Citation sources

Updated weekly. Details via Crossref
Crossref Scopus Google Scholar
512 369 Search
2023
Host species and microplastics differentiate the crop root endophytic antibiotic resistome
Journal of Hazardous Materials
2023
Metagenomics revealing molecular profiles of microbial community structure and metabolic capacity in Bamucuo lake, Tibet
Environmental Research
2023
Longitudinal metatranscriptomic sequencing of Southern California wastewater representing 16 million people from August 2020–21 reveals widespread transcription of antibiotic resistance genes
Water Research
2023
Anaerobic mercury methylators inhabit sinking particles of oxic water columns
Water Research
2022
Expressions of resistome is linked to the key functions and stability of active rumen microbiome
Animal Microbiome
2022
Meta-Analysis and Validation of a Colorectal Cancer Risk Prediction Model Using Deep Sequenced Fecal Metagenomes
Cancers
2022
A unique gut microbiota signature in pulmonary arterial hypertension: A pilot study
Pulmonary Circulation
2022
Optimisation and Application of a Novel Method to Identify Bacteriophages in Maternal Milk and Infant Stool Identifies Host-Phage Communities Within Preterm Infant Gut
Frontiers in Pediatrics
2022
Multi-Omics Strategies for Investigating the Microbiome in Toxicology Research
Toxicological Sciences
2022
Cobamide Sharing Is Predicted in the Human Skin Microbiome
mSystems
2022
Shotgun metagenomic sequencing of bulk tank milk filters reveals the role of Moraxellaceae and Enterobacteriaceae as carriers of antimicrobial resistance genes
Food Research International
2022
The Core Human Microbiome: Does It Exist and How Can We Find It? A Critical Review of the Concept
Nutrients
2022
Demeter: A Fast and Energy-Efficient Food Profiler Using Hyperdimensional Computing in Memory
IEEE Access
2022
Streptococcus bovis-bacteremia: subspecies distribution and association with colorectal cancer: a retrospective cohort study
Epidemiology and Infection
2022
A Wipe-Based Stool Collection and Preservation Kit for Microbiome Community Profiling
Frontiers in Immunology
2022
Disulfiram ameliorates nonalcoholic steatohepatitis by modulating the gut microbiota and bile acid metabolism
Nature Communications
2022
Ancient oral microbiomes support gradual Neolithic dietary shifts towards agriculture
Nature Communications
2022
MTD: a unique pipeline for host and meta-transcriptome joint and integrative analyses of RNA-seq data
Briefings in Bioinformatics
2022
Microbiota dynamics in a randomized trial of gut decontamination during allogeneic hematopoietic cell transplantation
JCI Insight
2022
Metagenomic Analysis of the Pediatric-Onset Multiple Sclerosis Gut Microbiome
Neurology
2022
Evaluation of sensitivity and specificity in RNA-Seq-based detection of grapevine viral pathogens
Journal of Virological Methods
2022
Metagenomic Sequencing of the Gallbladder Microbiome: Bacterial Diversity Does Not Vary by Surgical Pathology
Journal of Gastrointestinal Surgery
2022
The Chronic Wound Phageome: Phage Diversity and Associations with Wounds and Healing Outcomes
Microbiology Spectrum
2022
Improved gut microbiome recovery following drug therapy is linked to abundance and replication of probiotic strains
Gut Microbes
2022
microbioTA: an atlas of the microbiome in multiple disease tissues of Homo sapiens and Mus musculus
Nucleic Acids Research
2022
Genomic ancestry, diet and microbiomes of Upper Palaeolithic hunter-gatherers from San Teodoro cave
Communications Biology
2022
Species-resolved sequencing of low-biomass or degraded microbiomes using 2bRAD-M
Genome Biology
2022
Gut dysbiosis and inflammatory blood markers precede HIV with limited changes after early seroconversion
eBioMedicine
2022
Technical note: overcoming host contamination in bovine vaginal metagenomic samples with nanopore adaptive sequencing
Journal of Animal Science
2022
Benchmarking taxonomic classifiers with Illumina and Nanopore sequence data for clinical metagenomic diagnostic applications
Microbial Genomics
2022
Genetic Elements Orchestrating Lactobacillus crispatus Glycogen Metabolism in the Vagina
International Journal of Molecular Sciences
2022
Symbiotic bacteria of the gall-inducing mite Fragariocoptes setiger (Eriophyoidea) and phylogenomic resolution of the eriophyoid position among Acari
Scientific Reports
2022
HAYSTAC: A Bayesian framework for robust and rapid species identification in high-throughput sequencing data
PLOS Computational Biology
2022
Rare transmission of commensal and pathogenic bacteria in the gut microbiome of hospitalized adults
Nature Communications
2022
Metagenomic Assessment of the Pathogenic Risk of Microorganisms in Sputum of Postoperative Patients With Pulmonary Infection
Frontiers in Cellular and Infection Microbiology
2022
Impact of host age on viral and bacterial communities in a waterbird population
The ISME Journal
2022
Recovery of metagenome-assembled genomes from the phyllosphere of 110 rice genotypes
Scientific Data
2022
Developing whole cell standards for the microbiome field
Microbiome
2022
Increasing prediction performance of colorectal cancer disease status using random forests classification based on metagenomic shotgun sequencing data
Synthetic and Systems Biotechnology
2022
Adaptive sampling during sequencing reveals the origins of the bovine reproductive tract microbiome across reproductive stages and sexes
Scientific Reports
2022
Phyllosphere-associated microbiota in built environment: Do they have the potential to antagonize human pathogens?
