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2019
Encyclopedia of Bioinformatics and Computational Biology
2018
Genome-Centered Metagenomics Analysis Reveals the Symbiotic Organisms Possessing Ability to Cross-Feed with Anammox Bacteria in Anammox Consortia
Environmental Science & Technology
2018
Effect of ammonia on the active microbiome and metagenome from stable full-scale digesters
Bioresource Technology
2018
Methods in Enzymology
2018
MARVEL, a Tool for Prediction of Bacteriophage Sequences in Metagenomic Bins
Frontiers in Genetics
2018
Microbiome dynamics and adaptation of expression signatures during methane production failure and process recovery
Bioresource Technology
2018
Culture- and metagenomics-enabled analyses of the Methanosphaera genus reveals their monophyletic origin and differentiation according to genome size
The ISME Journal
2018
From proteins to polysaccharides: lifestyle and genetic evolution of Coprothermobacter proteolyticus
The ISME Journal
2018
Metagenomics Reveals Microbial Diversity and Metabolic Potentials of Seawater and Surface Sediment From a Hadal Biosphere at the Yap Trench
Frontiers in Microbiology
2018
Assessment of urban microbiome assemblies with the help of targeted in silico gold standards
Biology Direct
2018
A phylogenomic and ecological analysis of the globally abundant Marine Group II archaea (Ca. Poseidoniales ord. nov.)
The ISME Journal
2018
Metagenome Sequencing of Prokaryotic Microbiota from Two Hypersaline Soils of the Odiel Salt Marshes in Huelva, Southwestern Spain
Genome Announcements
2018
Spatial Distribution and Diverse Metabolic Functions of Lignocellulose-Degrading Uncultured Bacteria as Revealed by Genome-Centric Metagenomics
Applied and Environmental Microbiology
2018
AMBER: Assessment of Metagenome BinnERs
GigaScience
2018
DNA-SIP based genome-centric metagenomics identifies key long-chain fatty acid-degrading populations in anaerobic digesters with different feeding frequencies
The ISME Journal
2018
Genomic inference of the metabolism and evolution of the archaeal phylum Aigarchaeota
Nature Communications
2018
Fast Metagenomic Binning via Hashing and Bayesian Clustering
Journal of Computational Biology
2018
Galacturonate Metabolism in Anaerobic Chemostat Enrichment Cultures: Combined Fermentation and Acetogenesis by the Dominant sp. nov. “Candidatus Galacturonibacter soehngenii”
Applied and Environmental Microbiology
2018
Draft Genome Assembly of the Sheep Scab Mite, Psoroptes ovis
Genome Announcements
2018
GraftM: a tool for scalable, phylogenetically informed classification of genes within metagenomes
Nucleic Acids Research
2018
A methanotrophic archaeon couples anaerobic oxidation of methane to Fe(III) reduction
The ISME Journal
2018
High-quality genome sequences of uncultured microbes by assembly of read clouds
Nature Biotechnology
2018
Salinity-Aided Selection of Progressive Onset Denitrifiers as a Means of Providing Nitrite for Anammox
Environmental Science & Technology
2018
Deltaproteobacteria (Pelobacter) and Methanococcoides are responsible for choline-dependent methanogenesis in a coastal saltmarsh sediment
The ISME Journal
2018
Recovering Genomics Clusters of Secondary Metabolites from Lakes Using Genome-Resolved Metagenomics
Frontiers in Microbiology
2018
Single-cell metagenomics: challenges and applications
Protein & Cell
2018
Draft Genome Sequences of Two Basal Members of the Anaerolineae Class of Chloroflexi from a Sulfidic Hot Spring
Genome Announcements
2018
Dynamics of microbial populations mediating biogeochemical cycling in a freshwater lake
Microbiome
2018
Draft Genome Sequence of a Divergent Anaerobic Member of the Chloroflexi Class Ardenticatenia from a Sulfidic Hot Spring
Genome Announcements
2018
Mother-to-Infant Microbial Transmission from Different Body Sites Shapes the Developing Infant Gut Microbiome
Cell Host & Microbe
2018
New Biological Insights Into How Deforestation in Amazonia Affects Soil Microbial Communities Using Metagenomics and Metagenome-Assembled Genomes
Frontiers in Microbiology
2018
Interspecies cross-feeding orchestrates carbon degradation in the rumen ecosystem
Nature Microbiology
2018
Consensus assessment of the contamination level of publicly available cyanobacterial genomes
PLOS ONE
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
Performance and genome-centric metagenomics of thermophilic single and two-stage anaerobic digesters treating cheese wastes
Water Research
2018
Novel Autotrophic Organisms Contribute Significantly to the Internal Carbon Cycling Potential of a Boreal Lake
