Benchmarking metagenomics tools for taxonomic classification
HY Simon, KJ Siddle, DJ Park, PC Sabeti - Cell, 2019 - cell.com
Metagenomic sequencing is revolutionizing the detection and characterization of microbial
species, and a wide variety of software tools are available to perform taxonomic …
species, and a wide variety of software tools are available to perform taxonomic …
A survey of best practices for RNA-seq data analysis
Abstract RNA-sequencing (RNA-seq) has a wide variety of applications, but no single
analysis pipeline can be used in all cases. We review all of the major steps in RNA-seq data …
analysis pipeline can be used in all cases. We review all of the major steps in RNA-seq data …
The human tumor microbiome is composed of tumor type–specific intracellular bacteria
Bacteria were first detected in human tumors more than 100 years ago, but the
characterization of the tumor microbiome has remained challenging because of its low …
characterization of the tumor microbiome has remained challenging because of its low …
A reference map of potential determinants for the human serum metabolome
The serum metabolome contains a plethora of biomarkers and causative agents of various
diseases, some of which are endogenously produced and some that have been taken up …
diseases, some of which are endogenously produced and some that have been taken up …
Metabolomic and microbiome profiling reveals personalized risk factors for coronary artery disease
Complex diseases, such as coronary artery disease (CAD), are often multifactorial, caused
by multiple underlying pathological mechanisms. Here, to study the multifactorial nature of …
by multiple underlying pathological mechanisms. Here, to study the multifactorial nature of …
Potential roles of gut microbiome and metabolites in modulating ALS in mice
Amyotrophic lateral sclerosis (ALS) is a complex neurodegenerative disorder, in which the
clinical manifestations may be influenced by genetic and unknown environmental factors …
clinical manifestations may be influenced by genetic and unknown environmental factors …
Accuracy assessment of fusion transcript detection via read-mapping and de novo fusion transcript assembly-based methods
Background Accurate fusion transcript detection is essential for comprehensive
characterization of cancer transcriptomes. Over the last decade, multiple bioinformatic tools …
characterization of cancer transcriptomes. Over the last decade, multiple bioinformatic tools …
Scaling read aligners to hundreds of threads on general-purpose processors
B Langmead, C Wilks, V Antonescu, R Charles - Bioinformatics, 2019 - academic.oup.com
Motivation General-purpose processors can now contain many dozens of processor cores
and support hundreds of simultaneous threads of execution. To make best use of these …
and support hundreds of simultaneous threads of execution. To make best use of these …
Environment dominates over host genetics in shaping human gut microbiota
Human gut microbiome composition is shaped by multiple factors but the relative
contribution of host genetics remains elusive. Here we examine genotype and microbiome …
contribution of host genetics remains elusive. Here we examine genotype and microbiome …
[HTML][HTML] Personalized nutrition by prediction of glycemic responses
Elevated postprandial blood glucose levels constitute a global epidemic and a major risk
factor for prediabetes and type II diabetes, but existing dietary methods for controlling them …
factor for prediabetes and type II diabetes, but existing dietary methods for controlling them …