Journal of Advanced Research
2022
The standardisation of the approach to metagenomic human gut analysis: from sample collection to microbiome profiling
Scientific Reports
2022
Antibiotic resistomes in water supply reservoirs sediments of central China: main biotic drivers and distribution pattern
Environmental Science and Pollution Research
2022
Short- and long-read metagenomics of urban and rural South African gut microbiomes reveal a transitional composition and undescribed taxa
Nature Communications
2022
WGA-LP: a pipeline for whole genome assembly of contaminated reads
Bioinformatics
2022
Anatomy promotes neutral coexistence of strains in the human skin microbiome
Cell Host & Microbe
2022
Influences of Helicobacter pylori infection on diversity, heterogeneity, and composition of human gastric microbiomes across stages of gastric cancer development
Helicobacter
2022
Lake Erie field trials to advance autonomous monitoring of cyanobacterial harmful algal blooms
Frontiers in Marine Science
2022
Dose-dependent impact of enrofloxacin on broiler chicken gut resistome is mitigated by synbiotic application
Frontiers in Microbiology
2022
MetaTrass: A high‐quality metagenome assembler of the human gut microbiome by cobarcoding sequencing reads
iMeta
2022
Functional response to a microbial synbiotic in the gastrointestinal system of children: a randomized clinical trial
Pediatric Research
2022
Application of young maize plant residues alters the microbiome composition and its functioning in a soil under conservation agriculture: a metagenomics study
Archives of Microbiology
2022
Metagenomic DNA sequencing for semi-quantitative pathogen detection from urine: a prospective, laboratory-based, proof-of-concept study
The Lancet Microbe
2022
Longitudinal and Comparative Analysis of Gut Microbiota of Tunisian Newborns According to Delivery Mode
Frontiers in Microbiology
2022
An assessment of resistome and mobilome in wastewater treatment plants through temporal and spatial metagenomic analysis
Water Research
2022
Finding the right fit: evaluation of short-read and long-read sequencing approaches to maximize the utility of clinical microbiome data
Microbial Genomics
2022
Shotgun Metagenomics Study Suggests Alteration in Sulfur Metabolism and Oxidative Stress in Children with Autism and Improvement after Microbiota Transfer Therapy
International Journal of Molecular Sciences
2022
Nitrogen Fertilizer Application Alters the Root Endophyte Bacterial Microbiome in Maize Plants, but Not in the Stem or Rhizosphere Soil
Microbiology Spectrum
2022
Early Life Short-Term Exposure to Polychlorinated Biphenyl 126 in Mice Leads to Metabolic Dysfunction and Microbiota Changes in Adulthood
International Journal of Molecular Sciences
2022
Significant compositional and functional variation reveals the patterns of gut microbiota evolution among the widespread Asian honeybee populations
Frontiers in Microbiology
2022
Alterations of the Composition and Neurometabolic Profile of Human Gut Microbiota in Major Depressive Disorder
Biomedicines
2022
Carbendazim shapes microbiome and enhances resistome in the earthworm gut
Microbiome
2022
The gut microbiome, mild cognitive impairment, and probiotics: A randomized clinical trial in middle-aged and older adults
Clinical Nutrition
2022
Exploration of the Potential Relationship Between Gut Microbiota Remodeling Under the Influence of High-Protein Diet and Crohn’s Disease
Frontiers in Microbiology
2022
Metagenomics to characterize sediment microbial biodiversity associated with fishing exposure within the Stellwagen Bank National Marine Sanctuary
Scientific Reports
2022
Generation and application of pseudo–long reads for metagenome assembly
GigaScience
2022
Metabolomic, Lipidomic, Transcriptomic, and Metagenomic Analyses in Mice Exposed to PFOS and Fed Soluble and Insoluble Dietary Fibers
Environmental Health Perspectives
2022
The genus Serratia revisited by genomics
Nature Communications
2022
Meta-analysis of microbiome association networks reveal patterns of dysbiosis in diseased microbiomes
Scientific Reports
2022
Saliva and Lung Microbiome Associations with Electronic Cigarette Use and Smoking
Cancer Prevention Research
2022
Characterization of interactions of dietary cholesterol with the murine and human gut microbiome
Nature Microbiology
2022
Incipient Sympatric Speciation and Evolution of Soil Bacteria Revealed by Metagenomic and Structured Non-Coding RNAs Analysis
Biology
2022
Mutual Exclusion of Methanobrevibacter Species in the Human Gut Microbiota Facilitates Directed Cultivation of a Candidatus Methanobrevibacter Intestini Representative
Microbiology Spectrum
2022
Two microbiota subtypes identified in irritable bowel syndrome with distinct responses to the low FODMAP diet
Gut
2022
Design, construction, and in vivo augmentation of a complex gut microbiome
Cell
2022
Response of soil protozoa to acid mine drainage in a contaminated terrace
Journal of Hazardous Materials
2022
A mouse model of occult intestinal colonization demonstrating antibiotic-induced outgrowth of carbapenem-resistant Enterobacteriaceae
Microbiome
2022
Response of soil microbial compositional and functional heterogeneity to grazing exclusion in alpine shrub and meadows in the Qinghai–Tibet Plateau
Frontiers in Microbiology
2022
Enhanced survival of multi-species biofilms under stress is promoted by low-abundant but antimicrobial-resistant keystone species
Journal of Hazardous Materials
2022
Shared signatures and divergence in skin microbiomes of children with atopic dermatitis and their caregivers
Journal of Allergy and Clinical Immunology
2022
Evaluation of the kitchen microbiome and food safety behaviors of predominantly low-income families
Frontiers in Microbiology
2022
Auxiliary Metabolic Gene Functions in Pelagic and Benthic Viruses of the Baltic Sea
Frontiers in Microbiology
2022
Antimicrobial Resistance in Aquaculture Environments: Unravelling the Complexity and Connectivity of the Underlying Societal Drivers
Environmental Science & Technology
2022
Plastisphere showing unique microbiome and resistome different from activated sludge
Science of The Total Environment
2022
Antibiotic-Induced Treatments Reveal Stress-Responsive Gene Expression in the Endangered Lichen Lobaria pulmonaria
Journal of Fungi
2022
