[Embrio-list] Next All-hands seminar Dec. 6th

[Ladd, Brent Thomas]

Hello EMBRIOphytes,

I hope you all enjoyed a long holiday weekend. A reminder to use the 3-4pm scheduled time today for your project/thrust meetings. We will have our next all-hands meeting Monday Dec. 6th with Ph.D. Candidate and EMBRIO member, Javier Muñoz (Brubaker/Green Labs) presenting his thesis research that includes a computational framework for integrative modeling of multi-omics data titled:


Systems modeling for Multiomics Analysis Integration in Inflammatory Bowel Disease.

Javier Munoz-Briones and Doug Brubaker

Crohn’s disease and ulcerative colitis are chronic inflammatory bowel diseases (IBD) with a rising global prevalence, influenced by clinical and demographics factors. The pathogenesis of IBD involves complex interactions between gut microbiome dysbiosis, epithelial cell barrier disruption, and immune hyperactivity, which are poorly understood. This necessitates the development of novel approaches to integrate and model multiple clinical and molecular data modalities from patients, animal models, and in vitro systems to discover effective biomarkers for disease progression and drug response. For this presentation, my focus is on the lack of understanding of regarding the composition and functional interactions of the gut microbiome in IBD. As sequencing technologies advance, the amount of molecular and compositional data from paired measurements of host and microbiome systems is exploding. While it is become routine to generate such rich, deep datasets, tools for their interpretation lag behind. Here, I present a computational framework for integrative modeling of microbiome multi-omics data: Latent Interacting Variable Effects (LIVE) modeling. LIVE combines various types of microbiome multi-omics data using single-omic latent variables (LV) into a structured meta-model to determine the most predictive combinations of multi-omics features predicting an outcome, patient group, or phenotype. I implemented and tested LIVE using publicly available metagenomic and metabolomics data set from Crohn’s Disease(CD) and ulcerative colitis (UC) status patients in the PRISM and LLDeep cohorts. The findings show that LIVE reduced the number of features interactions from the original datasets for CD to tractable numbers and facilitated prioritization of biological associations between microbes, metabolites, enzymes, clinical variables, and a disease status outcome. LIVE modeling makes a distinct and complementary contribution to the current methods to integrate microbiome data to predict IBD status because of its flexibility to adapt to different types of microbiome multi-omics data, scalability for large and small cohort studies via reliance on latent variables and dimensionality reduction, and the intuitive interpretability of the meta-model integrating -omic data types.


Brent T. Ladd, Senior Research Program Manager, EMBRIO Institute<https://www.purdue.edu/research/embrio/>
Weldon School of Biomedical Engineering, Purdue University
Office: Hall for Discovery Learning and Research, Ste. 203
207 S. Martin Jischke Drive
West Lafayette, IN 47907
laddb at purdue.edu

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