regional Studies in Marine Science
2024
Unraveling New Frontiers and Advances in Bioinformatics
2024
The Role of Microbes and Microbiomes in Ecosystem Restoration
2024
Solving genomic puzzles: computational methods for metagenomic binning
Briefings in Bioinformatics
2024
Comparison of metagenomic and traditional methods for diagnosis of E. coli enteric infections
mBio
2024
Long-read powered viral metagenomics in the oligotrophic Sargasso Sea
Nature Communications
2024
Microbiome Drivers of Ecosystem Function
2024
Unraveling New Frontiers and Advances in Bioinformatics
2024
Methylotrophy in the Mire: direct and indirect routes for methane production in thawing permafrost
mSystems
2023
Exploring microbial functional biodiversity at the protein family level—From metagenomic sequence reads to annotated protein clusters
Frontiers in Bioinformatics
2023
Spatially and Temporally Explicit Metagenomes and Metagenome-Assembled Genomes from the Comau Fjord (42°S), Patagonia
Microbiology Resource Announcements
2023
2023 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
2023
Taxonomic Re-Classification and Expansion of the Phylum Chloroflexota Based on over 5000 Genomes and Metagenome-Assembled Genomes
Microorganisms
2023
Methods in Molecular Biology
2023
Microbiome of Finfish and Shellfish
2023
Identification of microbial metabolic functional guilds from large genomic datasets
Frontiers in Microbiology
2023
Genomic Surveillance and Pandemic Preparedness
2023
Bioinformatic approaches for studying the microbiome of fermented food
Critical Reviews in Microbiology
2023
Metagenomics to Bioremediation
2023
Closed genomes uncover a saltwater species of Candidatus Electronema and shed new light on the boundary between marine and freshwater cable bacteria
The ISME Journal
2022
Next-generation -omics approaches to drive carboxylate production by acidogenic fermentation of food waste: a review
Bioengineered
2022
Metagenomic-based surveillance systems for antibiotic resistance in non-clinical settings
Frontiers in Microbiology
2022
MetaConClust - Unsupervised Binning of Metagenomics Data using Consensus Clustering
Current Genomics
2022
Maternal inheritance of the koala gut microbiome and its compositional and functional maturation during juvenile development
Environmental Microbiology
2022
Computational analyses of bacterial strains from shotgun reads
Briefings in Bioinformatics
2022
Disentangle genus microdiversity within a complex microbial community by using a multi‐distance long‐read binning method: example of Candidatus Accumulibacter
Environmental Microbiology
2022
MetaCRS: unsupervised clustering of contigs with the recursive strategy of reducing metagenomic dataset’s complexity
BMC Bioinformatics
2022
HiCBin: binning metagenomic contigs and recovering metagenome-assembled genomes using Hi-C contact maps
Genome Biology
2022
Constructing metagenome-assembled genomes for almost all components in a real bacterial consortium for binning benchmarking
BMC Genomics
2022
High-Resolution Metagenomics of Human Gut Microbiota Generated by Nanopore and Illumina Hybrid Metagenome Assembly
Frontiers in Microbiology
2022
Accurate prediction of metagenome-assembled genome completeness by MAGISTA, a random forest model built on alignment-free intra-bin statistics
Environmental Microbiome
2022
Molecular Genetics and Genomics Tools in Biodiversity Conservation
2022
Comparative genomics reveals electron transfer and syntrophic mechanisms differentiating methanotrophic and methanogenic archaea
PLOS Biology
2022
Bioinformatics
2022
Current understanding and perspectives in anaerobic digestion based on genome-resolved metagenomic approaches
Bioresource Technology
2022
Music of metagenomics—a review of its applications, analysis pipeline, and associated tools
Functional & Integrative Genomics
2022
Microbes and Microbial Biotechnology for Green Remediation
2022
From Sequences to Graphs
2022
MetaDecoder: a novel method for clustering metagenomic contigs
Microbiome
2022
Advances in Bioremediation and Phytoremediation for Sustainable Soil Management
2021
Comprehensive Foodomics
2021
Development and characterization of an oral microbiome transplant among Australians for the treatment of dental caries and periodontal disease: A study protocol
PLOS ONE
2021
Methods in Molecular Biology
2021
Methods in Molecular Biology
2021
