4.7 Article

Optimizing UniFrac with OpenACC Yields Greater Than One Thousand Times Speed Increase

Related references

Note: Only part of the references are listed.
Review Mathematical & Computational Biology

Applications and Comparison of Dimensionality Reduction Methods for Microbiome Data

George Armstrong et al.

Summary: This review discusses the motivation, challenges, strategies, and successful applications of dimensionality reduction techniques in microbiome studies, highlighting the need for further development in incorporating phylogenetic analysis and addressing issues such as sparsity, compositionality, and non-normality. It also suggests the wider application of current techniques in future analyses.

FRONTIERS IN BIOINFORMATICS (2022)

Article Biochemical Research Methods

SciPy 1.0: fundamental algorithms for scientific computing in Python

Pauli Virtanen et al.

NATURE METHODS (2020)

Article Multidisciplinary Sciences

Host variables confound gut microbiota studies of human disease

Ivan Vujkovic-Cvijin et al.

NATURE (2020)

Review Gastroenterology & Hepatology

Microbiome 101: Studying, Analyzing, and Interpreting Gut Microbiome Data for Clinicians

Celeste Allaband et al.

CLINICAL GASTROENTEROLOGY AND HEPATOLOGY (2019)

Letter Biotechnology & Applied Microbiology

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

Evan Bolyen et al.

NATURE BIOTECHNOLOGY (2019)

Article Microbiology

redbiom: a Rapid Sample Discovery and Feature Characterization System

Daniel McDonald et al.

MSYSTEMS (2019)

Letter Biochemical Research Methods

Bioconda: sustainable and comprehensive software distribution for the life sciences

Bjoern Gruening et al.

NATURE METHODS (2018)

Article Microbiology

American Gut: an Open Platform for Citizen Science Microbiome Research

Daniel McDonald et al.

MSYSTEMS (2018)

Article Biochemical Research Methods

Qiita: rapid, web-enabled microbiome meta-analysis

Antonio Gonzalez et al.

NATURE METHODS (2018)

Letter Biochemical Research Methods

Striped UniFrac: enabling microbiome analysis at unprecedented scale

Daniel McDonald et al.

NATURE METHODS (2018)

Article Multidisciplinary Sciences

A communal catalogue reveals Earth's multiscale microbial diversity

Luke R. Thompson et al.

NATURE (2017)

Article Microbiology

Uncovering the Horseshoe Effect in Microbial Analyses

James T. Morton et al.

MSYSTEMS (2017)

Review Biochemistry & Molecular Biology

Microbial community profiling for human microbiome projects: Tools, techniques, and challenges

Micah Hamady et al.

GENOME RESEARCH (2009)

Article Biotechnology & Applied Microbiology

Quantitative and qualitative beta diversity measures lead to different insights into factors that structure microbial communities

Catherine A. Lozupone et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2007)

Article Biotechnology & Applied Microbiology

UniFrac: a new phylogenetic method for comparing microbial communities

C Lozupone et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2005)