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2024
An enterococcal phage-derived enzyme suppresses graft-versus-host disease
Nature
2024
Machine learning for microbiologists
Nature Reviews Microbiology
2024
Applications of Metagenomics
2024
Soil Microbiology, Ecology and Biochemistry
2024
MetageNN: a memory-efficient neural network taxonomic classifier robust to sequencing errors and missing genomes
BMC Bioinformatics
2024
Step-by-Step Metagenomics for Food Microbiome Analysis: A Detailed Review
Foods
2024
Review on computer-assisted biosynthetic capacities elucidation to assess metabolic interactions and communication within microbial communities
Critical Reviews in Microbiology
2023
Microbial Symbionts
2023
Influence of soil nutrients on the presence and distribution of CPR bacteria in a long-term crop rotation experiment
Frontiers in Microbiology
2023
Zero-shot-capable identification of phage–host relationships with whole-genome sequence representation by contrastive learning
Briefings in Bioinformatics
2023
Recent Advances in Metagenomic Approaches, Applications, and Challenges
Current Microbiology
2022
MetaCRS: unsupervised clustering of contigs with the recursive strategy of reducing metagenomic dataset’s complexity
BMC Bioinformatics
2022
BugSplit enables genome-resolved metagenomics through highly accurate taxonomic binning of metagenomic assemblies
Communications Biology
2022
Predominance of Methanomicrobiales and diverse hydrocarbon‐degrading taxa in the Appalachian coalbed biosphere revealed through metagenomics and genome‐resolved metabolisms
Environmental Microbiology
2022
Potential Use of Microbial Community Genomes in Various Dimensions of Agriculture Productivity and Its Management: A Review
Frontiers in Microbiology
2022
MetaDecoder: a novel method for clustering metagenomic contigs
Microbiome
2022
Binning Metagenomic Contigs Using Unsupervised Clustering and Reference Databases
Interdisciplinary Sciences: Computational Life Sciences
2021
Tutorial: assessing metagenomics software with the CAMI benchmarking toolkit
Nature Protocols
2021
Methods in Molecular Biology
2021
Functional Restoration of Bacteriomes and Viromes by Fecal Microbiota Transplantation
Gastroenterology
2021
Taxonomic classification of metagenomic sequences from Relative Abundance Index profiles using deep learning
Biomedical Signal Processing and Control
2021
The endophytome (plant-associated microbiome): methodological approaches, biological aspects, and biotech applications
World Journal of Microbiology and Biotechnology
2021
Wastewater Treatment Reactors
2021
Advances in Bioinformatics
2020
Carbon Assimilation Strategies in Ultrabasic Groundwater: Clues from the Integrated Study of a Serpentinization-Influenced Aquifer
mSystems
2020
Localized effect of treated wastewater effluent on the resistome of an urban watershed
GigaScience
2020
Implications of Error-Prone Long-Read Whole-Genome Shotgun Sequencing on Characterizing Reference Microbiomes
iScience
2020
Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analyses
Microbial Genomics
2020
Molecular and morphological characterization of a novel dihydroanatoxin-a producing Microcoleus species (cyanobacteria) from the Russian River, California, USA
Harmful Algae
2020
Metagenome Data on Intestinal Phage-Bacteria Associations Aids the Development of Phage Therapy against Pathobionts
Cell Host & Microbe
2020
A dynamic microbial sulfur cycle in a serpentinizing continental ophiolite
Environmental Microbiology
2020
Genomic Evidence for Formate Metabolism by Chloroflexi as the Key to Unlocking Deep Carbon in Lost City Microbial Ecosystems
Applied and Environmental Microbiology
2020
Metagenomics methods for the study of plant-associated microbial communities: A review
Journal of Microbiological Methods
2020
Metalign: efficient alignment-based metagenomic profiling via containment min hash
Genome Biology
2020
An Integrated Metagenome Catalog Reveals New Insights into the Murine Gut Microbiome
Cell Reports
2019
SeqDeχ: A Sequence Deconvolution Tool for Genome Separation of Endosymbionts From Mixed Sequencing Samples
Frontiers in Genetics
2019
Identifying accurate metagenome and amplicon software via a meta-analysis of sequence to taxonomy benchmarking studies
PeerJ
2019
Robust taxonomic classification of uncharted microbial sequences and bins with CAT and BAT
Genome Biology
2019
Niche Differentiation among Three Closely RelatedCompetibacteraceaeClades at a Full-Scale Activated Sludge Wastewater Treatment Plant and Putative Linkages to Process Performance
Applied and Environmental Microbiology
2019
Methods in Molecular Biology
2019
Machine Learning Approaches for Epidemiological Investigations of Food-Borne Disease Outbreaks
Frontiers in Microbiology
2019
Advances in Experimental Medicine and Biology
2019
2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
2019
Substrate specificities of aromatic ring-hydroxylating oxygenases of an uncultured gammaproteobacterium from chronically-polluted subantarctic sediments
International Biodeterioration & Biodegradation
2019
A review of methods and databases for metagenomic classification and assembly
Briefings in Bioinformatics
2019
Strain-level metagenomic assignment and compositional estimation for long reads with MetaMaps
Nature Communications
2018
BLAST-based validation of metagenomic sequence assignments
PeerJ
2018
Methods in Molecular Biology
2018
A closely-related clade of globally distributed bloom-forming cyanobacteria within the Nostocales
Harmful Algae
2018
Microbial effects of part-stream low-frequency ultrasonic pretreatment on sludge anaerobic digestion as revealed by high-throughput sequencing-based metagenomics and metatranscriptomics
Biotechnology for Biofuels
2018
Genomic Approaches in Earth and Environmental Sciences
2017
BusyBee Web: metagenomic data analysis by bootstrapped supervised binning and annotation
Nucleic Acids Research
2017
Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software
Nature Methods
2017
Bioinformatics for NGS-based metagenomics and the application to biogas research
Journal of Biotechnology
2017
Unexpected Dominance of Elusive Acidobacteria in Early Industrial Soft Coal Slags
Frontiers in Microbiology
2017
Draft Genome Sequences of Nine Cyanobacterial Strains from Diverse Habitats
Genome Announcements
2017
Advances in Virus Research
2017
A probabilistic model to recover individual genomes from metagenomes
PeerJ Computer Science
2017
A Metagenomic Approach to Cyanobacterial Genomics
Frontiers in Microbiology
2017
Origins and challenges of viral dark matter
Virus Research
2017
Methods in Molecular Biology
2016
‘Candidatus Adiutrix intracellularis’, an endosymbiont of termite gut flagellates, is the first representative of a deep‐branching clade of Deltaproteobacteria and a putative homoacetogen
Environmental Microbiology
2016
Comparing genome versus proteome-based identification of clinical bacterial isolates
Briefings in Bioinformatics
2016
Elucidation of Taste- and Odor-Producing Bacteria and Toxigenic Cyanobacteria in a Midwestern Drinking Water Supply Reservoir by Shotgun Metagenomic Analysis
Applied and Environmental Microbiology
2016
Novel Syntrophic Populations Dominate an Ammonia-Tolerant Methanogenic Microbiome
mSystems
2016
From Genomes to Phenotypes: Traitar, the Microbial Trait Analyzer
mSystems
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