Comparison of microbiome samples: methods and computational challenges
Briefings in Bioinformatics
2021
Chemosynthetic and photosynthetic bacteria contribute differentially to primary production across a steep desert aridity gradient
The ISME Journal
2021
Candidatus Eremiobacterota, a metabolically and phylogenetically diverse terrestrial phylum with acid-tolerant adaptations
The ISME Journal
2021
Post-weaning shifts in microbiome composition and metabolism revealed by over 25 000 pig gut metagenome-assembled genomes
Microbial Genomics
2021
A review of computational tools for generating metagenome-assembled genomes from metagenomic sequencing data
Computational and Structural Biotechnology Journal
2021
Antibiotic resistance: Time of synthesis in a post-genomic age
Computational and Structural Biotechnology Journal
2021
A review of the resistome within the digestive tract of livestock
Journal of Animal Science and Biotechnology
2021
A primer on metagenomics and next‐generation sequencing in fish gut microbiome research
Aquaculture Research
2021
CoCoNet: an efficient deep learning tool for viral metagenome binning
Bioinformatics
2021
Trends in Free‐access Genomic Data Accelerate Advances in Cyanobacteria Taxonomy
Journal of Phycology
2020
Reference Module in Food Science
2020
Strain-level epidemiology of microbial communities and the human microbiome
Genome Medicine
2020
What Is Metagenomics Teaching Us, and What Is Missed?
Annual Review of Microbiology
2020
Transcriptome reconstruction and functional analysis of eukaryotic marine plankton communities via high-throughput metagenomics and metatranscriptomics
Genome Research
2020
Evaluating metagenomics tools for genome binning with real metagenomic datasets and CAMI datasets
BMC Bioinformatics
2020
Metagenome-assembled genome distribution and key functionality highlight importance of aerobic metabolism in Svalbard permafrost
FEMS Microbiology Ecology
2020
Metagenomics: Techniques, Applications, Challenges and Opportunities
2020
Strain-resolved microbiome sequencing reveals mobile elements that drive bacterial competition on a clinical timescale
Genome Medicine
2020
Emerging Technologies in Environmental Bioremediation
2020
Encyclopedia of Marine Biotechnology
2020
Biases in genome reconstruction from metagenomic data
PeerJ
2020
Genomic and Transcriptomic Evidence Supports Methane Metabolism in Archaeoglobi
mSystems
2020
Comparative genome-centric analysis reveals seasonal variation in the function of coral reef microbiomes
The ISME Journal
2020
Community-led, integrated, reproducible multi-omics with anvi’o
Nature Microbiology
2020
Candidatus Mcinerneyibacterium aminivorans gen. nov., sp. nov., the first representative of the candidate phylum Mcinerneyibacteriota phyl. nov. recovered from a high temperature, high salinity tertiary oil reservoir in north central Oklahoma, USA
Systematic and Applied Microbiology
2020
MetaBMF: a scalable binning algorithm for large-scale reference-free metagenomic studies
Bioinformatics
2020
The spinal cord-gut-immune axis as a master regulator of health and neurological function after spinal cord injury
Experimental Neurology
2020
Characterization of a sponge microbiome using an integrative genome-centric approach
The ISME Journal
2020
Mini-review: Advances of metagenomics research for lake microbiomes
Journal of Lake Sciences
2019
Microbial Diversity in the Genomic Era
2019
Insights into microbiome research 4: The computational analysis
Multiple Sclerosis Journal
2019
A review of methods and databases for metagenomic classification and assembly
Briefings in Bioinformatics
2019
CAMISIM: simulating metagenomes and microbial communities
Microbiome
2019
Bioinformatics applied to biotechnology: A review towards bioenergy research
Biomass and Bioenergy
2019
bin3C: exploiting Hi-C sequencing data to accurately resolve metagenome-assembled genomes
Genome Biology
2019
The application of molecular tools to study the drinking water microbiome – Current understanding and future needs
Critical Reviews in Environmental Science and Technology
2019
Contrasting Pathways for Anaerobic Methane Oxidation in Gulf of Mexico Cold Seep Sediments
mSystems
2019
Optimizing sequencing protocols for leaderboard metagenomics by combining long and short reads
Genome Biology
2019
Methods in Molecular Biology
2019
Taxonomic and Functional Characterization of the Microbial Community During Spontaneous in vitro Fermentation of Riesling Must
