Computational methods for strain-level microbial detection in colony and metagenome sequencing data
Metagenomic sequencing is a powerful tool for examining the diversity and complexity of
microbial communities. Most widely used tools for taxonomic profiling of metagenomic …
microbial communities. Most widely used tools for taxonomic profiling of metagenomic …
A comparison of tools for the simulation of genomic next-generation sequencing data
Computer simulation of genomic data has become increasingly popular for assessing and
validating biological models or for gaining an understanding of specific data sets. Several …
validating biological models or for gaining an understanding of specific data sets. Several …
[HTML][HTML] Design, construction, and in vivo augmentation of a complex gut microbiome
Efforts to model the human gut microbiome in mice have led to important insights into the
mechanisms of host-microbe interactions. However, the model communities studied to date …
mechanisms of host-microbe interactions. However, the model communities studied to date …
Healthy human gut phageome
The role of bacteriophages in influencing the structure and function of the healthy human gut
microbiome is unknown. With few exceptions, previous studies have found a high level of …
microbiome is unknown. With few exceptions, previous studies have found a high level of …
Evolutionary dynamics of bacteria in the gut microbiome within and across hosts
Gut microbiota are shaped by a combination of ecological and evolutionary forces. While the
ecological dynamics have been extensively studied, much less is known about how species …
ecological dynamics have been extensively studied, much less is known about how species …
Single-molecule sequencing and optical mapping yields an improved genome of woodland strawberry (Fragaria vesca) with chromosome-scale contiguity
Background Although draft genomes are available for most agronomically important plant
species, the majority are incomplete, highly fragmented, and often riddled with assembly …
species, the majority are incomplete, highly fragmented, and often riddled with assembly …
A taxonomic signature of obesity in the microbiome? Getting to the guts of the matter
Obesity is an important and intractable public health problem. In addition to the well-known
risk factors of behavior, diet, and genetics, gut microbial communities were recently …
risk factors of behavior, diet, and genetics, gut microbial communities were recently …
Average genome size estimation improves comparative metagenomics and sheds light on the functional ecology of the human microbiome
S Nayfach, KS Pollard - Genome biology, 2015 - Springer
Average genome size is an important, yet often overlooked, property of microbial
communities. We developed MicrobeCensus to rapidly and accurately estimate average …
communities. We developed MicrobeCensus to rapidly and accurately estimate average …
Daring to be differential: metabarcoding analysis of soil and plant-related microbial communities using amplicon sequence variants and operational taxonomical units
Background Microorganisms are not only indispensable to ecosystem functioning, they are
also keystones for emerging technologies. In the last 15 years, the number of studies on …
also keystones for emerging technologies. In the last 15 years, the number of studies on …
Simulating Illumina metagenomic data with InSilicoSeq
Motivation The accurate in silico simulation of metagenomic datasets is of great importance
for benchmarking bioinformatics tools as well as for experimental design. Users are …
for benchmarking bioinformatics tools as well as for experimental design. Users are …