Metagenomics, metatranscriptomics, and metabolomics approaches for microbiome analysis: supplementary issue: bioinformatics methods and applications for big …

V Aguiar-Pulido, W Huang… - Evolutionary …, 2016 - journals.sagepub.com
Microbiomes are ubiquitous and are found in the ocean, the soil, and in/on other living
organisms. Changes in the microbiome can impact the health of the environmental niche in …

Computational meta'omics for microbial community studies

N Segata, D Boernigen, TL Tickle… - Molecular systems …, 2013 - embopress.org
Complex microbial communities are an integral part of the Earth's ecosystem and of our
bodies in health and disease. In the last two decades, culture‐independent approaches …

Bioinformatics tools for quantitative and functional metagenome and metatranscriptome data analysis in microbes

SY Niu, J Yang, A McDermaid, J Zhao… - Briefings in …, 2018 - academic.oup.com
Metagenomic and metatranscriptomic sequencing approaches are more frequently being
used to link microbiota to important diseases and ecological changes. Many analyses have …

Advances and challenges in metatranscriptomic analysis

M Shakya, CC Lo, PSG Chain - Frontiers in genetics, 2019 - frontiersin.org
Sequencing-based analyses of microbiomes have traditionally focused on addressing the
question of community membership and profiling taxonomic abundance through amplicon …

Current opportunities and challenges in microbial metagenome analysis—a bioinformatic perspective

H Teeling, FO Glöckner - Briefings in bioinformatics, 2012 - academic.oup.com
Metagenomics has become an indispensable tool for studying the diversity and metabolic
potential of environmental microbes, whose bulk is as yet non-cultivable. Continual progress …

Metatranscriptomic analysis of diverse microbial communities reveals core metabolic pathways and microbiome-specific functionality

Y Jiang, X Xiong, J Danska, J Parkinson - Microbiome, 2016 - Springer
Background Metatranscriptomics is emerging as a powerful technology for the functional
characterization of complex microbial communities (microbiomes). Use of unbiased RNA …

Towards biome-specific analysis of meta-omics data

Y Darzi, G Falony, S Vieira-Silva, J Raes - The ISME journal, 2016 - academic.oup.com
Microbial ecology has witnessed tremendous progress over the last decade empowered by
metaomics approaches and innovations in DNA/RNA sequencing as well as high-resolution …

gcMeta: a Global Catalogue of Metagenomics platform to support the archiving, standardization and analysis of microbiome data

W Shi, H Qi, Q Sun, G Fan, S Liu, J Wang… - Nucleic acids …, 2019 - academic.oup.com
Meta-omics approaches have been increasingly used to study the structure and function of
the microbial communities. A variety of large-scale collaborative projects are being …

The use of metagenomic approaches to analyze changes in microbial communities

G Neelakanta, H Sultana - Microbiology insights, 2013 - journals.sagepub.com
Microbes are the most abundant biological entities found in the biosphere. Identification and
measurement of microorganisms (including viruses, bacteria, archaea, fungi, and protists) in …

Toward accurate and quantitative comparative metagenomics

S Nayfach, KS Pollard - Cell, 2016 - cell.com
Shotgun metagenomics and computational analysis are used to compare the taxonomic and
functional profiles of microbial communities. Leveraging this approach to understand roles of …