Frontiers in Microbiology
2019
Microbial functional diversity: From concepts to applications
Ecology and Evolution
2019
Modelling approaches for studying the microbiome
Nature Microbiology
2019
Methods in Molecular Biology
2019
Phylogenomics of an uncultivated, aerobic and thermophilic, photoheterotrophic member of Chlorobia sheds light into the evolution of the phylum Chlorobi
Computational Biology and Chemistry
2019
Bacterial fermentation and respiration processes are uncoupled in anoxic permeable sediments
Nature Microbiology
2019
Computational profiling of the gut–brain axis: microflora dysbiosis insights to neurological disorders
Briefings in Bioinformatics
2019
MetaCon: unsupervised clustering of metagenomic contigs with probabilistic k-mers statistics and coverage
BMC Bioinformatics
2019
Resources and tools for the high-throughput, multi-omic study of intestinal microbiota
Briefings in Bioinformatics
2019
MG-RAST version 4—lessons learned from a decade of low-budget ultra-high-throughput metagenome analysis
Briefings in Bioinformatics
2019
Assessing alignment-based taxonomic classification of ancient microbial DNA
PeerJ
2018
The multi-omics promise in context: from sequence to microbial isolate
Critical Reviews in Microbiology
2018
Mechanisms of Persistence of the Ammonia-Oxidizing Bacteria Nitrosomonas to the Biocide Free Nitrous Acid
Environmental Science & Technology
2018
ezTree: an automated pipeline for identifying phylogenetic marker genes and inferring evolutionary relationships among uncultivated prokaryotic draft genomes
BMC Genomics
2018
Metabolic capability and in situ activity of microorganisms in an oil reservoir
Microbiome
2018
Population Genomics
2018
Excess labile carbon promotes the expression of virulence factors in coral reef bacterioplankton
The ISME Journal
2018
Methods in Molecular Biology
2018
Metagenomic Insights into the Phylogenetic and Metabolic Diversity of the Prokaryotic Community Dwelling in Hypersaline Soils from the Odiel Saltmarshes (SW Spain)
Genes
2018
A-GAME: improving the assembly of pooled functional metagenomics sequence data
BMC Genomics
2018
Metagenomics
2018
Metagenomic binning and association of plasmids with bacterial host genomes using DNA methylation
Nature Biotechnology
2018
MetaWRAP—a flexible pipeline for genome-resolved metagenomic data analysis
Microbiome
2018
Metagenomic assembly of new (sub)polar Cyanobacteria and their associated microbiome from non-axenic cultures
Microbial Genomics
2018
Lecture Notes in Computer Science
2018
Relative abundance of ‘Candidatus Tenderia electrophaga’ is linked to cathodic current in an aerobic biocathode community
Microbial Biotechnology
2018
Multi-scale characterization of symbiont diversity in the pea aphid complex through metagenomic approaches
Microbiome
2018
Consensus assessment of the contamination level of publicly available cyanobacterial genomes
PLOS ONE
2018
Computational Biology
2018
Microbial activity response to hydrogen injection in thermophilic anaerobic digesters revealed by genome-centric metatranscriptomics
Microbiome
2018
Genomes from uncultivated prokaryotes: a comparison of metagenome-assembled and single-amplified genomes
Microbiome
2018
New Biological Insights Into How Deforestation in Amazonia Affects Soil Microbial Communities Using Metagenomics and Metagenome-Assembled Genomes
Frontiers in Microbiology
2018
Metagenomic binning reveals the functional roles of core abundant microorganisms in twelve full-scale biogas plants
Water Research
2018
Spatial Distribution and Diverse Metabolic Functions of Lignocellulose-Degrading Uncultured Bacteria as Revealed by Genome-Centric Metagenomics
Applied and Environmental Microbiology
2017
Binning_refiner: improving genome bins through the combination of different binning programs
Bioinformatics
2017
High-resolution characterization of the human microbiome
Translational Research
2017
A Metagenomic Approach to Cyanobacterial Genomics
Frontiers in Microbiology
2017
Endozoicomonas genomes reveal functional adaptation and plasticity in bacterial strains symbiotically associated with diverse marine hosts
Scientific Reports
2017
Towards enhanced and interpretable clustering/classification in integrative genomics
Nucleic Acids Research
2017
Functional Metagenomics: Tools and Applications
2017
