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   Articles with "microbiome data" as a keyword



SuRF: A new method for sparse variable selection, with application in microbiome data analysis.

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recommendations! Published in 2020 at "Statistics in medicine"

DOI: 10.1002/sim.8809

Abstract: In this article, we present a new variable selection method for regression and classification purposes, particularly for microbiome analysis. Our method, called subsampling ranking forward selection (SuRF), is based on LASSO penalized regression, subsampling and… read more here.

Keywords: analysis; method; selection; variable selection ... See more keywords
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Processing and Analyzing Human Microbiome Data.

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recommendations! Published in 2017 at "Methods in molecular biology"

DOI: 10.1007/978-1-4939-7274-6_31

Abstract: The human microbiome is associated with complex disorders such as diabetes, cancer, obesity and cardiovascular disorders. Recent technological developments have allowed researchers to fully quantify the composition of the microbiome using culture-independent approaches, resulting in… read more here.

Keywords: processing analyzing; human microbiome; microbiome; analyzing human ... See more keywords

Fast and flexible analysis of linked microbiome data with mako.

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recommendations! Published in 2021 at "Nature methods"

DOI: 10.1038/s41592-021-01335-9

Abstract: Mako is a software tool that converts microbiome data and networks into a graph database and visualizes query results, thus allowing users without programming knowledge to carry out network-based queries. Mako is accompanied by a… read more here.

Keywords: fast flexible; flexible analysis; microbiome data; data mako ... See more keywords

Fox Insight at 5 years - a cohort of 54,000 participants contributing longitudinal patient-reported outcome, genetic, and microbiome data relating to Parkinson’s disease

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recommendations! Published in 2024 at "Scientific Data"

DOI: 10.1038/s41597-024-03407-9

Abstract: Fox Insight is an online, longitudinal study of over 54,000 people with and without Parkinson’s disease, facilitating discovery, validation, and reproducibility in Parkinson’s disease research. The study administers routine longitudinal assessments, one-time questionnaires on an… read more here.

Keywords: disease; microbiome data; fox insight; parkinson disease ... See more keywords

Quantifying the impact of workshops promoting microbiome data standards and data stewardship

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recommendations! Published in 2025 at "Scientific Reports"

DOI: 10.1038/s41598-025-89991-1

Abstract: The field of microbiome research continues to grow at a rapid pace, with multi-omics approaches becoming widely used to interrogate diverse microbiome samples. However, due to lagging awareness and implementation of standards and data stewardship,… read more here.

Keywords: data stewardship; cohort; microbiome data; standards data ... See more keywords

Mixtures of logistic normal multinomial regression models for microbiome data

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recommendations! Published in 2024 at "Journal of Applied Statistics"

DOI: 10.1080/02664763.2024.2383286

Abstract: In the realm of bioinformatics, we frequently encounter discrete data, particularly microbiome taxa count data obtained through 16S rRNA sequencing. These microbiome datasets are commonly characterized by their high dimensionality and the ability to provide… read more here.

Keywords: mixtures logistic; microbiome data; normal multinomial; multinomial regression ... See more keywords

A novel deep learning method for predictive modeling of microbiome data

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recommendations! Published in 2021 at "Briefings in bioinformatics"

DOI: 10.1093/bib/bbaa073

Abstract: With the development and decreasing cost of next-generation sequencing technologies, the study of the human microbiome has become a rapid expanding research field, which provides an unprecedented opportunity in various clinical applications such as drug… read more here.

Keywords: microbiome data; phylogenetic tree; method; deep learning ... See more keywords

Principal microbial groups: compositional alternative to phylogenetic grouping of microbiome data

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recommendations! Published in 2022 at "Briefings in bioinformatics"

DOI: 10.1093/bib/bbac328

Abstract: Statistical and machine learning techniques based on relative abundances have been used to predict health conditions and to identify microbial biomarkers. However, high dimensionality, sparsity and the compositional nature of microbiome data represent statistical challenges.… read more here.

Keywords: microbial groups; microbiome data; procedure; taxon grouping ... See more keywords

PLSDA-batch: a multivariate framework to correct for batch effects in microbiome data

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recommendations! Published in 2023 at "Briefings in Bioinformatics"

DOI: 10.1093/bib/bbac622

Abstract: Abstract Microbial communities are highly dynamic and sensitive to changes in the environment. Thus, microbiome data are highly susceptible to batch effects, defined as sources of unwanted variation that are not related to and obscure… read more here.

Keywords: batch effects; microbiome data; variation; plsda batch ... See more keywords

A novel normalization and differential abundance test framework for microbiome data

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recommendations! Published in 2020 at "Bioinformatics"

DOI: 10.1093/bioinformatics/btaa255

Abstract: MOTIVATION Microbial communities have been proved to have close relationship with many diseases. The identification of differentially abundant microbial species is clinically meaningful for finding disease-related pathogenic or probiotic bacteria. However, certain characteristics of microbiome… read more here.

Keywords: framework; abundance; size; microbiome data ... See more keywords

To rarefy or not to rarefy: robustness and efficiency trade-offs of rarefying microbiome data.

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recommendations! Published in 2022 at "Bioinformatics"

DOI: 10.1093/bioinformatics/btac127

Abstract: MOTIVATION Microbiome datasets provide rich information about microbial communities. However, vast library size variations across samples present great challenges for proper statistical comparisons. To deal with these challenges, rarefaction is often used in practice as… read more here.

Keywords: microbiome data; rarefying microbiome; rarefy; efficiency ... See more keywords