Microbiome datasets are compositional: and this is not optional
Datasets collected by high-throughput sequencing (HTS) of 16S rRNA gene amplimers,
metagenomes or metatranscriptomes are commonplace and being used to study human …
metagenomes or metatranscriptomes are commonplace and being used to study human …
[HTML][HTML] Network analysis methods for studying microbial communities: A mini review
MS Matchado, M Lauber, S Reitmeier… - Computational and …, 2021 - Elsevier
Microorganisms including bacteria, fungi, viruses, protists and archaea live as communities
in complex and contiguous environments. They engage in numerous inter-and intra …
in complex and contiguous environments. They engage in numerous inter-and intra …
NetCoMi: network construction and comparison for microbiome data in R
Motivation Estimating microbial association networks from high-throughput sequencing data
is a common exploratory data analysis approach aiming at understanding the complex …
is a common exploratory data analysis approach aiming at understanding the complex …
Understanding sequencing data as compositions: an outlook and review
Motivation Although seldom acknowledged explicitly, count data generated by sequencing
platforms exist as compositions for which the abundance of each component (eg gene or …
platforms exist as compositions for which the abundance of each component (eg gene or …
A field guide for the compositional analysis of any-omics data
Background Next-generation sequencing (NGS) has made it possible to determine the
sequence and relative abundance of all nucleotides in a biological or environmental …
sequence and relative abundance of all nucleotides in a biological or environmental …
Gut microbiome composition is predictive of incident type 2 diabetes in a population cohort of 5,572 Finnish adults
OBJECTIVE To examine the previously unknown long-term association between gut
microbiome composition and incident type 2 diabetes in a representative population cohort …
microbiome composition and incident type 2 diabetes in a representative population cohort …
ATTED-II v11: a plant gene coexpression database using a sample balancing technique by subagging of principal components
Abstract ATTED-II (https://atted. jp) is a gene coexpression database for nine plant species
based on publicly available RNAseq and microarray data. One of the challenges in …
based on publicly available RNAseq and microarray data. One of the challenges in …
Single-cell network biology for resolving cellular heterogeneity in human diseases
Understanding cellular heterogeneity is the holy grail of biology and medicine. Cells
harboring identical genomes show a wide variety of behaviors in multicellular organisms …
harboring identical genomes show a wide variety of behaviors in multicellular organisms …
The functional evolution of termite gut microbiota
Background Termites primarily feed on lignocellulose or soil in association with specific gut
microbes. The functioning of the termite gut microbiota is partly understood in a handful of …
microbes. The functioning of the termite gut microbiota is partly understood in a handful of …
Species-level analysis of human gut microbiota with metataxonomics
J Yang, J Pu, S Lu, X Bai, Y Wu, D **… - Frontiers in …, 2020 - frontiersin.org
The current understanding of human gut microbial community is mainly limited to taxonomic
features at the genus level. Here, we examined the human gut microbial community at the …
features at the genus level. Here, we examined the human gut microbial community at the …