R
Rob Knight
Researcher at University of California, San Diego
Publications - 1188
Citations - 322479
Rob Knight is an academic researcher from University of California, San Diego. The author has contributed to research in topics: Microbiome & Biology. The author has an hindex of 201, co-authored 1061 publications receiving 253207 citations. Previous affiliations of Rob Knight include Anschutz Medical Campus & University of Sydney.
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Using the nucleotide substitution rate matrix to detect horizontal gene transfer.
TL;DR: A new class of methods based on the changes in nucleotide substitution rates that occur when a gene is transferred to a new organism, which will be widely useful in detecting HGT events linked to the evolution of important bacterial traits, such as antibiotic resistance and pathogenicity.
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Emerging Trends for Microbiome Analysis: From Single-Cell Functional Imaging to Microbiome Big Data
TL;DR: It is argued that in the next decade, method development in microbiome analysis will be driven by three key changes in both ways of thinking and technological platforms: a shift from dissecting microbiota structure by sequencing to tracking microbiota state, function, and intercellular interaction via imaging.
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Intermittent Hypoxia and Hypercapnia Reproducibly Change the Gut Microbiome and Metabolome across Rodent Model Systems.
Anupriya Tripathi,Anupriya Tripathi,Zhenjiang Zech Xu,Jin Xue,Orit Poulsen,Antonio Gonzalez,Gregory Humphrey,Michael J. Meehan,Alexey V. Melnik,Gail Ackermann,Dan Zhou,Atul Malhotra,Gabriel G. Haddad,Gabriel G. Haddad,Pieter C. Dorrestein,Rob Knight +15 more
TL;DR: Time series multiomics data can be used to relate different animal models of disease using supervised machine learning techniques and can provide a pathway toward identifying robust microbiome and metabolome features that underpin translation from animal models to human disease.
Posted ContentDOI
Links between environment, diet, and the hunter-gatherer microbiome
Gabriela K. Fragiadakis,Samuel A. Smits,Erica D. Sonnenburg,Will Van Treuren,Gregor Reid,Rob Knight,Alphaxard Manjurano,John Changalucha,Maria Gloria Dominguez-Bello,Jeff Leach,Justin L. Sonnenburg +10 more
TL;DR: Additional observations from the Hadza microbiota and their lifestyle and environment are presented, including microbes detected on hands, water, and animal sources, how the microbiota varies with sex and age, and the shortterm effects of introducing agricultural products into the diet.
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SHOGUN: a modular, accurate and scalable framework for microbiome quantification
Benjamin Hillmann,Gabriel A. Al-Ghalith,Robin R. Shields-Cutler,Qiyun Zhu,Rob Knight,Dan Knights +5 more
TL;DR: The software pipeline SHOGUN profiles known taxonomic and gene abundances of short-read shotgun metagenomics sequencing data and produces both taxonomy and gene abundance profile tables with a single command, thus promoting convenient and reproducible metagenomic research.