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2025
Group-wise normalization in differential abundance analysis of microbiome samples
BMC Bioinformatics
2025
Schistosoma mansoni infection causes consistent changes to the fecal bacterial microbiota of mice across and within sites
PLOS One
2025
Adaptive dynamics of extrachromosomal circular DNA in rice under nutrient stress
Nature Communications
2025
Soil trenching – are microbial communities alike in experimental peatland plots measuring total and heterotrophic respiration?
Soil Biology and Biochemistry
2025
The role of greenhouse agricultural plastic waste as a reservoir of antibiotic resistance genes and vector of their environmental dissemination.
Environmental Chemistry and Ecotoxicology
2025
Methodology for microbiome data analysis: An overview
Computers in Biology and Medicine
2025
Zero inflated high dimensional compositional data with DeepInsight
PLOS ONE
2025
Degradation of rutin and genistein and the effect on human bacterial fecal populations of obese and non-obese
Journal of Functional Foods
2025
Urocanase-Positive Skin-Resident Bacteria Metabolize cis-Urocanic Acid and in Turn Reduce the Immunosuppressive Properties of UVR
Journal of Investigative Dermatology
2025
A workflow for statistical analysis and visualization of microbiome omics data using the R microeco package
Nature Protocols
2024
2dGBH: Two-dimensional group Benjamini–Hochberg procedure for false discovery rate control in two-way multiple testing of genomic data
Bioinformatics
2024
Evaluation of normalization methods for predicting quantitative phenotypes in metagenomic data analysis
Frontiers in Genetics
2024
Adaptive immune receptor repertoire analysis
Nature Reviews Methods Primers
2024
Soil and climatic characteristics and farming system shape fungal communities in European wheat fields
Agriculture, Ecosystems & Environment
2024
Comparison of the effectiveness of different normalization methods for metagenomic cross-study phenotype prediction under heterogeneity
Scientific Reports
2024
Current Trends and Challenges of Microbiome Research in Prostate Cancer
Current Oncology Reports
2024
Effect of no-till followed by crop diversification on the soil microbiome in a boreal short cereal rotation
Biology and Fertility of Soils
2024
mbtransfer: Microbiome intervention analysis using transfer functions and mirror statistics
PLOS Computational Biology
2024
A strategy for differential abundance analysis of sparse microbiome data with group-wise structured zeros
Scientific Reports
2024
Review and revamp of compositional data transformation: A new framework combining proportion conversion and contrast transformation
Computational and Structural Biotechnology Journal
2024
Distinct anal microbiome is correlated with anal cancer precursors in MSM with HIV
AIDS
2024
Oral administration of Lactobacillus casei DG® after ileostomy closure in restorative proctocolectomy: a randomized placebo-controlled trial (microbiota and immune microenvironment in pouchitis -MEP1)
Gut Microbes
2024
Cluster-specific associations between the gut microbiota and behavioral outcomes in preschool-aged children
Microbiome
2024
Treatment response in rheumatoid arthritis is predicted by the microbiome: a large observational study in UK DMARD-naive patients
Rheumatology
2024
Preoperative vaginal microbiome as a predictor of postoperative urinary tract infection
Scientific Reports
2024
The integration of omics and cultivation-dependent methods could effectively determine the biological risks associated with the utilization of soil conditioners in agriculture
Journal of Hazardous Materials
2024
mbDecoda: a debiased approach to compositional data analysis for microbiome surveys
Briefings in Bioinformatics
2024
A comprehensive, large-scale analysis of “terroir” cheese and milk microbiota reveals profiles strongly shaped by both geographical and human factors
ISME Communications
2024
Crohn’s Disease–Associated Pathogenic Mutation in the Manganese Transporter ZIP8 Shifts the Ileal and Rectal Mucosal Microbiota Implicating Aberrant Bile Acid Metabolism
Inflammatory Bowel Diseases
2024
TimeNorm: a novel normalization method for time course microbiome data
Frontiers in Genetics
2023
Benchmarking differential abundance analysis methods for correlated microbiome sequencing data
