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Microbiome data
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Links between colorectal cancer (CRC) and the gut microbiome have been established, but the specific microbial species and their role in carcinogenesis remain an active area of inquiry. Our understanding would be enhanced by better accounting for tumor subtype, microbial community interactions, metabolism, and ecology.
13p
vibransone
28-03-2024
5
2
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Understanding longitudinal variability of the microbiome in ill patients is critical to moving microbiomebased measurements and therapeutics into clinical practice. However, the vast majority of data regarding microbiome stability are derived from healthy subjects.
14p
vioraclene
31-03-2024
3
2
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The association between microbes and cancer has been reported repeatedly; however, it is not clear if molecular tumour properties are connected to specific microbial colonisation patterns. This is due mainly to the current technical and analytical strategy limitations to characterise tumour-associated bacteria.
19p
vicwell
29-02-2024
4
1
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Ebook "Anthocyanins and human health: Biomolecular and therapeutic aspects" presents comprehensive coverage of anthocyanins. The text covers the scientific literature and clinical significance of this Flavonoid sub-group, with a special focus on their therapeutic aspects. In focusing on secondary metabolites in plants, this work aims to cover the resulting therapeutic potential for humans by referencing the numerous herbal-derived substances which have been evaluated and the rapidly growing data on the interactions of anthocyanins with the microbiome.
145p
lamquandat
28-12-2023
4
2
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Phylogenetically informed distances are commonly used in the analysis of microbiome data, and analysts have many options to choose from. Although all phylogenetic distances share the goal of incorporating the phylogenetic relationships among the bacteria, they do so in different ways and give different pictures of the relationships between the bacterial communities.
16p
vigalileogalilei
27-02-2022
10
1
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Vector-borne diseases (VBDs) impact both human and veterinary medicine and pose special public health challenges. The main bacterial vector-borne pathogens (VBPs) of importance in veterinary medicine include Anaplasma spp., Bartonella spp., Ehrlichia spp., and Spotted Fever Group Rickettsia.
10p
vidarwin
23-02-2022
11
1
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Longitudinal studies are crucial for discovering causal relationships between the microbiome and human disease. We present MITRE, the Microbiome Interpretable Temporal Rule Engine, a supervised machine learning method for microbiome time-series analysis that infers human-interpretable rules linking changes in abundance of clades of microbes over time windows to binary descriptions of host status, such as the presence/absence of disease.
15p
vielonmusk
30-01-2022
13
0
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Comparative data from non-human primates provide insight into the processes that shaped the evolution of the human gut microbiome and highlight microbiome traits that differentiate humans from other primates.
12p
vielonmusk
30-01-2022
11
0
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Studies of the microbiome have become increasingly sophisticated, and multiple sequence-based, molecular methods as well as culture-based methods exist for population-scale microbiome profiles. To link the resulting host and microbial data types to human health, several experimental design considerations, data analysis challenges, and statistical epidemiological approaches must be addressed.
16p
vialfrednobel
29-01-2022
8
0
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Existing workflows for the analysis of multi-omic microbiome datasets are lab-specific and often result in sub-optimal data usage. Here we present IMP, a reproducible and modular pipeline for the integrated and reference-independent analysis of coupled metagenomic and metatranscriptomic data.
21p
vialfrednobel
29-01-2022
9
0
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Predicting dynamics of host-microbial ecosystems is crucial for the rational design of bacteriotherapies. We present MDSINE, a suite of algorithms for inferring dynamical systems models from microbiome time-series data and predicting temporal behaviors. Using simulated data, we demonstrate that MDSINE significantly outperforms the existing inference method.
17p
viaristotle
29-01-2022
11
0
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The correct identification of differentially abundant microbial taxa between experimental conditions is a methodological and computational challenge. Recent work has produced methods to deal with the high sparsity and compositionality characteristic of microbiome data, but independent benchmarks comparing these to alternatives developed for RNA-seq data analysis are lacking.
31p
viarchimedes
26-01-2022
11
2
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Microbiome meta-analysis and crossdisease comparison enabled by the SIAMCAT machine learning toolbox
The human microbiome is increasingly mined for diagnostic and therapeutic biomarkers using machine learning (ML). However, metagenomics-specific software is scarce, and overoptimistic evaluation and limited cross-study generalization are prevailing issues.
27p
viarchimedes
26-01-2022
14
0
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Structured RNAs play varied bioregulatory roles within microbes. To date, hundreds of candidate structured RNAs have been predicted using informatic approaches that search for motif structures in genomic sequence data. The human microbiome contains thousands of species and strains of microbes.
16p
viarchimedes
26-01-2022
9
1
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African populations provide a unique opportunity to interrogate hostmicrobe co-evolution and its impact on adaptive phenotypes due to their genomic, phenotypic, and cultural diversity. We integrate gut microbiome 16S rRNA amplicon and shotgun metagenomic sequence data with quantification of pathogen burden and measures of immune parameters for 575 ethnically diverse Africans from Cameroon.
32p
viarchimedes
26-01-2022
8
0
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Exploration of large data sets, such as shotgun metagenomic sequence or expression data, by biomedical experts and medical professionals remains as a major bottleneck in the scientific discovery process. Although tools for this purpose exist for 16S ribosomal RNA sequencing analysis, there is a growing but still insufficient number of user-friendly interactive visualization workflows for easy data exploration and figure generation. The development of such platforms for this purpose is necessary to accelerate and streamline microbiome laboratory research.
11p
vibeauty
23-10-2021
10
1
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Modern metagenomic analysis of complex microbial communities produces large amounts of sequence data containing information on the microbiome in terms of bacterial, archaeal, viral and eukaryotic composition. The bioinformatics tools available are mainly devoted to profiling the bacterial and viral fractions and only a few software packages consider fungi.
7p
visilicon2711
20-08-2021
10
1
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Metagenomic sequencing is a powerful technology for studying the mixture of microbes or the microbiomes on human and in the environment. One basic task of analyzing metagenomic data is to identify the component genomes in the community.
9p
visilicon2711
20-08-2021
11
1
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The explosive growth of microbiome data provides ample opportunities to gain a better understanding of the microbes and their interactions in microbial communities. Given these massive data, optimized data mining methods become important and necessary to perform deep and comprehensive analysis.
9p
visilicon2711
20-08-2021
11
1
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One of the major challenges in microbial studies is detecting associations between microbial communities and a specific disease. A specialized feature of microbiome count data is that intestinal bacterial communities form clusters called as “enterotype”, which are characterized by differences in specific bacterial taxa, making it difficult to analyze these data under health and disease conditions.
13p
visilicon2711
20-08-2021
10
1
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