Metaproteomics as a tool for studying the protein landscape of human-gut bacterial species
PLOS Computational Biology
2022
Variations in Bacterial Communities and Antibiotic Resistance Genes Across Diverse Recycled and Surface Water Irrigation Sources in the Mid-Atlantic and Southwest United States: A CONSERVE Two-Year Field Study
Environmental Science & Technology
2022
Bacterial low-abundant taxa are key determinants of a healthy airway metagenome in the early years of human life
Computational and Structural Biotechnology Journal
2022
Targeted suppression of human IBD-associated gut microbiota commensals by phage consortia for treatment of intestinal inflammation
Cell
2022
Function-Based Rhizosphere Assembly along a Gradient of Desiccation in the Former Aral Sea
mSystems
2022
RiboTaxa: combined approaches for rRNA genes taxonomic resolution down to the species level from metagenomics data revealing novelties
NAR Genomics and Bioinformatics
2022
Host diet shapes functionally differentiated gut microbiomes in sympatric speciation of blind mole rats in Upper Galilee, Israel
Frontiers in Microbiology
2022
Distribution of soil viruses across China and their potential role in phosphorous metabolism
Environmental Microbiome
2022
Arabinoxylan and Pectin Metabolism in Crohn’s Disease Microbiota: An In Silico Study
International Journal of Molecular Sciences
2022
Inhalable Antibiotic Resistome from Wastewater Treatment Plants to Urban Areas: Bacterial Hosts, Dissemination Risks, and Source Contributions
Environmental Science & Technology
2022
Evaluation of Host Depletion and Extraction Methods for Shotgun Metagenomic Analysis of Bovine Vaginal Samples
Microbiology Spectrum
2022
Changes in systolic blood pressure, postprandial glucose, and gut microbial composition following mango consumption in individuals with overweight and obesity
Applied Physiology, Nutrition, and Metabolism
2022
Evolution of phenotypic variance in response to a novel hot environment
Molecular Ecology
2022
AGAMEMNON: an Accurate metaGenomics And MEtatranscriptoMics quaNtificatiON analysis suite
Genome Biology
2022
Early Life Polychlorinated Biphenyl 126 Exposure Disrupts Gut Microbiota and Metabolic Homeostasis in Mice Fed with High-Fat Diet in Adulthood
Metabolites
2022
Metagenomics Approaches for Improving Food Safety: A Review
Journal of Food Protection
2022
Emu: species-level microbial community profiling of full-length 16S rRNA Oxford Nanopore sequencing data
Nature Methods
2022
Anthropogenic impact accelerates antibiotic resistome diversity in the mangrove sediment of Indian Sundarban
Chemosphere
2022
The swine enteric virome in a commercial production system and its association with neonatal diarrhea
Veterinary Microbiology
2022
Fungal biodiversity in commercial table olive packages
Food Microbiology
2022
The Carbon Footprint of Bioinformatics
Molecular Biology and Evolution
2022
Comparison of the Respiratory Resistomes and Microbiota in Children Receiving Short versus Standard Course Treatment for Community-Acquired Pneumonia
mBio
2022
Multi-kingdom microbiota analyses identify bacterial–fungal interactions and biomarkers of colorectal cancer across cohorts
Nature Microbiology
2022
Incorporating genome‐based phylogeny and functional similarity into diversity assessments helps to resolve a global collection of human gut metagenomes
Environmental Microbiology
2022
MinION™ Nanopore Sequencing of Skin Microbiome 16S and 16S-23S rRNA Gene Amplicons
Frontiers in Cellular and Infection Microbiology
2022
Phylogeny-Aware Analysis of Metagenome Community Ecology Based on Matched Reference Genomes while Bypassing Taxonomy
mSystems
2022
PathoLive—Real-Time Pathogen Identification from Metagenomic Illumina Datasets
Life
2022
High-quality metagenome-assembled genomes from proximal colonic microbiomes of synbiotic-treated korean native black pigs reveal changes in functional capacity
Scientific Reports
2022
Prospective study of oral microbiome and gastric cancer risk among Asian, African American and European American populations
International Journal of Cancer
2022
Drinking water chlorination has minor effects on the intestinal flora and resistomes of Bangladeshi children
Nature Microbiology
2022
Microbial functional genes are driven by gradients in sediment stoichiometry, oxygen, and salinity across the Baltic benthic ecosystem
Microbiome
2022
Cerebral Intraparenchymal Hemorrhage Changes Patients’ Gut Bacteria Composition and Function
Frontiers in Cellular and Infection Microbiology
2022
Insights into the Unique Lung Microbiota Profile of Pulmonary Tuberculosis Patients Using Metagenomic Next-Generation Sequencing
Microbiology Spectrum
2022
Exploring the universal healthy human gut microbiota around the World
Computational and Structural Biotechnology Journal
2022
Potential metabolic and genetic interaction among viruses, methanogen and methanotrophic archaea, and their syntrophic partners
ISME Communications
2022
Microalgae and Bacteria Interaction—Evidence for Division of Diligence in the Alga Microbiota
Microbiology Spectrum
2022
Patient-Reported Outcomes Correlate With Microbial Community Composition Independent of Mucosal Inflammation in Pediatric Inflammatory Bowel Disease
Inflammatory Bowel Diseases
2022
Metagenomic Sequencing for the Diagnosis of Plasmodium spp. with Different Levels of Parasitemia in EDTA Blood of Malaria Patients—A Proof-of-Principle Assessment
International Journal of Molecular Sciences
2022
Differential Oral Microbial Input Determines Two Microbiota Pneumo‐Types Associated with Health Status
Advanced Science
2022
Spatiotemporal Investigation of Antibiotic Resistance in the Urban Water Cycle Influenced by Environmental and Anthropogenic Activity
Microbiology Spectrum
2022
The microbiome-derived metabolite TMAO drives immune activation and boosts responses to immune checkpoint blockade in pancreatic cancer
Science Immunology
2022
Honeybee intestines retain low yeast titers, but no bacterial mutualists, at emergence
Yeast
2022
Characterization and Demonstration of Mock Communities as Control Reagents for Accurate Human Microbiome Community Measurements
Microbiology Spectrum
2022
The gut microbiome-metabolome dataset collection: a curated resource for integrative meta-analysis
npj Biofilms and Microbiomes
2022
Bacteroides abundance drives birth mode dependent infant gut microbiota developmental trajectories