Briefings in Bioinformatics
2023
A new method for mining information of gut microbiome with probabilistic topic models
Multimedia Tools and Applications
2023
Pairwise ratio-based differential abundance analysis of infant microbiome 16S sequencing data
NAR Genomics and Bioinformatics
2023
2023 IEEE 6th International Conference on Pattern Recognition and Artificial Intelligence (PRAI)
2023
Out of site, out of mind: Changes in feather moss phyllosphere microbiota in mine offsite boreal landscapes
Frontiers in Microbiology
2023
Soil microbiome analysis reveals effects of periodic waterlogging stress on sugarcane growth
PLOS ONE
2023
Clonal dynamics limits detection of selection in tumour xenograft CRISPR/Cas9 screens
Cancer Gene Therapy
2023
RSim: A reference-based normalization method via rank similarity
PLOS Computational Biology
2023
Microbial community structural and functional differentiation in capped thickened oil sands tailings planted with native boreal species
Frontiers in Microbiology
2023
Robust Differential Abundance Analysis of Microbiome Sequencing Data
Genes
2023
Statistical normalization methods in microbiome data with application to microbiome cancer research
Gut Microbes
2023
Uncover a microbiota signature of upper respiratory tract in patients with SARS-CoV-2 + 
Scientific Reports
2023
Overview of data preprocessing for machine learning applications in human microbiome research
Frontiers in Microbiology
2023
Waterlogging may reduce chemical soil C stabilization in forested peatlands
Soil Biology and Biochemistry
2023
Exploration of fMRI brain responses to oral sucrose after Roux-en-Y gastric bypass in obese yucatan minipigs in relationship with microbiota and metabolomics profiles
Clinical Nutrition
2023
Tree islands enhance biodiversity and functioning in oil palm landscapes
Nature
2023
Rapid nitrification involving comammox and canonical Nitrospira at extreme pH in saline‐alkaline lakes
Environmental Microbiology
2023
BIC: a database for the transcriptional landscape of bacteria in cancer
Nucleic Acids Research
2023
Pitfalls in the statistical analysis of microbiome amplicon sequencing data
Molecular Ecology Resources
2023
Climate warming has direct and indirect effects on microbes associated with carbon cycling in northern lakes
Global Change Biology
2023
A review of normalization and differential abundance methods for microbiome counts data
WIREs Computational Statistics
2023
Biogeographical effect on the diversity of vaginal microbiome in preterm birth: A systematic review and meta-analysis
Medicine in Microecology
2023
The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models
Cell
2023
Change in Cutibacterium acnes phylotype abundance and improvement of clinical parameters using a new dermocosmetic product containing Myrtus communis and Celastrol enriched plant cell culture extracts in patients with acne vulgaris
Journal of the European Academy of Dermatology and Venereology
2023
Interpretable Machine Learning for Personalized Medical Recommendations: A LIME-Based Approach
Diagnostics
2023
Characterization of Gut Microbiome Composition in Patients with Triple-Negative Breast Cancer Treated with Neoadjuvant Chemotherapy
The Oncologist
2023
Improved understanding on biochar effect in electron supplied anaerobic soil as evidenced by dechlorination and methanogenesis processes
Science of The Total Environment
2023
Bioinformatic and Statistical Analysis of Microbiome Data
2023
Patient-Reported Outcomes Correlate With Microbial Community Composition Independent of Mucosal Inflammation in Pediatric Inflammatory Bowel Disease
Inflammatory Bowel Diseases
2023
Metagenomic analysis of the fecal microbiome in colorectal cancer patients compared to healthy controls as a function of age
Cancer Medicine
2023
Accommodating multiple potential normalizations in microbiome associations studies
BMC Bioinformatics
2023
Impacts of coniferous bark-derived organic soil amendments on microbial communities in arable soil – a microcosm study
FEMS Microbiology Ecology
2023
Substituting meat for mycoprotein reduces genotoxicity and increases the abundance of beneficial microbes in the gut: Mycomeat, a randomised crossover control trial
European Journal of Nutrition
2023
