Author: Rob Knight

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Preprints

Challenges in Benchmarking Metagenomic Profilers

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Enabling high-accuracy long-read amplicon sequences using unique molecular identifiers with Nanopore or PacBio sequencing

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Structure-Based Function Prediction using Graph Convolutional Networks

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Evaluating the information content of shallow shotgun metagenomics

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BugBase Predicts Organism Level Microbiome Phenotypes

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American Gut: an Open Platform for Citizen-Science Microbiome Research

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Taxonomic Signatures of Long-Term Mortality Risk in Human Gut Microbiota

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Ultra-low input single tube linked-read library method enables short-read NGS systems to generate highly accurate and economical long-range sequencing information for de novo genome assembly and haplotype phasing

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Quantifying and understanding well-to-well contamination in microbiome research

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Bacterial modification of the host glycosaminoglycan heparan sulfate modulates SARS-CoV-2 infectivity

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Chemically-informed Analyses of Metabolomics Mass Spectrometry Data with Qemistree

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Genetics of human gut microbiome composition

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Algorithmic Learning for Auto-deconvolution of GC-MS Data to Enable Molecular Networking within GNPS.

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Chemical Impacts of the Microbiome Across Scales Reveal Novel Conjugated Bile Acids

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Links between environment, diet, and the hunter-gatherer microbiome

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The development of gut microbiota in ostriches and its association with juvenile growth

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Dramatic differences in gut bacterial densities help to explain the relationship between diet and habitat in rainforest ants

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Metagenomic covariation along densely sampled environmental gradients in the Red Sea

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Deep metagenomics examines the oral microbiome during dental caries, revealing novel taxa and co-occurrences with host molecules

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Species abundance information improves sequence taxonomy classification accuracy

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Age and sex-dependent patterns of gut microbial diversity in human adults

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Bacterial community composition and dynamics spanning five years in freshwater bog lakes

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Repository-scale Co- and Re-analysis of Tandem Mass Spectrometry Data

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SARS-CoV-2 Infection Among Symptom-Free Healthcare Workers

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MetaRiPPquest: A Peptidogenomics Approach for the Discovery of Ribosomally Synthesized and Post-translationally Modified Peptides

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Feasibility of SARS-CoV-2 virus detection from consumer-grade cotton swabs

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Reference data based insights expand understanding of human metabolomes

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Microbial ecology of Atlantic salmon, Salmo salar, hatcheries: impacts of the built environment on fish mucosal microbiota

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A Sensitive, Rapid, and Portable CasRx-based Diagnostic Assay for SARS-CoV2

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Combined effects of host genetics and diet on human gut microbiota and incident disease in a single population cohort

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Revisiting microbe-metabolite interactions: doing better than random

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Microbe-metabolite associations linked to the rebounding murine gut microbiome post-colonization with vancomycin resistant Enterococcus faecium

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Visualizing 'omic feature rankings and log-ratios using Qurro

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Early prediction of liver disease using conventional risk factors and gut microbiome-augmented gradient boosting

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Temporal, environmental, and biological drivers of the mucosal microbiome in a wild marine fish, Scomber japonicus

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Expanding magnetic organelle biogenesis in the domain Bacteria

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The Molecular and Microbial Microenvironments in Chronically Diseased Lungs

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Links between gut microbiome composition and fatty liver disease in a large population sample

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Multiple sclerosis-associated changes in the composition and immune functions of spore-forming bacteria

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A comparison of DNA/RNA extraction protocols for high-throughput sequencing of microbial communities

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Metabolome-informed microbiome analysis refines metadata classifications and reveals unexpected medication transfer in captive cheetahs

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The Southern Bluefin Tuna mucosal microbiome is influenced by husbandry method, net pen location, and anti-parasite treatment

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Red Sea SAR11 and Prochlorococcus Single-cell Genomes Reflect Globally Distributed Pangenomes

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Microbial context predicts SARS-CoV-2 prevalence in patients and the hospital built environment

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EMPress enables tree-guided, interactive, and exploratory analyses of multi-omic datasets

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High throughput wastewater SARS-CoV-2 detection enables forecasting of community infection dynamics in San Diego county

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Characterizing the response of Acinetobacter baumannii ATCC 17978 to azithromycin in multiple in vitro growth conditions

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Identifying the effect of vancomycin on HA-MRSA strains using bacteriological and physiological media

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Profiling the effect of nafcillin on HA-MRSA D592 using bacteriological and physiological media

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A scale-free, fully connected global transition network underlies known microbiome diversity

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