Frontiers in Microbiology
2022
Personalized microbiome-driven effects of non-nutritive sweeteners on human glucose tolerance
Cell
2022
Microbiome Profiling of Enterotoxigenic Escherichia coli (ETEC) Carriers Highlights Signature Differences between Symptomatic and Asymptomatic Individuals
mBio
2022
Metagenome Sequencing Reveals the Microbiome of Aedes albopictus and Its Possible Relationship With Dengue Virus Susceptibility
Frontiers in Microbiology
2022
Viral Metagenomics Reveals Widely Diverse Viral Community of Freshwater Amazonian Lake
Frontiers in Public Health
2022
Oxygen‐deficient water zones in the Baltic Sea promote uncharacterized Hg methylating microorganisms in underlying sediments
Limnology and Oceanography
2022
Tetracycline-induced mitohormesis mediates disease tolerance against influenza
Journal of Clinical Investigation
2022
MTSv: rapid alignment-based taxonomic classification and high-confidence metagenomic analysis
PeerJ
2022
Critical Assessment of Metagenome Interpretation: the second round of challenges
Nature Methods
2022
Whole-Genome Sequencing Reveals Age-Specific Changes in the Human Blood Microbiota
Journal of Personalized Medicine
2022
Metagenomic Approaches Reveal Strain Profiling and Genotyping of Klebsiella pneumoniae from Hospitalized Patients in China
Microbiology Spectrum
2022
Clinical Metagenomics Is Increasingly Accurate and Affordable to Detect Enteric Bacterial Pathogens in Stool
Microorganisms
2022
Metagenomics reveals contrasting energy utilization efficiencies of captive and wild camels ( Camelus ferus )
Integrative Zoology
2022
Primary Succession Changes the Composition and Functioning of the Protist Community on Mine Tailings, Especially Phototrophic Protists
ACS Environmental Au
2022
Metagenome analysis using the Kraken software suite
Nature Protocols
2022
Microbial and human transcriptome in vaginal fluid at midgestation: Association with spontaneous preterm delivery
Clinical and Translational Medicine
2022
First insight into oral microbiome diversity in Papua New Guineans reveals a specific regional signature
Molecular Ecology
2022
Maize seed endophytes
Molecular Plant Pathology
2022
Marine Microbial Communities of North and South Shelves of Iceland
Frontiers in Marine Science
2022
Collective effects of human genomic variation on microbiome function
Scientific Reports
2022
Strain level microbial detection and quantification with applications to single cell metagenomics
Nature Communications
2022
Nivolumab plus ipilimumab with or without live bacterial supplementation in metastatic renal cell carcinoma: a randomized phase 1 trial
Nature Medicine
2022
Pan-Genome Analysis of Staphylococcus aureus Reveals Key Factors Influencing Genomic Plasticity
Microbiology Spectrum
2022
The Mouse Gastrointestinal Bacteria Catalogue enables translation between the mouse and human gut microbiotas via functional mapping
Cell Host & Microbe
2022
Clinical evaluation of metagenomic next-generation sequencing for detecting pathogens in bronchoalveolar lavage fluid collected from children with community-acquired pneumonia
Frontiers in Medicine
2022
Response of soil viral communities to land use changes
Nature Communications
2022
Gut microbiota composition in chemotherapy and targeted therapy of patients with metastatic colorectal cancer
Frontiers in Oncology
2022
Risk assessment of three sheep stocking modes via identification of bacterial genomes carrying antibiotic resistance genes and virulence factor genes
Journal of Environmental Management
2022
Genomic reconstruction of short-chain fatty acid production by the human gut microbiota
Frontiers in Molecular Biosciences
2022
Comparison Between Full-Length 16S rRNA Metabarcoding and Whole Metagenome Sequencing Suggests the Use of Either Is Suitable for Large-Scale Microbiome Studies
Foodborne Pathogens and Disease
2022
Genome-centric analysis of short and long read metagenomes reveals uncharacterized microbiome diversity in Southeast Asians
Nature Communications
2022
Metatranscriptomic Analysis of the Chicken Gut Resistome Response to In-Feed Antibiotics and Natural Feed Additives
Frontiers in Microbiology
2022
The healthy female microbiome across body sites: effect of hormonal contraceptives and the menstrual cycle
Human Reproduction
2022
Subgingival host–microbiome metatranscriptomic changes following scaling and root planing in grade II / III periodontitis
Journal of Clinical Periodontology
2022
Metagenomic investigation of the equine faecal microbiome reveals extensive taxonomic diversity
PeerJ
2021
Bacterial Diversity in House Dust: Characterization of a Core Indoor Microbiome
Frontiers in Environmental Science
2021
Characterization of the Blood and Cerebrospinal Fluid Microbiome in Children with Bacterial Meningitis and Its Potential Correlation with Inflammation
mSystems
2021
Streptozotocin-induced hyperglycemia alters the cecal metabolome and exacerbates antibiotic-induced dysbiosis
Cell Reports
2021
Ontology-Enriched Specifications Enabling Findable, Accessible, Interoperable, and Reusable Marine Metagenomic Datasets in Cyberinfrastructure Systems
Frontiers in Microbiology
2021
The Abundance and Diversity of Fungi in a Hypersaline Microbial Mat from Guerrero Negro, Baja California, México
Journal of Fungi
2021
High throughput shotgun sequencing of eRNA reveals taxonomic and derived functional shifts across a benthic productivity gradient
Molecular Ecology
2021
A unified catalog of 204,938 reference genomes from the human gut microbiome
Nature Biotechnology
2021
Gut microbiome is associated with the clinical response to anti-PD-1 based immunotherapy in hepatobiliary cancers
Journal for ImmunoTherapy of Cancer
2021
Correlation of Salmonella enterica and Listeria monocytogenes in Irrigation Water to Environmental Factors, Fecal Indicators, and Bacterial Communities
Frontiers in Microbiology
2021
Combined metagenomic and archaeobotanical analyses on human dental calculus: A cross-section of lifestyle conditions in a Copper Age population of central Italy
Quaternary International
2021
Combining Culture-Dependent and Culture-Independent Methods: New Methodology Insight on the Vibrio Community of Ruditapes philippinarum
Foods
2021
DNA traces the origin of honey by identifying plants, bacteria and fungi
Scientific Reports
2021