mBio
2018
Genomes from uncultivated prokaryotes: a comparison of metagenome-assembled and single-amplified genomes
Microbiome
2018
Lysogeny is prevalent and widely distributed in the murine gut microbiota
The ISME Journal
2018
Genome-enabled metabolic reconstruction of dominant chemosynthetic colonizers in deep-sea massive sulfide deposits
Environmental Microbiology
2018
Inferring Ancient Relationships with Genomic Data: A Commentary on Current Practices
Integrative and Comparative Biology
2018
Methanotrophy across a natural permafrost thaw environment
The ISME Journal
2018
Optimizing body fluid recognition from microbial taxonomic profiles
Forensic Science International: Genetics
2018
Excess labile carbon promotes the expression of virulence factors in coral reef bacterioplankton
The ISME Journal
2018
Profiling microbial strains in urban environments using metagenomic sequencing data
Biology Direct
2018
IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes
Nucleic Acids Research
2018
Hidden in plain sight—highly abundant and diverse planktonic freshwater Chloroflexi
Microbiome
2018
Removal of selenate from brine using anaerobic bacteria and zero valent iron
Journal of Environmental Management
2018
Integrated multi-omic analysis of host-microbiota interactions in acute oak decline
Microbiome
2018
A metagenomics roadmap to the uncultured genome diversity in hypersaline soda lake sediments
Microbiome
2018
MEGAN-LR: new algorithms allow accurate binning and easy interactive exploration of metagenomic long reads and contigs
Biology Direct
2018
Genomic profiling of four cultivated Candidatus Nitrotoga spp. predicts broad metabolic potential and environmental distribution
The ISME Journal
2018
Bacterial contributions to delignification and lignocellulose degradation in forest soils with metagenomic and quantitative stable isotope probing
The ISME Journal
2018
Genome-centric view of carbon processing in thawing permafrost
Nature
2018
Characterization of Bathyarchaeota genomes assembled from metagenomes of biofilms residing in mesophilic and thermophilic biogas reactors
Biotechnology for Biofuels
2018
Genomic expansion of magnetotactic bacteria reveals an early common origin of magnetotaxis with lineage-specific evolution
The ISME Journal
2018
Metagenome analysis of Russian and Georgian Pyophage cocktails and a placebo-controlled safety trial of single phage versus phage cocktail in healthy Staphylococcus aureus carriers
Environmental Microbiology
2018
Relative abundance of ‘Candidatus Tenderia electrophaga’ is linked to cathodic current in an aerobic biocathode community
Microbial Biotechnology
2018
Mechanisms of Persistence of the Ammonia-Oxidizing Bacteria Nitrosomonas to the Biocide Free Nitrous Acid
Environmental Science & Technology
2018
Ongoing Transposon-Mediated Genome Reduction in the Luminous Bacterial Symbionts of Deep-Sea Ceratioid Anglerfishes
mBio
2018
Highlighting Clinical Metagenomics for Enhanced Diagnostic Decision-making: A Step Towards Wider Implementation
Computational and Structural Biotechnology Journal
2018
Dynamic membrane bioreactor (DMBR) for the treatment of landfill leachate; bioreactor's performance and metagenomic insights into microbial community evolution
Environmental Pollution
2018
Binning enables efficient host genome reconstruction in cnidarian holobionts
GigaScience
2018
Functional Microbial Features Driving Community Assembly During Seed Germination and Emergence
Frontiers in Plant Science
2018
BMC3C: binning metagenomic contigs using codon usage, sequence composition and read coverage
Bioinformatics
2018
A metagenomic analysis of the camel rumen’s microbiome identifies the major microbes responsible for lignocellulose degradation and fermentation
Biotechnology for Biofuels
2018
Metagenomic Characterization of the Human Intestinal Microbiota in Fecal Samples from STEC-Infected Patients
Frontiers in Cellular and Infection Microbiology
2018
Stable Isotope and Metagenomic Profiling of a Methanogenic Naphthalene-Degrading Enrichment Culture
Microorganisms
2018
Two identical copies of the hydrazine synthase gene clusters found in the genomes of anammox bacteria
International Biodeterioration & Biodegradation
2018
Single-cell genomics of co-sorted Nanoarchaeota suggests novel putative host associations and diversification of proteins involved in symbiosis
Microbiome
2018
Review: The application of omics to rumen microbiota function
animal
2018
Metagenomic binning reveals the functional roles of core abundant microorganisms in twelve full-scale biogas plants
