Microbiome

Locally sparse varying coefficient mixed model with application to longitudinal microbiome differential abundance
Differential abundance (DA) analysis in microbiome studies has recently been used to uncover a plethora of associations between …
Simon Fontaine, Nisha J. D'Silva, Marcell Costa De Medeiros, Grace Y. Chen, Ji Zhu, Gen Li
October, 2025 Under revision at Biometrics Microbiome
Code Project Paper code
Loss of salivary agglutinin induces changes in the salivary microbiome and accelerates development of oral cancer

Background: Salivary agglutinin, also known as deleted in malignant brain tumors 1 (DMBT1), is an anti-microbial protein. Salivary DMBT1 is low in saliva from patients with oral cancer and dramatically increases after treatment with accompanying microbial changes. While suppression of DMBT1 has been associated with oral microbial dysbiosis and oral cancer, direct effect has not been established.
Marcell Costa De Medeiros, Simon Fontaine, Erika Danella, Ethan Hillman, Thomas Schmidt, Allison Furgal, Deneen M Wellik, Gen Li, Naohiro Inohara, Gabriel Nunez, Grace Y. Chen, Nisha J. D’Silva
October, 2025 Under review at Microbiome Applied, Microbiome
Project
Bayesian Fréchet Regression
While linear regression focuses on studying the relationship between a set of covariates and a real-valued response, Fréchet regression …
Jun 15, 2025 10:00 AM ICSA 2025 Storrs, CT, USA
Simon Fontaine, Lingzhou Xue, Bing Li
ADAPT: Analysis of Microbiome Differential Abundance by Pooling Tobit Models
Microbiome differential abundance analysis remains a challenging problem despite multiple methods proposed in the literature. The …
Mukai Wang, Simon Fontaine, Hui Jiang, Gen Li
November, 2024 Bioinformatics Microbiome
Code Project DOI Paper code
Locally sparse varying coefficient mixed model for longitudinal differential abundance analysis
Differential abundance (DA) analysis in microbiome studies has recently been used to uncover a plethora of associations between …
Jul 18, 2024 10:00 AM EcoSta 2024 Beijing, China
Simon Fontaine, Nisha J D'Silva, Marcell Costa De Medeiros, Ji Zhu, Gen Li
Locally sparse varying coefficient mixed model for longitudinal differential abundance analysis
Differential abundance (DA) analysis in microbiome studies has recently been used to uncover a plethora of associations between …
Aug 8, 2023 10:00 AM JSM 2023 Toronto, ON, Canada
Simon Fontaine, Nisha J D'Silva, Marcell Costa De Medeiros, Ji Zhu, Gen Li
Slides
POLDA: Pooling Overdispersed Logistic Regressions for Microbiome Differential Abundance Analysis
Differential abundance (DA) analysis aims to identify microbiome taxa whose abundances are different between two or more conditions. …
Jun 13, 2023 10:00 AM ICSA Applied Symposium 2023 Ann Arbor, MI
Mukai Wang, Simon Fontaine, Hui Jiang, Gen Li