MetaGen: reference-free learning with multiple metagenomic samples
Genome Biology
2017
Effect of antibiotics on bacterial populations: a multi-hierarchical selection process
F1000Research
2017
Bioinformatics strategies for taxonomy independent binning and visualization of sequences in shotgun metagenomics
Computational and Structural Biotechnology Journal
2017
ICoVeR – an interactive visualization tool for verification and refinement of metagenomic bins
BMC Bioinformatics
2017
CoMet: a workflow using contig coverage and composition for binning a metagenomic sample with high precision
BMC Bioinformatics
2017
Microbial strain-level population structure and genetic diversity from metagenomes
Genome Research
2017
Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea
Nature Biotechnology
2017
COCACOLA: binning metagenomic contigs using sequence COmposition, read CoverAge, CO-alignment and paired-end read LinkAge
Bioinformatics
2017
VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data
Microbiome
2017
Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life
Nature Microbiology
2017
Global Distribution Patterns and Pangenomic Diversity of the Candidate Phylum “Latescibacteria” (WS3)
Applied and Environmental Microbiology
2017
Unsupervised Binning of Metagenomic Assembled Contigs Using Improved Fuzzy C-Means Method
IEEE/ACM Transactions on Computational Biology and Bioinformatics
2017
Methane-Fueled Syntrophy through Extracellular Electron Transfer: Uncovering the Genomic Traits Conserved within Diverse Bacterial Partners of Anaerobic Methanotrophic Archaea
mBio
2017
The Brazilian Microbiome
2017
Optimizing and evaluating the reconstruction of Metagenome-assembled microbial genomes
BMC Genomics
2017
BinSanity: unsupervised clustering of environmental microbial assemblies using coverage and affinity propagation
PeerJ
2017
Towards long-read metagenomics: complete assembly of three novel genomes from bacteria dependent on a diazotrophic cyanobacterium in a freshwater lake co-culture
Standards in Genomic Sciences
2017
Shotgun metagenomics, from sampling to analysis
Nature Biotechnology
2017
Improving contig binning of metagenomic data using $$ {d}_2^S $$ oligonucleotide frequency dissimilarity
BMC Bioinformatics
2017
Organismal and spatial partitioning of energy and macronutrient transformations within a hypersaline mat
FEMS Microbiology Ecology
2017
Genomic and metagenomic technologies to explore the antibiotic resistance mobilome
Annals of the New York Academy of Sciences
2017
DNA Sequencing as a Tool to Monitor Marine Ecological Status
Frontiers in Marine Science
2017
Comparative metagenomics of hydrocarbon and methane seeps of the Gulf of Mexico
Scientific Reports
2017
Methods in Molecular Biology
2017
Atmospheric trace gases support primary production in Antarctic desert surface soil
Nature
2017
Integrated metabolism in sponge–microbe symbiosis revealed by genome-centered metatranscriptomics
The ISME Journal
2017
Interpreting Microbial Biosynthesis in the Genomic Age: Biological and Practical Considerations
Marine Drugs
2017
kmerPyramid: an interactive visualization tool for nucleobase and k-mer frequencies
Bioinformatics
2017
A probabilistic model to recover individual genomes from metagenomes
PeerJ Computer Science
2016
Accurate binning of metagenomic contigs via automated clustering sequences using information of genomic signatures and marker genes
Scientific Reports
2016
From Genomes to Phenotypes: Traitar, the Microbial Trait Analyzer
mSystems
2016
Age decreases mitochondrial motility and increases mitochondrial size in vascular smooth muscle
The Journal of Physiology
2016
Reconstruction of Bacterial and Viral Genomes from Multiple Metagenomes
Frontiers in Microbiology
2016
Methylotrophic methanogenesis discovered in the archaeal phylum Verstraetearchaeota
Nature Microbiology
2016
Permafrost Meta-Omics and Climate Change
Annual Review of Earth and Planetary Sciences
2016
Targeted metagenomics of active microbial populations with stable-isotope probing
Current Opinion in Biotechnology
2016
Metagenomics: Probing pollutant fate in natural and engineered ecosystems
Biotechnology Advances
2016
Deconvoluting simulated metagenomes: the performance of hard- and soft- clustering algorithms applied to metagenomic chromosome conformation capture (3C)
PeerJ
2016