Water Research
2018
On the Road to Strain-Resolved Comparative Metagenomics
mSystems
2018
Co-cultivation of the strictly anaerobic methanogen Methanosarcina barkeri with aerobic methanotrophs in an oxygen-limited membrane bioreactor
Applied Microbiology and Biotechnology
2018
Genomic Approaches in Earth and Environmental Sciences
2018
Methods in Molecular Biology
2018
MetaWRAP—a flexible pipeline for genome-resolved metagenomic data analysis
Microbiome
2018
Genome-resolved metagenomics of sugarcane vinasse bacteria
Biotechnology for Biofuels
2018
Metagenomic assembly of new (sub)polar Cyanobacteria and their associated microbiome from non-axenic cultures
Microbial Genomics
2018
Species classifier choice is a key consideration when analysing low-complexity food microbiome data
Microbiome
2018
Gammaproteobacterial methanotrophs dominate methanotrophy in aerobic and anaerobic layers of boreal lake waters
Aquatic Microbial Ecology
2018
Viral and metabolic controls on high rates of microbial sulfur and carbon cycling in wetland ecosystems
Microbiome
2018
Development and characterization of stable anaerobic thermophilic methanogenic microbiomes fermenting switchgrass at decreasing residence times
Biotechnology for Biofuels
2018
Single cell genomic and transcriptomic evidence for the use of alternative nitrogen substrates by anammox bacteria
The ISME Journal
2018
Lecture Notes in Computer Science
2018
Metabolic versatility of small archaea Micrarchaeota and Parvarchaeota
The ISME Journal
2017
A probabilistic model to recover individual genomes from metagenomes
PeerJ Computer Science
2017
Ecophysiology of Freshwater Verrucomicrobia Inferred from Metagenome-Assembled Genomes
mSphere
2017
A review of methods and databases for metagenomic classification and assembly
Briefings in Bioinformatics
2017
Comparative metagenomics of hydrocarbon and methane seeps of the Gulf of Mexico
Scientific Reports
2017
Draft Genome Sequences of Two Unclassified Bacteria, Sphingomonas sp. Strains IBVSS1 and IBVSS2, Isolated from Environmental Samples
Genome Announcements
2017
Marine Animal Microbiomes: Toward Understanding Host–Microbiome Interactions in a Changing Ocean
Frontiers in Marine Science
2017
Applied Genomics of Foodborne Pathogens
2017
From complex gut communities to minimal microbiomes via cultivation
Current Opinion in Microbiology
2017
The Brazilian Microbiome
2017
Draft Genome Sequence of Uncultured Upland Soil Cluster Gammaproteobacteria Gives Molecular Insights into High-Affinity Methanotrophy
Genome Announcements
2017
The Tale of a Neglected Energy Source: Elevated Hydrogen Exposure Affects both Microbial Diversity and Function in Soil
Applied and Environmental Microbiology
2017
Rokubacteria: Genomic Giants among the Uncultured Bacterial Phyla
Frontiers in Microbiology
2017
MetaGen: reference-free learning with multiple metagenomic samples
Genome Biology
2017
Metagenome sequencing and 98 microbial genomes from Juan de Fuca Ridge flank subsurface fluids
Scientific Data
2017
Functional Metagenomics: Tools and Applications
2017
Metagenomic binning and association of plasmids with bacterial host genomes using DNA methylation
Nature Biotechnology
2017
ICoVeR – an interactive visualization tool for verification and refinement of metagenomic bins
BMC Bioinformatics
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
Genomic and metagenomic technologies to explore the antibiotic resistance mobilome
Annals of the New York Academy of Sciences
2017
On the origins of oxygenic photosynthesis and aerobic respiration in Cyanobacteria
Science
2017
A Metagenomic Approach to Cyanobacterial Genomics
Frontiers in Microbiology
2017
Global Distribution Patterns and Pangenomic Diversity of the Candidate Phylum “Latescibacteria” (WS3)
Applied and Environmental Microbiology
2017
Bacterial colonization and succession in a newly opened hospital
Science Translational Medicine
2017
Bioinformatics strategies for taxonomy independent binning and visualization of sequences in shotgun metagenomics
Computational and Structural Biotechnology Journal
2017
Chemical dispersants enhance the activity of oil- and gas condensate-degrading marine bacteria
The ISME Journal
2017
BusyBee Web: metagenomic data analysis by bootstrapped supervised binning and annotation
Nucleic Acids Research
2017
Genomic diversification of giant enteric symbionts reflects host dietary lifestyles
Proceedings of the National Academy of Sciences
2017