Vegan vs. omnivore diets paradox: A whole-metagenomic approach for defining metabolic networks during the race in ultra-marathoners- a before and after study design
PLOS ONE
2021
Frontiers in Probability and the Statistical Sciences
2021
Tumor microbiome contributes to an aggressive phenotype in the basal-like subtype of pancreatic cancer
Communications Biology
2021
Metformin Strongly Affects Gut Microbiome Composition in High-Fat Diet-Induced Type 2 Diabetes Mouse Model of Both Sexes
Frontiers in Endocrinology
2021
Shotgun-metagenomics based prediction of antibiotic resistance and virulence determinants in Staphylococcus aureus from periprosthetic tissue on blood culture bottles
Scientific Reports
2021
Phenotypes, Lung Microbiota and Cytokine Responses in Pneumonia After Hematopoietic Stem Cell Transplantation
Journal of Inflammation Research
2021
Vertebrate host phylogeny influences gut archaeal diversity
Nature Microbiology
2021
Soil Disturbance Affects Plant Productivity via Soil Microbial Community Shifts
Frontiers in Microbiology
2021
Nanopore-Based Surveillance of Zoonotic Bacterial Pathogens in Farm-Dwelling Peridomestic Rodents
Pathogens
2021
Metabarcoding analysis of gut microbiota of healthy individuals reveals impact of probiotic and maltodextrin consumption
Beneficial Microbes
2021
High-resolution microbiome analysis enabled by linking of 16S rRNA gene sequences with adjacent genomic contexts
Microbial Genomics
2021
Distribution patterns of antibiotic resistance genes and their bacterial hosts in pig farm wastewater treatment systems and soil fertilized with pig manure
Science of The Total Environment
2021
Bog ecosystems as a playground for plant–microbe coevolution: bryophytes and vascular plants harbour functionally adapted bacteria
Microbiome
2021
Characterization of Bacterial Community Dynamics of the Human Mouth Throughout Decomposition via Metagenomic, Metatranscriptomic, and Culturing Techniques
Frontiers in Microbiology
2021
Alterations in the Composition of Intestinal DNA Virome in Patients With COVID-19
Frontiers in Cellular and Infection Microbiology
2021
Enhanced metal recovery by efficient agglomeration of precipitates in an up-flow fixed-bed bioreactor
Chemical Engineering Journal
2021
Microbial river-to-sea continuum: gradients in benthic and planktonic diversity, osmoregulation and nutrient cycling
Microbiome
2021
Exploring bacterial diversity via a curated and searchable snapshot of archived DNA sequences
PLOS Biology
2021
Microbiomes of commercially-available pine nuts and sesame seeds
PLOS ONE
2021
Extensive microbial diversity within the chicken gut microbiome revealed by metagenomics and culture
PeerJ
2021
A Statistical Perspective on the Challenges in Molecular Microbial Biology
Journal of Agricultural, Biological and Environmental Statistics
2021
Cold Acclimation in Brachypodium Is Accompanied by Changes in Above-Ground Bacterial and Fungal Communities
Plants
2021
Surveillance of Listeria monocytogenes: Early Detection, Population Dynamics, and Quasimetagenomic Sequencing during Selective Enrichment
Applied and Environmental Microbiology
2021
Characterization of gut microbial structural variations as determinants of human bile acid metabolism
Cell Host & Microbe
2021
Analysis of metagenome-assembled viral genomes from the human gut reveals diverse putative CrAss-like phages with unique genomic features
Nature Communications
2021
Long-term gut microbiome dynamics in Drosophila melanogaster reveal environment-specific associations between bacterial taxa at the family level
Proceedings of the Royal Society B: Biological Sciences
2021
Elevated rates of horizontal gene transfer in the industrialized human microbiome
Cell
2021
Gut microbiome stability and dynamics in healthy donors and patients with non-gastrointestinal cancers
Journal of Experimental Medicine
2021
Metagenome-Wide Analysis of Rural and Urban Surface Waters and Sediments in Bangladesh Identifies Human Waste as a Driver of Antibiotic Resistance
mSystems
2021
Diverse methanogens, bacteria and tannase genes in the feces of the endangered volcano rabbit (Romerolagus diazi)
PeerJ
2021
Imported human norovirus in travelers, Shanghai port, China 2018: An epidemiological and whole genome sequencing study
Travel Medicine and Infectious Disease
2021
A Fructo-Oligosaccharide Prebiotic Is Well Tolerated in Adults Undergoing Allogeneic Hematopoietic Stem Cell Transplantation: A Phase I Dose-Escalation Trial
Transplantation and Cellular Therapy
2021
Diversity and composition of the North Sikkim hot spring mycobiome using a culture-independent method
Folia Microbiologica
2021
Metataxonomic Profiling of Native and Starter Microbiota During Ripening of Gouda Cheese Made With Listeria monocytogenes-Contaminated Unpasteurized Milk
Frontiers in Microbiology
2021
Reduced metagenome sequencing for strain-resolution taxonomic profiles
Microbiome
2021
NanoCLUST: a species-level analysis of 16S rRNA nanopore sequencing data
Bioinformatics
2021
Using RNA-Sequencing Data to Examine Tissue-Specific Garlic Microbiomes
International Journal of Molecular Sciences
2021
Struo2: efficient metagenome profiling database construction for ever-expanding microbial genome datasets
PeerJ
2021
Origin Sample Prediction and Spatial Modeling of Antimicrobial Resistance in Metagenomic Sequencing Data
Frontiers in Genetics
2021
Metagenomic Analyses Expand Bacterial and Functional Profiling Biomarkers for Colorectal Cancer in a Hainan Cohort, China
Current Microbiology
2021
Evidence for the Widespread Occurrence of Bacteria Implicated in Acute Oak Decline from Incidental Genetic Sampling
Forests
2021
Population structure and transmission of Mycobacterium bovis in Ethiopia
Microbial Genomics
2021
Isolation and characterization of fast‐growing green snow bacteria from coastal East Antarctica
MicrobiologyOpen
2021
Endophytic Bacterial Communities in Apple Leaves Are Minimally Impacted by Streptomycin Use for Fire Blight Management
Phytobiomes Journal
2021
Comparative Study of Metagenomics and Metatranscriptomics to Reveal Microbiomes in Overwintering Pepper Fruits
International Journal of Molecular Sciences
2021
Comparison of bacterial communities and antibiotic resistance genes in oxidation ditches and membrane bioreactors
Scientific Reports
2021
TIPP2: metagenomic taxonomic profiling using phylogenetic markers
