Best practices for analysing microbiomes

R Knight, A Vrbanac, BC Taylor, A Aksenov… - Nature Reviews …, 2018 - nature.com
Complex microbial communities shape the dynamics of various environments, ranging from
the mammalian gastrointestinal tract to the soil. Advances in DNA sequencing technologies …

A tutorial review: Metabolomics and partial least squares-discriminant analysis–a marriage of convenience or a shotgun wedding

PS Gromski, H Muhamadali, DI Ellis, Y Xu, E Correa… - Analytica chimica …, 2015 - Elsevier
The predominance of partial least squares-discriminant analysis (PLS-DA) used to analyze
metabolomics datasets (indeed, it is the most well-known tool to perform classification and …

mixOmics: An R package for 'omics feature selection and multiple data integration

F Rohart, B Gautier, A Singh… - PLoS computational …, 2017 - journals.plos.org
The advent of high throughput technologies has led to a wealth of publicly available 'omics
data coming from different sources, such as transcriptomics, proteomics, metabolomics …

Integrated omics: tools, advances and future approaches

BB Misra, C Langefeld, M Olivier… - Journal of molecular …, 2019 - jme.bioscientifica.com
With the rapid adoption of high-throughput omic approaches to analyze biological samples
such as genomics, transcriptomics, proteomics, and metabolomics, each analysis can …

From big data analysis to personalized medicine for all: challenges and opportunities

A Alyass, M Turcotte, D Meyre - BMC medical genomics, 2015 - Springer
Recent advances in high-throughput technologies have led to the emergence of systems
biology as a holistic science to achieve more precise modeling of complex diseases. Many …

Multi-omics data integration considerations and study design for biological systems and disease

S Graw, K Chappell, CL Washam, A Gies, J Bird… - Molecular omics, 2021 - pubs.rsc.org
With the advancement of next-generation sequencing and mass spectrometry, there is a
growing need for the ability to merge biological features in order to study a system as a …

Methods for the integration of multi-omics data: mathematical aspects

M Bersanelli, E Mosca, D Remondini, E Giampieri… - BMC …, 2016 - Springer
Background Methods for the integrative analysis of multi-omics data are required to draw a
more complete and accurate picture of the dynamics of molecular systems. The complexity …

Prospects and challenges of multi-omics data integration in toxicology

S Canzler, J Schor, W Busch, K Schubert… - Archives of …, 2020 - Springer
Exposure of cells or organisms to chemicals can trigger a series of effects at the regulatory
pathway level, which involve changes of levels, interactions, and feedback loops of …

Morphometric, behavioral, and genomic evidence for a new orangutan species

A Nater, MP Mattle-Greminger, A Nurcahyo, MG Nowak… - Current Biology, 2017 - cell.com
Six extant species of non-human great apes are currently recognized: Sumatran and
Bornean orangutans, eastern and western gorillas, and chimpanzees and bonobos [1] …

Early‐life establishment of the swine gut microbiome and impact on host phenotypes

N Mach, M Berri, J Estellé, F Levenez… - Environmental …, 2015 - Wiley Online Library
Early bacterial colonization and succession within the gastrointestinal tract has been
suggested to be crucial in the establishment of specific microbiota composition and the …