A novel archaeal species belonging to Methanoculleus genus identified via de-novo assembly and metagenomic binning process in biogas reactors
Anaerobe
2017
Draft Genome Sequences of Two Unclassified Bacteria, Hydrogenophaga sp. Strains IBVHS1 and IBVHS2, Isolated from Environmental Samples
Genome Announcements
2017
Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software
Nature Methods
2017
Methane-Fueled Syntrophy through Extracellular Electron Transfer: Uncovering the Genomic Traits Conserved within Diverse Bacterial Partners of Anaerobic Methanotrophic Archaea
mBio
2017
Thermodynamically diverse syntrophic aromatic compound catabolism
Environmental Microbiology
2017
Genomics insights into production of 2-methylisoborneol and a putative cyanobactin by Planktothricoides sp. SR001
Standards in Genomic Sciences
2017
Binning_refiner: improving genome bins through the combination of different binning programs
Bioinformatics
2017
Computational profiling of the gut–brain axis: microflora dysbiosis insights to neurological disorders
Briefings in Bioinformatics
2017
MG-RAST version 4—lessons learned from a decade of low-budget ultra-high-throughput metagenome analysis
Briefings in Bioinformatics
2017
MetaSort untangles metagenome assembly by reducing microbial community complexity
Nature Communications
2017
Metagenomics of Two Severe Foodborne Outbreaks Provides Diagnostic Signatures and Signs of Coinfection Not Attainable by Traditional Methods
Applied and Environmental Microbiology
2017
Methanogenesis in oxygenated soils is a substantial fraction of wetland methane emissions
Nature Communications
2017
Mimicking microbial interactions under nitrate-reducing conditions in an anoxic bioreactor: enrichment of novel Nitrospirae bacteria distantly related to Thermodesulfovibrio
Environmental Microbiology
2017
Simulation ofDeepwater Horizonoil plume reveals substrate specialization within a complex community of hydrocarbon degraders
Proceedings of the National Academy of Sciences
2017
High-resolution characterization of the human microbiome
Translational Research
2017
BinSanity: unsupervised clustering of environmental microbial assemblies using coverage and affinity propagation
PeerJ
2017
Draft Genome Sequences of Two Unclassified Chitinophagaceae Bacteria, IBVUCB1 and IBVUCB2, Isolated from Environmental Samples
Genome Announcements
2017
CoMet: a workflow using contig coverage and composition for binning a metagenomic sample with high precision
BMC Bioinformatics
2017
Optimizing and evaluating the reconstruction of Metagenome-assembled microbial genomes
BMC Genomics
2017
Members of the Candidate Phyla Radiation are functionally differentiated by carbon- and nitrogen-cycling capabilities
Microbiome
2017
Metagenomic Analysis of Therapeutic PYO Phage Cocktails from 1997 to 2014
Viruses
2017
Giant viruses with an expanded complement of translation system components
Science
2017
A clinician's guide to microbiome analysis
Nature Reviews Gastroenterology & Hepatology
2017
Genetic adaptation of microbial populations present in high-intensity catfish production systems with therapeutic oxytetracycline treatment
Scientific Reports
2017
Atmospheric trace gases support primary production in Antarctic desert surface soil
Nature
2017
Towards enhanced and interpretable clustering/classification in integrative genomics
Nucleic Acids Research
2017
Machine learning for metagenomics: methods and tools
Metagenomics
2017
HgtSIM: a simulator for horizontal gene transfer (HGT) in microbial communities
PeerJ
2017
Chemolithotrophic processes in the bacterial communities on the surface of mineral-enriched biochars
The ISME Journal
2017
A submarine volcanic eruption leads to a novel microbial habitat
Nature Ecology & Evolution
2017
Resources and tools for the high-throughput, multi-omic study of intestinal microbiota
Briefings in Bioinformatics
2017
Vitamin and Amino Acid Auxotrophy in Anaerobic Consortia Operating under Methanogenic Conditions
mSystems
2017
Dietary energy drives the dynamic response of bovine rumen viral communities
Microbiome
2017
Metabolic network analysis reveals microbial community interactions in anammox granules
Nature Communications
2017
Benefits of Genomic Insights and CRISPR-Cas Signatures to Monitor Potential Pathogens across Drinking Water Production and Distribution Systems
Frontiers in Microbiology
2017
Shotgun metagenomics, from sampling to analysis
Nature Biotechnology
2017
High-Quality Draft Genome Sequence of “ Candidatus Methanoperedens sp.” Strain BLZ2, a Nitrate-Reducing Anaerobic Methane-Oxidizing Archaeon Enriched in an Anoxic Bioreactor