Bioinformatics
2021
Active DNRA and denitrification in oxic hypereutrophic waters
Water Research
2021
Metagenomics: a path to understanding the gut microbiome
Mammalian Genome
2021
Conversion of dietary inositol into propionate and acetate by commensal Anaerostipes associates with host health
Nature Communications
2021
The Gut Microbiome of Healthy Vietnamese Adults and Children Is a Major Reservoir for Resistance Genes Against Critical Antimicrobials
The Journal of Infectious Diseases
2021
HumGut: a comprehensive human gut prokaryotic genomes collection filtered by metagenome data
Microbiome
2021
The Formation of Antibiotic Resistance Genes in Bacterial Communities During Garlic Powder Processing
Frontiers in Nutrition
2021
Foam shares antibiotic resistomes and bacterial pathogens with activated sludge in wastewater treatment plants
Journal of Hazardous Materials
2021
Disease-induced changes in plant microbiome assembly and functional adaptation
Microbiome
2021
Enlightening the taxonomy darkness of human gut microbiomes with a cultured biobank
Microbiome
2021
Long-term dynamics of the human oral microbiome during clinical disease progression
BMC Biology
2021
Whole-Genome Sequencing Analysis to Identify Infection with Multiple Species of Nontuberculous Mycobacteria
Pathogens
2021
Metagenomic Geolocation Prediction Using an Adaptive Ensemble Classifier
Frontiers in Genetics
2021
Probiotics Improve Gastrointestinal Function and Life Quality in Pregnancy
Nutrients
2021
Probiotics impact the antibiotic resistance gene reservoir along the human GI tract in a person-specific and antibiotic-dependent manner
Nature Microbiology
2021
Microbiome degrading linear alkylbenzene sulfonate in activated sludge
Journal of Hazardous Materials
2021
Nickel complexation as an innovative approach for nickel-cobalt selective recovery using sulfate-reducing bacteria
Journal of Hazardous Materials
2021
Metagenomic insights into the microbial communities of inert and oligotrophic outdoor pier surfaces of a coastal city
Microbiome
2021
Uncovering the genomic and metagenomic research potential in old ethanol-preserved snakes
PLOS ONE
2021
A primer and discussion on DNA-based microbiome data and related bioinformatics analyses
Peer Community Journal
2021
Diversity and Function of Wolf Spider Gut Microbiota Revealed by Shotgun Metagenomics
Frontiers in Microbiology
2021
Tianwang Buxin Granules Influence the Intestinal Flora in Perimenopausal Insomnia
BioMed Research International
2021
Metagenome-assembled genomes and gene catalog from the chicken gut microbiome aid in deciphering antibiotic resistomes
Communications Biology
2021
A review of computational tools for generating metagenome-assembled genomes from metagenomic sequencing data
Computational and Structural Biotechnology Journal
2021
An accessible, efficient and global approach for the large-scale sequencing of bacterial genomes
Genome Biology
2021
TaxonKit: A practical and efficient NCBI taxonomy toolkit
Journal of Genetics and Genomics
2021
Beware of pharyngeal Fusobacterium nucleatum in COVID-19
BMC Microbiology
2021
A comprehensive approach for microbiota and health monitoring in mouse colonies using metagenomic shotgun sequencing
Animal Microbiome
2021
Tracking the transition to agriculture in Southern Europe through ancient DNA analysis of dental calculus
Proceedings of the National Academy of Sciences
2021
Mapping the Terrain for Pathogen Persistence and Proliferation in Non-potable Reuse Distribution Systems: Interactive Effects of Biofiltration, Disinfection, and Water Age
Environmental Science & Technology
2021
Tutorial: assessing metagenomics software with the CAMI benchmarking toolkit
Nature Protocols
2021
Application of computational approaches to analyze metagenomic data
Journal of Microbiology
2021
Manure Microbial Communities and Resistance Profiles Reconfigure after Transition to Manure Pits and Differ from Those in Fertilized Field Soil
mBio
2021
Genomic Insights into Adaptations of Trimethylamine-Utilizing Methanogens to Diverse Habitats, Including the Human Gut
mSystems
2021
Long-read sequencing revealed cooccurrence, host range, and potential mobility of antibiotic resistome in cow feces
Proceedings of the National Academy of Sciences
2021
Challenges in benchmarking metagenomic profilers
Nature Methods
2021
Gulf of Mexico blue hole harbors high levels of novel microbial lineages
The ISME Journal
2021
Functional and Taxonomic Effects of Organic Amendments on the Restoration of Semiarid Quarry Soils
mSystems
2021
Colonization Dynamics of Multidrug-Resistant Klebsiella pneumoniae Are Dictated by Microbiota-Cluster Group Behavior over Individual Antibiotic Susceptibility: A Metataxonomic Analysis
Antibiotics
2021
Performance of Multiple Metagenomics Pipelines in Understanding Microbial Diversity of a Low-Biomass Spacecraft Assembly Facility
Frontiers in Microbiology
2021
Metagenomic Survey Reveals More Diverse and Abundant Antibiotic Resistance Genes in Municipal Wastewater Than Hospital Wastewater
Frontiers in Microbiology
2021
A genomic surveillance framework and genotyping tool for Klebsiella pneumoniae and its related species complex
Nature Communications
2021
Genomic and temporal analyses of Mycobacterium bovis in southern Brazil
Microbial Genomics
2021
Plasma metagenomic sequencing to detect and quantify bacterial DNA in ICU patients suspected of sepsis: A proof-of-principle study
Journal of Trauma and Acute Care Surgery
2021
The oral microbiota of wild bears in Sweden reflects the history of antibiotic use by humans
Current Biology
2021
The Postmedieval Latvian Oral Microbiome in the Context of Modern Dental Calculus and Modern Dental Plaque Microbial Profiles
Genes
2021
A catalogue of 1,167 genomes from the human gut archaeome
Nature Microbiology
2021
High Potential for Biomass-Degrading Enzymes Revealed by Hot Spring Metagenomics
Frontiers in Microbiology
2021
Multiplexed functional metagenomic analysis of the infant microbiome identifies effectors of NF-κB, autophagy, and cellular redox state
Cell Reports
2021
Assessing Gut Microbiota in an Infant with Congenital Propionic Acidemia before and after Probiotic Supplementation
Microorganisms
2021
Identification of Reductive Dehalogenases That Mediate Complete Debromination of Penta- and Tetrabrominated Diphenyl Ethers in Dehalococcoides spp.
