preprints
A Statistical Analysis of Compositional Surveys. arXiv
Microbiota responses to different prebiotics are conserved within individuals and associated with habitual fiber intake. bioRxiv
2022
Multiomics implicate gut microbiota in altered lipid and energy metabolism in Parkinson’s disease. NPJ Parkinsson’s Disease
2021
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
2020
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.
2019
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
2018
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
2017
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