Genome Announcements
2017
A review of existing whole genome data suggests lichen mycelia may be haploid or diploid
The Bryologist
2017
Interpreting Microbial Biosynthesis in the Genomic Age: Biological and Practical Considerations
Marine Drugs
2017
Bioinformatics for NGS-based metagenomics and the application to biogas research
Journal of Biotechnology
2016
Draft Genome Sequence of a Tropical Freshwater Cyanobacterium, Limnothrix sp. Strain P13C2
Genome Announcements
2016
Integrative microbial community analysis reveals full-scale enhanced biological phosphorus removal under tropical conditions
Scientific Reports
2016
Metagenomics and Bioinformatics in Microbial Ecology: Current Status and Beyond
Microbes and environments
2016
Metagenomic survey of methanesulfonic acid (MSA) catabolic genes in an Atlantic Ocean surface water sample and in a partial enrichment
PeerJ
2016
Recovering complete and draft population genomes from metagenome datasets
Microbiome
2016
Methylotrophic methanogenesis discovered in the archaeal phylum Verstraetearchaeota
Nature Microbiology
2016
Validation of picogram- and femtogram-input DNA libraries for microscale metagenomics
PeerJ
2016
From Genomes to Phenotypes: Traitar, the Microbial Trait Analyzer
mSystems
2016
Identifying contamination with advanced visualization and analysis practices: metagenomic approaches for eukaryotic genome assemblies
PeerJ
2016
Reconstruction of Bacterial and Viral Genomes from Multiple Metagenomes
Frontiers in Microbiology
2016
High definition for systems biology of microbial communities: metagenomics gets genome-centric and strain-resolved
Current Opinion in Biotechnology
2016
Draft Genome Sequence of Uncultured SAR324 Bacterium lautmerah10, Binned from a Red Sea Metagenome
Genome Announcements
2016
Metagenomics: Probing pollutant fate in natural and engineered ecosystems
Biotechnology Advances
2016
Identification and genome reconstruction of abundant distinct taxa in microbiomes from one thermophilic and three mesophilic production-scale biogas plants
Biotechnology for Biofuels
2016
Draft Genome Sequence of the Anaerobic Ammonium-Oxidizing Bacterium “ Candidatus Brocadia sp. 40”
Genome Announcements
2016
Accurate binning of metagenomic contigs via automated clustering sequences using information of genomic signatures and marker genes
Scientific Reports
2016
Genomic characterization of the uncultured Bacteroidales family S24-7 inhabiting the guts of homeothermic animals
Microbiome
2016
Draft Genome Sequences of Two Benthic Cyanobacteria, Oscillatoriales USR 001 and Nostoc sp. MBR 210, Isolated from Tropical Freshwater Lakes
Genome Announcements
2016
COCACOLA: binning metagenomic contigs using sequence COmposition, read CoverAge, CO-alignment and paired-end read LinkAge
Bioinformatics
2016
IMP: a pipeline for reproducible reference-independent integrated metagenomic and metatranscriptomic analyses
Genome Biology
2016
Metagenomic analysis and functional characterization of the biogas microbiome using high throughput shotgun sequencing and a novel binning strategy
Biotechnology for Biofuels
2016
MetaG: a graph-based metagenomic gene analysis for big DNA data
Network Modeling Analysis in Health Informatics and Bioinformatics
2016
MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets
Bioinformatics
2016
Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses
Nature
2016
Genome-wide selective sweeps and gene-specific sweeps in natural bacterial populations
The ISME Journal
2016
2016 IEEE Symposium Series on Computational Intelligence (SSCI)
2016
A catalogue of 136 microbial draft genomes from Red Sea metagenomes
Scientific Data
2016
New Genomic Insights into “Entotheonella” Symbionts in Theonella swinhoei: Mixotrophy, Anaerobic Adaptation, Resilience, and Interaction
Frontiers in Microbiology
2016
Identification, Recovery, and Refinement of Hitherto Undescribed Population-Level Genomes from the Human Gastrointestinal Tract
Frontiers in Microbiology
2016
Insights into human evolution from ancient and contemporary microbiome studies
Current Opinion in Genetics & Development
2015
Experimental Design and Bioinformatics Analysis for the Application of Metagenomics in Environmental Sciences and Biotechnology
Environmental Science & Technology
2015
gbtools: Interactive Visualization of Metagenome Bins in R
Frontiers in Microbiology
2015
Methane metabolism in the archaeal phylum Bathyarchaeota revealed by genome-centric metagenomics
Science
2015
Anvi’o: an advanced analysis and visualization platform for ‘omics data
PeerJ