Rob D. Knight

Homology-aware average nucleotide identity estimation at scale with TurboANI

TurboANI is a fast, homology-aware ANI estimator with up to ~40,000x speedup over alignment-based methods and better accuracy than FastANI and skani.

Replication of Host St6galnac1-Microbiome Association Across Distinct Experimental Conditions in Heterogeneous Stock Rats

The paper replicates the association between St6galnac1 and Paraprevotella abundance in stool samples from non-fasted HS rats, confirming the association across different experimental conditions.

Genome-resolved ecology and evolution of the microbiome enabled by quantitative long-read metagenomics

This paper introduces LRQ, a long-read metagenomics method that enables absolute strain abundance measurement and resolves microbial evolution in a Crohn's disease patient over eight years.

Integrated multi-omics analysis identifies microbial and metabolic signatures and drivers of CNS autoimmunity

This paper integrates microbiomic and metabolomic data to identify microbial and metabolic drivers of CNS autoimmunity in a mouse model of MS.

Multi-omics Analyses of Facial Skin in Acne Identify Distinct Microbial and Metabolic Features at Lesional and Non-lesional Sites

This study identifies distinct microbial and metabolic features in non-lesional acne skin using multi-omics analyses, showing molecular dysbiosis extends beyond visible lesions.

Alkamines reveal a hidden layer of steroid and drug metabolism

The paper identifies alkamines as a previously hidden class of metabolites formed via reductive amination, revealing significant gaps in metabolomics and drug metabolism understanding.

An expansive animal gut microbiome dataset elucidates major compositional shifts across bilaterian evolution

The paper presents a large-scale gut microbiome dataset across 1,553 host species and identifies major compositional shifts in gut microbiomes during animal evolution.

Antibiotic Exposure Through Human Milk Influences the Infant Gut Microbiome

This study examines how maternal antibiotic use during breastfeeding affects the infant gut microbiome and metabolome, finding altered microbial profiles and increased BMI in some infants.

Farnesoid X receptor-dependent microbiome-bile acid signaling mediates obstructive sleep apnea-induced atherosclerosis

This study shows that FXR deficiency prevents IHC-induced atherosclerosis by disrupting microbiome-bile acid signaling in ApoE-/- mice.

A Multi-Omics Processing Pipeline (MOPP) for Extracting Taxonomic and Functional Insights from Metaribosome Profiling (metaRibo-Seq) data

The paper introduces MOPP, a pipeline for processing metaRibo-Seq data to improve taxonomic and functional analysis by reducing false positives through coverage breadth filtering.

Pan-repository analysis reveals a drug-activating function of microbial bile acid conjugation

The paper identifies microbial bile acid conjugation as a drug-activating function for 5-ASA, revealing its therapeutic relevance through metabolomics analysis.

Enabling Megascale Microbiome Analysis with DartUniFrac

DartUniFrac is a fast, scalable algorithm for microbiome analysis that matches the statistical performance of exact UniFrac methods.

Community assembly modeling of microbial evolution within Barrett's esophagus and esophageal adenocarcinoma

The paper models microbial community assembly dynamics in Barrett's esophagus and esophageal adenocarcinoma, finding neutral dynamics in normal tissue and BE but not EAC, with H. pylori showing non-neutral behavior in BE non-cancer outcomes.

A searchable metadata network graph for microbiome metabolomics

The paper introduces microbiomeMASST, a metadata network graph linking metabolites across datasets, enabling cross-study analysis of microbial metabolites and their biological context.

Community Curation of Microbial Metabolites Enables Biological Insights of Metabolomics Data

The paper introduces a collaborative platform for curating microbial metabolite knowledge to enhance metabolomics data interpretation.

Novel insights into the genetic architecture and mechanisms of host/microbiome interactions from a multi-cohort analysis of outbred laboratory rats

The paper identifies host genetic effects on microbiome composition in rats and finds evidence of indirect genetic effects contributing to missing heritability.

Personalised whole-body modelling links gut microbiota to metabolic perturbations in Alzheimer's disease

The paper uses whole-body metabolic models to link gut microbiota to metabolic changes in Alzheimer's disease, identifying key microbial drivers and metabolites involved.

Industrialization drives convergent microbial and physiological shifts in the human metaorganism

The paper investigates how industrialization affects microbial and physiological traits in the human gut across diverse populations, finding homogenized microbiomes, reduced diversity, and impaired disease prediction accuracy in less industrialized groups.

The microbiome shapes immunity in a sex-specific manner in mouse models of Alzheimer's disease

This study shows that the microbiome influences immune responses and cognitive deficits in sex-specific ways in mouse models of Alzheimer's disease.

Environmental and Maternal Imprints on Infant Gut Metabolic Programming

The paper examines how environmental and maternal factors influence infant gut metabolism through microbiome and metabolome profiling in Bangladeshi mother-infant pairs.

A three-country analysis of the gut microbiome indicates taxon associations with diet vary by location and strain

The paper analyzes gut microbiome data from three countries to show diet-microbiota associations vary by location and strain.

Microbiome variations in osteoarthritis reflect aging and metabolic factors, not the disease

This study analyzes microbiome data from multiple OA cohorts and finds no significant differences between OA patients and controls, attributing microbiome changes to age and BMI instead of OA.

Ultra-fast and Efficient Network Embedding for Gigascale Biological Datasets

The paper introduces GraphEmbed, a scalable network embedding tool that efficiently handles large biological datasets with speed and accuracy improvements over existing methods.

A Multi-Organ Murine Metabolomics Atlas Reveals Molecular Dysregulations in Alzheimer's Disease

The paper presents a multi-organ metabolomics atlas in AD mouse models, identifying dysregulated metabolites and microbiome associations linked to oxidative stress and cognitive impairment.

Gut Microbiota and Derived Metabolites Mediate Obstructive Sleep Apnea Induced Atherosclerosis

This study shows that gut microbiota and their metabolites contribute to OSA-induced atherosclerosis, particularly in the aorta, through specific bacterial imbalances and bile acid dysregulation.

Human untargeted metabolomics in the gut microbiome era: ethanol vs methanol

The paper compares ethanol and methanol extraction methods for fecal metabolomics, showing ethanol is safer for off-site collection and preserves metabolic profiles.

Ecological relationships between human gut bacteria predicted from analysis of dense microbiome time series data from US travelers in Bangladesh

This study predicts ecological relationships between human gut bacteria using time-series data from US travelers in Bangladesh, identifying both cooperative and competitive interactions with metabolic and genomic support.

To impute or not to impute in untargeted metabolomics - that is the compositional question

This study evaluates imputation methods for untargeted metabolomics data, finding that kNN and RF imputation perform poorly with missing data, especially MNAR, and that missing data proportion significantly affects accuracy.

TEMPTED: Time-Informed Dimensionality Reduction for Longitudinal Microbiome Studies

TEMPTED improves analysis of longitudinal microbiome data by incorporating time as a continuous variable, achieving high accuracy in phenotype classification and identifying microbial markers linked to birth outcomes.

The microbiome diversifies N-acyl lipid pools - including short-chain fatty acid-derived compounds

The paper creates a spectral library of N-acyl lipids from metabolomics data, identifies novel compounds, and links them to health conditions like HIV and cognitive impairment.