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Haris Zafeiropoulos, Daniel Garza
Flux sampling is an analysis that, based on a distribution, picks randomly an efficient number of points from the solution space of a metabolic model. Unlike most constraint-based analyses, flux sampling does not require an objective function to optimize, allowing for the …
Haris Zafeiropoulos, Daniel Garza
Flux sampling is an analysis that, based on a distribution, picks randomly an efficient number of points from the solution space of a metabolic model. Unlike most constraint-based analyses, flux sampling does not require an objective function to optimize, allowing for the …
be, fr (code pays fourni par la source)
Andrew Radev, Julia Casado Gómez-Pallete, Sofia Duarte, Karoline Faust et autres
Abstract Microbial growth curve data contain valuable information about microorganisms’ physiology and metabolism. However, they are currently reported in various formats scattered across publications. A generic resource that allows querying and comparing microbial growth curve data is currently missing. For this reason, …
be (code pays fourni par la source)
Robert D. Finn, Bachir Balech, Josephine Burgin, Physilia Chua et autres
Microbiome research has grown substantially over the past decade in terms of the range of biomes sampled, identified taxa, and the volume of data derived from the samples. In particular, experimental approaches such as metagenomics, metabarcoding, metatranscriptomics and metaproteomics have provided profound …
gb, it, us, fr, pt, nl, si, de, lu, ni, Afrique du Sud, gr, be, no (code pays fourni par la source)
In this repository we keep internal data for the microbetag microbial co-occurrence network annotator. microbetag makes use of 2-column files for each genome, indicating the KO term found and a KEGG module in which this terms takes part into. As a single …
Haris Zafeiropoulos, Ermis Ioannis Michail Delopoulos, Andi Erega, Aline Schneider et autres
Microbial co-occurrence network inference is often hindered by low accuracy and tool dependency. We introduce microbetag, a comprehensive software ecosystem designed to annotate microbial networks. Nodes, representing taxa, are enriched with phenotypic traits, while edges are enhanced with metabolic complementarities, highlighting potential …
be, ch, us (code pays fourni par la source)
Robert D. Finn, Bachir Balech, Josephine Burgin, Physilia Chua et autres
Microbiome research has grown substantially over the past decade in terms of the range of biomes sampled, identified taxa, and the volume of data derived from the samples. In particular, experimental approaches such as metagenomics, metabarcoding, metatranscriptomics and metaproteomics have provided profound …
gb, it, us, fr, pt, nl, si, de, lu, ni, Afrique du Sud, gr, be, no (code pays fourni par la source)
ROBERT FINN, Bachir Balech, Josephine Burgin, Physilia Chua et autres
Microbiome research has grown substantially over the past decade in terms of the range of biomes sampled, identified taxa, and the volume of data derived from the samples. In particular, experimental approaches such as metagenomics, metabarcoding, metatranscriptomics and metaproteomics have provided profound …
gb, it, us, fr, pt, nl, si, de, lu, ni, Afrique du Sud, gr, be, no (code pays fourni par la source)
In this repo, the crest4 and the RDPClassifier oriented databases used in PEMA will be versioned. We list the provided databases per marker gene: Marker Gene crest4 Databases RDPClassifier Databases Version COI midori2 (darn processed) midori1, midori2 16S Silva128, Silvamod138pr2 (SILVA v138 …
Nauras Daraghmeh, Katrina Exter, Justine Pagnier, Piotr Bałazy et autres
Molecular methods such as DNA/eDNA metabarcoding have emerged as useful tools to document the biodiversity of complex communities over large spatio-temporal scales. We established an international Marine Biodiversity Observation Network (ARMS-MBON) combining standardised sampling using autonomous reef monitoring structures (ARMS) with metabarcoding …
se, be, es, pl, gr, gb, fr, fi, il, si, no, dk (code pays fourni par la source)
Dimitrios Skliros, Maria Kostakou, Constantina Kokkari, Maria Ioanna Tsertou et autres
The importance of microbial communities in fish hatcheries for fish health and welfare has been recognized, with several studies mapping these communities during healthy rearing conditions and disease outbreaks. In this study, we analyzed the bacteriome of the live feeds, such as …
gr, de, fr, be (code pays fourni par la source)
Meine D. Boer, Chrats Melkonian, Haris Zafeiropoulos, Andreas F. Haas et autres
Deciphering microbial metabolism is essential for understanding ecosystem functions. Genome-scale metabolic models (GSMMs) predict metabolic traits from genomic data, but constructing GSMMs for uncultured bacteria is challenging due to incomplete metagenome-assembled genomes, resulting in many gaps. We introduce the deep neural network …
nl, be, fr, de (code pays fourni par la source)
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