A Single Intranasal Dose of Bacterial Therapeutics to Calves Confers Longitudinal Modulation of the Nasopharyngeal Microbiota: a Pilot Study
mSystems
2022
A specific microbiota signature is associated to various degrees of ulcerative colitis as assessed by a machine learning approach
Gut Microbes
2022
Selective induction of human gut-associated acetogenic/butyrogenic microbiota based on specific microbial colonization of indigestible starch granules
The ISME Journal
2022
Impact of Aligner, Normalization Method, and Sequencing Depth on TempO-seq Accuracy
Bioinformatics and Biology Insights
2022
A metagenomics study of hexabromocyclododecane degradation with a soil microbial community
Journal of Hazardous Materials
2022
Machine Learning and Canine Chronic Enteropathies: A New Approach to Investigate FMT Effects
Veterinary Sciences
2022
The Microbiome in Bronchial Biopsies from Smokers and Ex-Smokers with Stable COPD - A Metatranscriptomic Approach
COPD: Journal of Chronic Obstructive Pulmonary Disease
2022
A comprehensive evaluation of microbial differential abundance analysis methods: current status and potential solutions
Microbiome
2022
The lung microbiome regulates brain autoimmunity
Nature
2022
Presence of Blastocystis in gut microbiota is associated with cognitive traits and decreased executive function
The ISME Journal
2022
Multiregion transcriptomic profiling of the primate brain reveals signatures of aging and the social environment
Nature Neuroscience
2022
Gut microbial β-glucuronidases regulate host luminal proteases and are depleted in irritable bowel syndrome
Nature Microbiology
2022
Analysis of microbiome in gastrointestinal stromal tumors: Looking for different players in tumorigenesis and novel therapeutic options
Cancer Science
2022
Gut Steroids and Microbiota: Effect of Gonadectomy and Sex
Biomolecules
2022
LinDA: linear models for differential abundance analysis of microbiome compositional data
Genome Biology
2022
Drivers of gut microbiome variation within and between groups of a wild Malagasy primate
Microbiome
2022
Predicting measures of soil health using the microbiome and supervised machine learning
Soil Biology and Biochemistry
2022
MZINBVA: variational approximation for multilevel zero-inflated negative-binomial models for association analysis in microbiome surveys
Briefings in Bioinformatics
2022
Association Between the Gut Microbiome and Their Metabolites With Human Blood Pressure Variability
Hypertension
2022
Unraveling negative biotic interactions determining soil microbial community assembly and functioning
The ISME Journal
2022
Testing microbiome associations with survival times at both the community and individual taxon levels
PLOS Computational Biology
2022
Potential Role of Inflammation-Promoting Biliary Microbiome in Primary Sclerosing Cholangitis and Cholangiocarcinoma
Cancers
2022
Spatial distribution of live gut microbiota and bile acid metabolism in various parts of human large intestine
Scientific Reports
2022
Beware to ignore the rare: how imputing zero-values can improve the quality of 16S rRNA gene studies results
BMC Bioinformatics
2022
Ensuring That Fundamentals of Quantitative Microbiology Are Reflected in Microbial Diversity Analyses Based on Next-Generation Sequencing
Frontiers in Microbiology
2022
Multivariate statistical monitoring system for microbial population dynamics
Physical Biology
2022
Investigating differential abundance methods in microbiome data: A benchmark study
PLOS Computational Biology
2022
DNA- and RNA-based bacterial communities and geochemical zonation under changing sediment porewater dynamics on the Aldabra Atoll
Scientific Reports
2022
Analysis of Gut Microbiome Structure Based on GMPR+Spectrum
Applied Sciences
2021
Characterization of the Luminal and Mucosa-Associated Microbiome along the Gastrointestinal Tract: Results from Surgically Treated Preterm Infants and a Murine Model
Nutrients
2021
A Bayesian zero-inflated negative binomial regression model for the integrative analysis of microbiome data
Biostatistics
2021
Alcohol Use Is Associated With Intestinal Dysbiosis and Dysfunctional CD8+ T-Cell Phenotypes in Persons With Human Immunodeficiency Virus
The Journal of Infectious Diseases
2021
Microbiome diversity predicts surgical success in patients with rectovaginal fistula
International Urogynecology Journal
2021
