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BinaRena: a dedicated interactive platform for human-guided exploration and binning of metagenomes
BackgroundExploring metagenomic contigs and “binning” them into metagenome-assembled genomes (MAGs) are essential for the delineation of functional...
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Integrating metagenomic binning with flux balance analysis to unravel syntrophies in anaerobic CO2 methanation
BackgroundCarbon fixation through biological methanation has emerged as a promising technology to produce renewable energy in the context of the...
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Optimal Binning for Finding High Risk Cut-offs (1445 Families)
Optimal binning is a so-called non-metric method for describing a continuous predictor variable in the form of best fit categories for making...
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A human antibody epitope map of the malaria vaccine antigen Pfs25
Pfs25 is a leading antigen for a malaria transmission-blocking vaccine and shows moderate transmission-blocking activity and induction of rapidly...
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Unraveling metagenomics through long-read sequencing: a comprehensive review
The study of microbial communities has undergone significant advancements, starting from the initial use of 16S rRNA sequencing to the adoption of...
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A novel amplitude binning strategy to handle irregular breathing during 4DMRI acquisition: improved imaging for radiotherapy purposes
BackgroundFor radiotherapy of abdominal cancer, four-dimensional magnetic resonance imaging (4DMRI) is desirable for tumor definition and the...
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Investigation of fiber utilization in the rumen of dairy cows based on metagenome-assembled genomes and single-cell RNA sequencing
BackgroundDairy cows utilize human-inedible, low-value plant biomass to produce milk, a low-cost product with rich nutrients and high proteins. This...
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Metagenomic insights into microbial adaptation to the salinity gradient of a typical short residence-time estuary
BackgroundMicrobial adaptation to salinity has been a classic inquiry in the field of microbiology. It has been demonstrated that microorganisms can...
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Recovery of strain-resolved genomes from human microbiome through an integration framework of single-cell genomics and metagenomics
BackgroundObtaining high-quality (HQ) reference genomes from microbial communities is crucial for understanding the phylogeny and function of...
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Compendium of 5810 genomes of sheep and goat gut microbiomes provides new insights into the glycan and mucin utilization
BackgroundRuminant gut microbiota are critical in ecological adaptation, evolution, and nutrition utilization because it regulates energy metabolism,...
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Characterization of diazotrophic root endophytes in Chinese silvergrass (Miscanthus sinensis)
BackgroundPhytoremediation is a potentially cost-effective way to remediate highly contaminated mine tailing sites. However, nutrient limitations,...
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Analysis of the anaerobic digestion metagenome under environmental stresses stimulating prophage induction
BackgroundThe viral community has the potential to influence the structure of the microbiome and thus the yield of the anaerobic digestion process....
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Visualization-assisted binning of metagenome assemblies reveals potential new pathogenic profiles in idiopathic travelers’ diarrhea
BackgroundTravelers’ diarrhea (TD) is often caused by enterotoxigenic Escherichia coli , enteroaggregative E . coli , other bacterial pathogens,...
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High-quality bacterial genomes of a partial-nitritation/anammox system by an iterative hybrid assembly method
BackgroundGenome-centric approaches are widely used to investigate microbial compositions, dynamics, ecology, and interactions within various...
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Oxygen Assessment in Tumors In Vivo Using Phosphorescence Lifetime Imaging Microscopy
The oxygen level in a tumor is a crucial factor for its development and response to therapies. Phosphorescence lifetime imaging (PLIM) with the use...
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Genome-resolved metagenomics: a game changer for microbiome medicine
Recent substantial evidence implicating commensal bacteria in human diseases has given rise to a new domain in biomedical research: microbiome...
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Freshwater Viral Metagenome Analyses Targeting dsDNA Viruses
Viral metagenomics is one of the most widely used approaches to study viral population genomics. With the recent development of bioinformatic tools,...
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In Vivo Bioluminescence and Fluorescence Imaging: Optical Tool for Cancer Research
In vivo whole-body imaging, using optical tools based on bioluminescence and fluorescence detection, offers tremendous opportunities to specifically...
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Microbiome Data Analysis and Interpretation: Correlation Inference and Dynamic Pattern Discovery
Microbial communities are everywhere within our bodies and in the environments (Byrd et al. n.d.), which play a key role in human health and all...
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Shotgun metagenomic analysis reveals new insights into bacterial community profiles in tempeh
ObjectiveAmplicon sequencing targeting 16S ribosomal RNA (rRNA) has been widely used to profile the microbial community from fermented food samples....