Applied and Environmental Microbiology
2021
Evaluation of the Microba Community Profiler for Taxonomic Profiling of Metagenomic Datasets From the Human Gut Microbiome
Frontiers in Microbiology
2021
High-throughput next-generation sequencing for identifying pathogens during early-stage post-lung transplantation
BMC Pulmonary Medicine
2021
The gut microbiome in konzo
Nature Communications
2021
PuffAligner: a fast, efficient and accurate aligner based on the Pufferfish index
Bioinformatics
2021
Treatments of porcine fecal samples affect high-throughput virome sequencing results
Journal of Virological Methods
2021
Long-Term Effects of a Web-Based Low-FODMAP Diet Versus Probiotic Treatment for Irritable Bowel Syndrome, Including Shotgun Analyses of Microbiota: Randomized, Double-Crossover Clinical Trial
Journal of Medical Internet Research
2021
Nanopore sequencing and its application to the study of microbial communities
Computational and Structural Biotechnology Journal
2021
Characterization of the public transit air microbiome and resistome reveals geographical specificity
Microbiome
2021
Skin Microbiota and Clinical Associations in Netherton Syndrome
JID Innovations
2021
Microbiome-based environmental monitoring of a dairy processing facility highlights the challenges associated with low microbial-load samples
npj Science of Food
2021
Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3
eLife
2021
Microbial Community Dynamics during Biodegradation of Crude Oil and Its Response to Biostimulation in Svalbard Seawater at Low Temperature
Microorganisms
2021
Baseline Gut Metagenomic Functional Gene Signature Associated with Variable Weight Loss Responses following a Healthy Lifestyle Intervention in Humans
mSystems
2021
Identifying biases and their potential solutions in human microbiome studies
Microbiome
2021
Comparative Metagenomics Reveals Microbial Signatures of Sugarcane Phyllosphere in Organic Management
Frontiers in Microbiology
2021
Dental calculus as a proxy for animal microbiomes
Quaternary International
2021
Full Issue PDF
Phytobiomes Journal
2021
Species-Specific Quality Control, Assembly and Contamination Detection in Microbial Isolate Sequences with AQUAMIS
Genes
2020
LEMMI: a continuous benchmarking platform for metagenomics classifiers
Genome Research
2020
Next-generation sequencing as a screening tool for foodborne pathogens in fresh produce
Journal of Microbiological Methods
2020
The distribution of microbiomes and resistomes across farm environments in conventional and organic dairy herds in Pennsylvania
Environmental Microbiome
2020
SHOGUN: a modular, accurate and scalable framework for microbiome quantification
Bioinformatics
2020
Proximal colon–derived O-glycosylated mucus encapsulates and modulates the microbiota
Science
2020
Oral microbiome-systemic link studies: perspectives on current limitations and future artificial intelligence-based approaches
Critical Reviews in Microbiology
2020
A big data approach to metagenomics for all-food-sequencing
BMC Bioinformatics
2020
Meeting report of the third annual Tri-Service Microbiome Consortium symposium
Environmental Microbiome
2020
Distinct microbiome composition and metabolome exists across subgroups of elite Irish athletes
Journal of Science and Medicine in Sport
2020
Tracking resistomes, virulence genes, and bacterial pathogens in long-term manure-amended greenhouse soils
Journal of Hazardous Materials
2020
Prevalence of methanogens in the uncultured Sikkim hot spring solfataric mud archaeal microbiome
Environmental Sustainability
2020
Sorghum Growth Promotion by Paraburkholderia tropica and Herbaspirillum frisingense: Putative Mechanisms Revealed by Genomics and Metagenomics
Microorganisms
2020
Ultrafast and accurate 16S rRNA microbial community analysis using Kraken 2
Microbiome
2020
Syntrophy via Interspecies H 2 Transfer between Christensenella and Methanobrevibacter Underlies Their Global Cooccurrence in the Human Gut
mBio
2020
Dairy Products and Dairy-Processing Environments as a Reservoir of Antibiotic Resistance and Quorum-Quenching Determinants as Revealed through Functional Metagenomics
mSystems
2020
Multiple approaches for massively parallel sequencing of SARS-CoV-2 genomes directly from clinical samples
Genome Medicine
2020
Impact of narrow-spectrum penicillin V on the oral and faecal resistome in a young child treated for otitis media
Journal of Global Antimicrobial Resistance
2020
Large-Scale Metagenome Assembly Reveals Novel Animal-Associated Microbial Genomes, Biosynthetic Gene Clusters, and Other Genetic Diversity
mSystems
2020
Evaluation of methods for the reduction of contaminating host reads when performing shotgun metagenomic sequencing of the milk microbiome
Scientific Reports
2020
Probabilistic model based on circular statistics for quantifying coverage depth dynamics originating from DNA replication
PeerJ
2020
Colony-Level Effects of Amygdalin on Honeybees and Their Microbes
Insects
2020
Big Data in metagenomics: Apache Spark vs MPI
PLOS ONE
2020
IDseq—An open source cloud-based pipeline and analysis service for metagenomic pathogen detection and monitoring
GigaScience
2020
Computational Approaches for Unraveling the Effects of Variation in the Human Genome and Microbiome
Annual Review of Biomedical Data Science
2020
The impact of contaminants on the accuracy of genome skimming and the effectiveness of exclusion read filters
Molecular Ecology Resources
2020
Gut bacterial deamination of residual levodopa medication for Parkinson’s disease
BMC Biology
2020
Shotgun-Metagenomics on Positive Blood Culture Bottles Inoculated With Prosthetic Joint Tissue: A Proof of Concept Study
Frontiers in Microbiology
2020
Improving Oral Health and Modulating the Oral Microbiome to Reduce Bloodstream Infections from Oral Organisms in Pediatric and Young Adult Hematopoietic Stem Cell Transplantation Recipients: A Randomized Controlled Trial
Biology of Blood and Marrow Transplantation
2020
Enterobacteriaceae predominate in the endophytic microbiome and contribute to the resistome of strawberry
Science of The Total Environment
2020
Metalign: efficient alignment-based metagenomic profiling via containment min hash
Genome Biology
2020
Thermus thermophilus DNA can be used as internal control for process monitoring of clinical metagenomic next-generation sequencing of urine samples
Journal of Microbiological Methods
2020
A shotgun metagenomic investigation of the microbiota of udder cleft dermatitis in comparison to healthy skin in dairy cows
PLOS ONE
2020
Microbiota composition data of imago and larval stage of the anhydrobiotic midge
Data in Brief
2020
Systematic evaluation of supervised machine learning for sample origin prediction using metagenomic sequencing data
Biology Direct
2020
Metagenomic Association Analysis of Gut Symbiont Limosilactobacillus reuteri Without Host-Specific Genome Isolation
Frontiers in Microbiology
2020
Campylobacter Abundance in Breastfed Infants and Identification of a New Species in the Global Enterics Multicenter Study
mSphere
2020
Mutations inMycobacterium tuberculosisIsolates with Discordant Results for Drug-Susceptibility Testing in Peru
International Journal of Microbiology
2020
Do you cov me? Effect of coverage reduction on metagenome shotgun sequencing studies
F1000Research
2020
Developing standards for the microbiome field
Microbiome
2020
Sensitivity of shotgun metagenomics to host DNA: abundance estimates depend on bioinformatic tools and contamination is the main issue
Access Microbiology
2020