Comparison of microbiome samples: methods and computational challenges
Briefings in Bioinformatics
2021
Statistical analysis of microbiome data: The challenge of sparsity
Current Opinion in Endocrine and Metabolic Research
2021
Exploring the mechanisms by which reindeer droppings induce fen peat methane production
Soil Biology and Biochemistry
2021
Pulp and paper mill sludges decrease soil erodibility
Journal of Environmental Quality
2021
Benchmarking microbiome transformations favors experimental quantitative approaches to address compositionality and sampling depth biases
Nature Communications
2021
mbImpute: an accurate and robust imputation method for microbiome data
Genome Biology
2021
A novel deep learning method for predictive modeling of microbiome data
Briefings in Bioinformatics
2021
Meta-analysis of the Parkinson’s disease gut microbiome suggests alterations linked to intestinal inflammation
npj Parkinson's Disease
2021
Determining Gut Microbial Dysbiosis: a Review of Applied Indexes for Assessment of Intestinal Microbiota Imbalances
Applied and Environmental Microbiology
2021
Lactobacillus crispatus thrives in pregnancy hormonal milieu in a Nigerian patient cohort
Scientific Reports
2021
Faecal Microbiome Transplantation as a Solution to Chronic Enteropathies in Dogs: A Case Study of Beneficial Microbial Evolution
Animals
2021
Bacterial Signatures of Paediatric Respiratory Disease: An Individual Participant Data Meta-Analysis
Frontiers in Microbiology
2021
Challenges, Strategies, and Perspectives for Reference-Independent Longitudinal Multi-Omic Microbiome Studies
Frontiers in Genetics
2021
Boreal soil microbial diversity and seed onion mycorrhizal colonization is unaffected by preceding one season crop cultivation
European Journal of Soil Biology
2021
Glucose but Not Fructose Alters the Intestinal Paracellular Permeability in Association With Gut Inflammation and Dysbiosis in Mice
Frontiers in Immunology
2021
Predominance of Atopobium vaginae at Midtrimester: a Potential Indicator of Preterm Birth Risk in a Nigerian Cohort
mSphere
2021
Distinct Changes in Gut Microbiota Are Associated with Estradiol-Mediated Protection from Diet-Induced Obesity in Female Mice
Metabolites
2021
Site fertility and soil water‐table level affect fungal biomass production and community composition in boreal peatland forests
Environmental Microbiology
2021
Long-term impacts of organic and conventional farming on the soil microbiome in boreal arable soil
European Journal of Soil Biology
2021
Model‐based biclustering for overdispersed count data with application in microbial ecology
Methods in Ecology and Evolution
2021
Ecological memory of recurrent drought modifies soil processes via changes in soil microbial community
Nature Communications
2021
Uncovering multi-faceted taxonomic and functional diversity of soil bacteriomes in tropical Southeast Asian countries
Scientific Reports
2021
Chemical composition controls the decomposition of organic amendments and influences the microbial community structure in agricultural soils
Carbon Management
2021
The Interplay between Campylobacter and the Caecal Microbial Community of Commercial Broiler Chickens over Time
Microorganisms
2021
Esophageal microbiome in active eosinophilic esophagitis and changes induced by different therapies
Scientific Reports
2021
Ethnic variability associating gut and oral microbiome with obesity in children
Gut Microbes
2021
The Gut Microbiota and Their Metabolites in Human Arterial Stiffness
Heart, Lung and Circulation
2021
Opposing Effects of Climate and Permafrost Thaw on CH4 and CO2 Emissions From Northern Lakes
AGU Advances
2021
Microbial and geo-archaeological records reveal the growth rate, origin and composition of desert rock surface communities
Biogeosciences
2020
Sick Individuals and Sick (Microbial) Populations: Challenges in Epidemiology and the Microbiome
Annual Review of Public Health
2020
Dissimilarity of Airway and Lung Tissue Microbiota in Smokers Undergoing Surgery for Lung Cancer
Microorganisms
2020
Soil bacterial community structures in relation to different oil palm management practices
Scientific Data
2020
Alterations of the bile microbiome in primary sclerosing cholangitis
Gut
2020
Identification of microbial interaction network: zero-inflated latent Ising model based approach
BioData Mining
