A Statistical Analysis of Compositional Surveys. arXiv

Microbiota responses to different prebiotics are conserved within individuals and associated with habitual fiber intake. bioRxiv


Multiomics implicate gut microbiota in altered lipid and energy metabolism in Parkinson’s disease. NPJ Parkinsson’s Disease


Scalable estimation of microbial co-occurrence networks with Variational Autoencoders. NeurIPS

Bayesian Multinomial Logistic Normal Models through Marginally Latent Matrix-T Processes. Journal of Machine Learning Resarch (Accepted)

Measuring and Mitigating PCR Bias in Microbiome Data. PLoS Computational Biology

Naught all zeros in sequence count data are the same. Computational and Structural Biotechnology Journal

DNA Extraction and Host Depletion Methods Significantly Impact and Potentially Bias Bacterial Detection in a Biological Fluid. mSystems

The Pediatric Obesity Microbiome and Metabolism Study (POMMS): Methods, Baseline Data, and Early Insights. Obesity

Analysis and visualization of epidemics on the timescale of burden: derivation and application of Epidemic Resistance Lines (ERLs) to COVID-19 outbreaks in the US. medRxiv


Using influenza surveillance networks to estimate state-specific prevalence of SARS-CoV-2 in the United States. Science Translational Medicine

Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England Science

Short-Chain Fatty Acid Production by Gut Micro- biota from Children with Obesity Differs According to Prebiotic Choice and Bacterial Community Composition. mBio

Inter-individual variation in dietary carbohydrate metabolism by gut bacteria revealed with droplet microfluidic culture. mSystems.


Establishing microbial measurement standards with reference frames. Nature Communications

Statistical Considerations in the Design and Analysis of Longitudinal Microbiome Studies. bioRxiv

Allogenic fecal microbiota transplantation in patients with non-alcoholic fatty liver disease improves abnormal small intestinal permeability: a randomized control trial. The American Journal of Gastroenterology


Dynamic linear models guide design and analysis of microbiota studies within artificial human guts. Microbiome

Modeling the temporal dynamics of the gut microbial community in adults and infants. PLoS Computational Biology

Phylofactorization: a graph partitioning algorithm to identify phylogenetic scales of ecological data. Ecololgical Monographs

The Bayesian Sorting Hat: A Decision-Theoretic Approach to Size-Constrained Clustering. arXiv


Human gut microbiota predicts susceptibility to Vibrio cholerae infection. Journal of Infectious Diseases

Phylogenetic factorization of compositional data yields lineage-level associations in microbiome datasets. PeerJ

A phylogenetic transform enhances analysis of compositional microbiota data. eLife