The road to metagenomics: from microbiology to DNA sequencing technologies and bioinformatics
A Escobar-Zepeda, A Vera-Ponce de León… - Frontiers in …, 2015 - frontiersin.org
The study of microorganisms that pervade each and every part of this planet has
encountered many challenges through time such as the discovery of unknown organisms …
encountered many challenges through time such as the discovery of unknown organisms …
Metagenome analysis: a powerful tool for enzyme bioprospecting
A Madhavan, R Sindhu, B Parameswaran… - Applied biochemistry …, 2017 - Springer
Microorganisms are found throughout every corner of nature, and vast number of
microorganisms is difficult to cultivate by classical microbiological techniques. The advent of …
microorganisms is difficult to cultivate by classical microbiological techniques. The advent of …
[PDF][PDF] MicrobiomeAnalyst: a web-based tool for comprehensive statistical, visual and meta-analysis of microbiome data
The widespread application of next-generation sequencing technologies has revolutionized
microbiome research by enabling high-throughput profiling of the genetic contents of …
microbiome research by enabling high-throughput profiling of the genetic contents of …
Glycine-based treatment ameliorates NAFLD by modulating fatty acid oxidation, glutathione synthesis, and the gut microbiome
Nonalcoholic fatty liver disease (NAFLD) including nonalcoholic steatohepatitis (NASH) has
reached epidemic proportions with no pharmacological therapy approved. Lower circulating …
reached epidemic proportions with no pharmacological therapy approved. Lower circulating …
[HTML][HTML] Bioconductor workflow for microbiome data analysis: from raw reads to community analyses
High-throughput sequencing of PCR-amplified taxonomic markers (like the 16S rRNA gene)
has enabled a new level of analysis of complex bacterial communities known as …
has enabled a new level of analysis of complex bacterial communities known as …
Rhea: a transparent and modular R pipeline for microbial profiling based on 16S rRNA gene amplicons
The importance of 16S rRNA gene amplicon profiles for understanding the influence of
microbes in a variety of environments coupled with the steep reduction in sequencing costs …
microbes in a variety of environments coupled with the steep reduction in sequencing costs …
Pavian: interactive analysis of metagenomics data for microbiome studies and pathogen identification
FP Breitwieser, SL Salzberg - Bioinformatics, 2020 - academic.oup.com
Pavian is a web application for exploring classification results from metagenomics
experiments. With Pavian, researchers can analyze, visualize and transform results from …
experiments. With Pavian, researchers can analyze, visualize and transform results from …
[HTML][HTML] ranacapa: An R package and Shiny web app to explore environmental DNA data with exploratory statistics and interactive visualizations
Environmental DNA (eDNA) metabarcoding is becoming a core tool in ecology and
conservation biology, and is being used in a growing number of education, biodiversity …
conservation biology, and is being used in a growing number of education, biodiversity …
Fish skin and gut microbiomes show contrasting signatures of host species and habitat
Teleost fish represent an invaluable repertoire of host species to study the factors shaping
animal-associated microbiomes. Several studies have shown that the phylogenetic structure …
animal-associated microbiomes. Several studies have shown that the phylogenetic structure …
Recent past, present, and future of the food microbiome
Sequencing technologies have deeply changed our approach to the study of food microbial
communities. This review describes recent exploitations of high-throughput sequencing …
communities. This review describes recent exploitations of high-throughput sequencing …