2020
Influences of Climate on Phyllosphere Endophytic Bacterial Communities of Wild Poplar
Frontiers in Plant Science
2020
Salmonella Typhimurium infection disrupts but continuous feeding of Bacillus based probiotic restores gut microbiota in infected hens
Journal of Animal Science and Biotechnology
2020
Alterations of the Rectal Microbiome Are Associated with the Development of Postoperative Ileus in Patients Undergoing Colorectal Surgery
Journal of Gastrointestinal Surgery
2020
Early Signs of Gut Microbiome Aging: Biomarkers of Inflammation, Metabolism, and Macromolecular Damage in Young Adulthood
The Journals of Gerontology: Series A
2020
Naught all zeros in sequence count data are the same
Computational and Structural Biotechnology Journal
2020
Progress in Molecular Biology and Translational Science
2020
Combined effects of HIV and obesity on the gastrointestinal microbiome of young men who have sex with men
HIV Medicine
2020
A disease‐specific decline of the relative abundance of Bifidobacterium in patients with autoimmune hepatitis
Alimentary Pharmacology & Therapeutics
2020
Gut bacterial taxonomic abundances vary with cognition, personality, and mood in the Wisconsin Longitudinal Study
Brain, Behavior, & Immunity - Health
2020
Diversity of bacteria populations associated with different thallus regions of the brown alga Laminaria digitata
PLOS ONE
2020
Post‐natal co‐development of the microbiota and gut barrier function follows different paths in the small and large intestine in piglets
The FASEB Journal
2020
Incorporating Phylogenetic Information in Microbiome Differential Abundance Studies Has No Effect on Detection Power and FDR Control
Frontiers in Microbiology
2020
Effect of a Multispecies Probiotic on Intestinal and Skin Colonization by Multidrug-Resistant Gram-Negative Bacteria in Patients in a Long-Term Care Facility: A Pilot Study
Nutrients
2020
Modeling microbial abundances and dysbiosis with beta-binomial regression
The Annals of Applied Statistics
2020
Characterizing the cancer-associated microbiome with small RNA sequencing data
Biochemical and Biophysical Research Communications
2020
Maternal Linoleic Acid Overconsumption Alters Offspring Gut and Adipose Tissue Homeostasis in Young but Not Older Adult Rats
Nutrients
2020
Ecotype differences in aggression, neural activity and behaviorally relevant gene expression in cichlid fish
Genes, Brain and Behavior
2019
Postmenopause as a key factor in the composition of the Endometrial Cancer Microbiome (ECbiome)
Scientific Reports
2019
Estradiol and high fat diet associate with changes in gut microbiota in female ob/ob mice
Scientific Reports
2019
Effects of HIV viremia on the gastrointestinal microbiome of young MSM
AIDS
2019
metamicrobiomeR: an R package for analysis of microbiome relative abundance data using zero-inflated beta GAMLSS and meta-analysis across studies using random effects models
BMC Bioinformatics
2019
Caries-associated oral microbiome in head and neck cancer radiation patients: a longitudinal study
Journal of Oral Microbiology
2019
Sourcepredict: Prediction of metagenomic sample sources using dimension reduction followed by machine learning classification
Journal of Open Source Software
2019
2019
The origin and role of biological rock crusts in rocky desert weathering
Biogeosciences
2019
Phospho‐RNA‐seq: a modified small RNA‐seq method that reveals circulating mRNA and lncRNA fragments as potential biomarkers in human plasma
The EMBO Journal
2019
Alterations to the Gastrointestinal Microbiome Associated with Methamphetamine Use among Young Men who have Sex with Men
Scientific Reports
2019
Small intestinal microbial dysbiosis underlies symptoms associated with functional gastrointestinal disorders
Nature Communications
2019
Outlier Detection for Minor Compositional Variations in Taxonomic Abundance Data
Applied Sciences
2018
Enrichment of gut-derived Fusobacterium is associated with suboptimal immune recovery in HIV-infected individuals
Scientific Reports
2018
A Phylogeny-Regularized Sparse Regression Model for Predictive Modeling of Microbial Community Data
Frontiers in Microbiology
2018
Predictive Modeling of Microbiome Data Using a Phylogeny-Regularized Generalized Linear Mixed Model
Frontiers in Microbiology
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