Phylogenomic analysis of Candidatus ‘Izimaplasma’ species: free-living representatives from a Tenericutes clade found in methane seeps
The ISME Journal
2016
Identification and Resolution of Microdiversity through Metagenomic Sequencing of Parallel Consortia
Applied and Environmental Microbiology
2016
Proteomic Stable Isotope Probing Reveals Biosynthesis Dynamics of Slow Growing Methane Based Microbial Communities
Frontiers in Microbiology
2016
A Phylogenomic Analysis of the Bacterial Phylum Fibrobacteres
Frontiers in Microbiology
2016
HoloVir: A Workflow for Investigating the Diversity and Function of Viruses in Invertebrate Holobionts
Frontiers in Microbiology
2016
IMP: a pipeline for reproducible reference-independent integrated metagenomic and metatranscriptomic analyses
Genome Biology
2016
Uncovering oral Neisseria tropism and persistence using metagenomic sequencing
Nature Microbiology
2016
Metagenomic analysis and functional characterization of the biogas microbiome using high throughput shotgun sequencing and a novel binning strategy
Biotechnology for Biofuels
2016
Genome‐centric resolution of microbial diversity, metabolism and interactions in anaerobic digestion
Environmental Microbiology
2016
MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets
Bioinformatics
2016
Genome-Based Microbial Taxonomy Coming of Age
Cold Spring Harbor Perspectives in Biology
2016
High definition for systems biology of microbial communities: metagenomics gets genome-centric and strain-resolved
Current Opinion in Biotechnology
2016
Metagenomic applications in environmental monitoring and bioremediation
Journal of Industrial Microbiology and Biotechnology
2016
Recovering complete and draft population genomes from metagenome datasets
Microbiome
2016
Improved metagenome assemblies and taxonomic binning using long-read circular consensus sequence data
Scientific Reports
2016
Diversity and function of prevalent symbiotic marine bacteria in the genus Endozoicomonas
Applied Microbiology and Biotechnology
2016
Comparative Genomics of Candidate Phylum TM6 Suggests That Parasitism Is Widespread and Ancestral in This Lineage
Molecular Biology and Evolution
2016
Reading the Underlying Information From Massive Metagenomic Sequencing Data
Proceedings of the IEEE
2015
gbtools: Interactive Visualization of Metagenome Bins in R
Frontiers in Microbiology
2015
First genomic insights into members of a candidate bacterial phylum responsible for wastewater bulking
PeerJ
2015
The changing landscape of microbial biodiversity exploration and its implications for systematics
Systematic and Applied Microbiology
2015
Strain recovery from metagenomes
Nature Biotechnology
2015
Greater than the sum of their parts: characterizing plant microbiomes at the community-level
Current Opinion in Plant Biology
2015
Networks of energetic and metabolic interactions define dynamics in microbial communities
Proceedings of the National Academy of Sciences
2015
Unraveling interactions in microbial communities - from co-cultures to microbiomes
Journal of Microbiology
2015
VizBin - an application for reference-independent visualization and human-augmented binning of metagenomic data
Microbiome
2015
Advances in Microbial Physiology
2015
ConStrains identifies microbial strains in metagenomic datasets
Nature Biotechnology
2015
Metagenome-assembled genomes uncover a global brackish microbiome
Genome Biology
2015
Detection of low-abundance bacterial strains in metagenomic datasets by eigengenome partitioning
Nature Biotechnology
2015
2015 International Joint Conference on Neural Networks (IJCNN)
2015
MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities
PeerJ
2015
Exploring microbial dark matter to resolve the deep archaeal ancestry of eukaryotes
Philosophical Transactions of the Royal Society B: Biological Sciences
2015
Experimental Design and Bioinformatics Analysis for the Application of Metagenomics in Environmental Sciences and Biotechnology
Environmental Science & Technology
2015
Metagenomic Chromosome Conformation Capture (3C): techniques, applications, and challenges
F1000Research
2015
‘Metagenomics 2.0’
Environmental Microbiology Reports
2015
Ecological speciation in bacteria: reverse ecology approaches reveal the adaptive part of bacterial cladogenesis
Research in Microbiology
2015
CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes
Genome Research
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