RNA sequencing of whole blood in dogs with primary immune-mediated hemolytic anemia (IMHA) reveals novel insights into disease pathogenesis
PLOS ONE
2020
A quasimetagenomics method for concerted detection and subtyping of Salmonella enterica and E. coli O157:H7 from romaine lettuce
Food Microbiology
2020
Contaminant DNA in bacterial sequencing experiments is a major source of false genetic variability
BMC Biology
2020
Microbiome-Informed Food Safety and Quality: Longitudinal Consistency and Cross-Sectional Distinctiveness of Retail Chicken Breast Microbiomes
mSystems
2020
Improved Metagenomic Taxonomic Profiling Using a Curated Core Gene-Based Bacterial Database Reveals Unrecognized Species in the Genus Streptococcus
Pathogens
2020
Genomic characterization of a diazotrophic microbiota associated with maize aerial root mucilage
PLOS ONE
2020
Improved gastrointestinal health for irritable bowel syndrome with metagenome-guided interventions
Precision Clinical Medicine
2020
Difference in the rhizosphere microbiome of Melia azedarach during removal of benzo(a)pyrene from cadmium co-contaminated soil
Chemosphere
2020
Low Abundance of Methanotrophs in Sediments of Shallow Boreal Coastal Zones With High Water Methane Concentrations
Frontiers in Microbiology
2020
Consumption of a Western-Style Diet Modulates the Response of the Murine Gut Microbiome to Ciprofloxacin
mSystems
2020
Stratification of microbiomes during the holomictic period of Lake Fuxian, an alpine monomictic lake
Limnology and Oceanography
2020
A Pilot Study of the Effect of Deployment on the Gut Microbiome and Traveler’s Diarrhea Susceptibility
Frontiers in Cellular and Infection Microbiology
2020
The trans-kingdom battle between donor and recipient gut microbiome influences fecal microbiota transplantation outcome
Scientific Reports
2020
Rapid and Accurate Species Identification of Mitis Group Streptococci Using the MinION Nanopore Sequencer
Frontiers in Cellular and Infection Microbiology
2020
Metavirome and its functional diversity analysis through microbiome study of the Sikkim Himalayan hot spring solfataric mud sediments
Current Research in Microbial Sciences
2020
Detection of Antimicrobial Resistance Genes in the Milk Production Environment: Impact of Host DNA and Sequencing Depth
Frontiers in Microbiology
2020
Skin Microbiome in Cutaneous T-Cell Lymphoma by 16S and Whole-Genome Shotgun Sequencing
Journal of Investigative Dermatology
2020
Salmonella Genomic Island 1 is Broadly Disseminated within Gammaproteobacteriaceae
Microorganisms
2020
Acquisition, transmission and strain diversity of human gut-colonizing crAss-like phages
Nature Communications
2020
The Role of the Gut Microbiome in Resisting Norovirus Infection as Revealed by a Human Challenge Study
mBio
2020
Soil microbial diversity drops with land‐use change in a high mountain temperate forest: a metagenomics survey
Environmental Microbiology Reports
2020
Assessment of In Vitro and In Silico Protocols for Sequence-Based Characterization of the Human Vaginal Microbiome
mSphere
2020
Whole genomic sequencing and sex-dependent abundance estimation of Cardinium sp., a common and hyperabundant bacterial endosymbiont of the American house dust mite, Dermatophagoides farinae
Experimental and Applied Acarology
2020
Antimicrobial Resistance Gene Prevalence in a Population of Patients with Advanced Dementia Is Related to Specific Pathobionts
iScience
2020
The Nubeam reference-free approach to analyze metagenomic sequencing reads
Genome Research
2019
Improved metagenomic analysis with Kraken 2
Genome Biology
2019
The fecal resistome of dairy cattle is associated with diet during nursing
Nature Communications
2019
Direct transmission of within-host Mycobacterium tuberculosis diversity to secondary cases can lead to variable between-host heterogeneity without de novo mutation: A genomic investigation
EBioMedicine
2019
Host immunoglobulin G selectively identifies pathobionts in pediatric inflammatory bowel diseases
Microbiome
2019
The Rice Leaf Microbiome Has a Conserved Community Structure Controlled by Complex Host-Microbe Interactions
SSRN Electronic Journal
2019
Optimizing sequencing protocols for leaderboard metagenomics by combining long and short reads
Genome Biology
2019
Benchmarking Metagenomics Tools for Taxonomic Classification
Cell
2019
SEPATH: benchmarking the search for pathogens in human tissue whole genome sequence data leads to template pipelines
Genome Biology
2019
MetaPheno: A critical evaluation of deep learning and machine learning in metagenome-based disease prediction
Methods
2019
Intestinal microbiota domination under extreme selective pressures characterized by metagenomic read cloud sequencing and assembly
BMC Bioinformatics
2019
Microfluidics-Based Enrichment and Whole-Genome Amplification Enable Strain-Level Resolution for Airway Metagenomics
mSystems
2019
Shotgun sequencing of clinical biofilm following scanning electron microscopy identifies bacterial community composition
Pathogens and Disease
2019
Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth
Nature
2019
Alzheimer’s Disease Microbiome Is Associated with Dysregulation of the Anti-Inflammatory P-Glycoprotein Pathway
mBio
2019
The diverse and extensive plant polysaccharide degradative apparatuses of the rumen and hindgut Prevotella species: A factor in their ubiquity?
Systematic and Applied Microbiology
2019
Ultrafast search of all deposited bacterial and viral genomic data
Nature Biotechnology
2019
Taxonomic and Functional Characterization of the Microbial Community During Spontaneous in vitro Fermentation of Riesling Must
Frontiers in Microbiology
2019
Strain-level metagenomic assignment and compositional estimation for long reads with MetaMaps
Nature Communications
2019
Do you cov me? Effect of coverage reduction on species identification and genome reconstruction in complex biological matrices by metagenome shotgun high-throughput sequencing
F1000Research
2019
Microbial Metabolism Modulates Antibiotic Susceptibility within the Murine Gut Microbiome
Cell Metabolism
2019
Exploration of the antibiotic resistome in a wastewater treatment plant by a nine-year longitudinal metagenomic study
Environment International
2019
MSC: a metagenomic sequence classification algorithm
Bioinformatics
2019
Microbial abundance, activity and population genomic profiling with mOTUs2
Nature Communications
2019
Mycobacterium avium Complex Diversity within Lung Disease, as Revealed by Whole-Genome Sequencing
American Journal of Respiratory and Critical Care Medicine
2019
A review of methods and databases for metagenomic classification and assembly
Briefings in Bioinformatics
2018
American Gut: an Open Platform for Citizen Science Microbiome Research
mSystems
2018
RefSeq database growth influences the accuracy of k-mer-based lowest common ancestor species identification
Genome Biology
2018
MetaWRAP—a flexible pipeline for genome-resolved metagenomic data analysis
Microbiome
2018
taxMaps: comprehensive and highly accurate taxonomic classification of short-read data in reasonable time
Genome Research
2018
Bone formation transcripts dominate the differential gene expression profile in an equine osteoporotic condition associated with pulmonary silicosis
PLOS ONE
2017
DNA Sequencing as a Tool to Monitor Marine Ecological Status
Frontiers in Marine Science
2017
Abundance estimation and differential testing on strain level in metagenomics data
Bioinformatics
2017
Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology,and Health Informatics
Additional cited-by details will be shown when available from Crossref