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2025
Microorganisms for Sustainability
2025
Optimization of Mapping Tools and Investigation of Ribosomal RNA Influence for Data-Driven Gene Expression Analysis in Complex Microbiomes
Microorganisms
2025
Environmental RNA‐Based Metatranscriptomics as a Novel Biomonitoring Tool: A Case Study of Glyphosate‐Based Herbicide Effects on Freshwater Eukaryotic Communities
Molecular Ecology
2025
Core cooperative metabolism in low-complexity CO2-fixing anaerobic microbiota
The ISME Journal
2025
Predicting functions of uncharacterized gene products from microbial communities
Nature Biotechnology
2025
Multiomics Integration Reveals Microbial Gene Interactions Shaping Host Responses in a DSS-Induced Colitis Mouse Model
Journal of Microbiology and Biotechnology
2025
Sublethal systemic LPS in mice enables gut-luminal pathogens to bloom through oxygen species-mediated microbiota inhibition
Nature Communications
2025
QS molecules change the planktonic/mineral subpopulations distribution of moderately thermophilic leaching bacteria in pyrite and decrease leaching in chalcopyrite
Frontiers in Microbiology
2025
Functional stability of Spirochaetota symbionts in the precious octocoral Corallium rubrum under heat stress
Environmental Microbiome
2024
Heterogeneous lineage-specific arginine deiminase expression within dental microbiome species
Microbiology Spectrum
2024
Diverse epistatic effects in barley-powdery mildew interactions localize to host chromosome hotspots
iScience
2024
Structural and functional analysis of the active cow rumen’s microbial community provides a catalogue of genes and microbes participating in the deconstruction of cardoon biomass
Biotechnology for Biofuels and Bioproducts
2024
Taxanorm: a novel taxa-specific normalization approach for microbiome data
BMC Bioinformatics
2024
Prevotella copri and microbiota members mediate the beneficial effects of a therapeutic food for malnutrition
Nature Microbiology
2023
Metatranscriptomics-guided genome-scale metabolic modeling of microbial communities
Cell Reports Methods
2023
Physiological and evolutionary contexts of a new symbiotic species from the nitrogen-recycling gut community of turtle ants
The ISME Journal
2023
Current concepts, advances, and challenges in deciphering the human microbiota with metatranscriptomics
Trends in Genetics
2023
Consistency across multi‐omics layers in a drug‐perturbed gut microbial community
Molecular Systems Biology
2023
The hitchhikers’ guide to RNA sequencing and functional analysis
Briefings in Bioinformatics
2022
A Framework for Comparison and Assessment of Synthetic RNA-Seq Data
Genes
2022
Marine Microeukaryote Metatranscriptomics: Sample Processing and Bioinformatic Workflow Recommendations for Ecological Applications
Frontiers in Marine Science
2021
Metatranscriptomics for the Human Microbiome and Microbial Community Functional Profiling
Annual Review of Biomedical Data Science
2021
Disruption of barley immunity to powdery mildew by an in-frame Lys-Leu deletion in the essential protein SGT1
Genetics
2021
Insights into rumen microbial biosynthetic gene cluster diversity through genome-resolved metagenomics
Communications Biology
2021
Microbial Metatranscriptomics Belowground
2021
Statistical approaches for differential expression analysis in metatranscriptomics
Bioinformatics
2020
Reverse engineering directed gene regulatory networks from transcriptomics and proteomics data of biomining bacterial communities with approximate Bayesian computation and steady-state signalling simulations
BMC Bioinformatics
2020
Systems biology of acidophile biofilms for efficient metal extraction
Scientific Data
2020
Mining the proliferative diabetic retinopathy-associated genes and pathways by integrated bioinformatic analysis
International Ophthalmology
2019
Determining Microbial Roles in Ecosystem Function: Redefining Microbial Food Webs and Transcending Kingdom Barriers
mSystems
2019
Meta-transcriptomics reveals a diverse antibiotic resistance gene pool in avian microbiomes
BMC Biology
2019
Advances and Challenges in Metatranscriptomic Analysis
Frontiers in Genetics
2018
Automated Microscopic Analysis of Metal Sulfide Colonization by Acidophilic Microorganisms
Applied and Environmental Microbiology
2018
Weak Iron Oxidation by Sulfobacillus thermosulfidooxidans Maintains a Favorable Redox Potential for Chalcopyrite Bioleaching
Frontiers in Microbiology
2018
Novel soil bacteria possess diverse genes for secondary metabolite biosynthesis
Nature
2018
Gene expression of indoor fungal communities under damp building conditions: Implications for human health
Indoor Air
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