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A statistical perspective on the challenges in microbiome multi-domain data
					
 Mar 30, 2022 
 3:30PM to 5:00PM

									

				

					Event Categories   2022 Seminars and   CSE Seminars Page
				

			


	

	

		

			

				

					

						

														

															

						

						

	

		


	Date/Time

	Date(s) - 30/03/2022
3:30 pm - 5:00 pm







Speaker: Prof. Pratheepa Jeganathan


Topic: A statistical perspective on the challenges in microbiome multi-domain data


Date of Presentation: Wednesday, March 30, 2022


Location:  Online


Abstract:


High-throughput sequencing generates massive microbiome multi-domain datasets that pose several challenges. As a result, statistical and computational methods have been developed to address contamination sequences from reagents, unequal sampling, strain switching (present as one taxon in one set of specimens and a close, distinct strain appears in the other set of specimens), sparsity, heterogeneity, and multiple tables. One of the important goals in microbiome research is to find taxonomic differences across environments or groups. In the first part of the talk, we’ll demonstrate how to use topic models to provide useful aggregates for differential abundance analysis when strain switching can be an impediment. Multi-domain data are massive and have multiple scales. In the second part of the talk, we’ll show R/Bioconductor containers and variance stabilizing transformations for integrating microbiome multi-domain data.


This talk is based on


1. Jeganathan, P., & Holmes, S. P. (2021). A statistical perspective on the challenges in molecular microbial biology. Journal of Agricultural, Biological and Environmental Statistics, 26(2), 131-160 and R package diffTop available on Github.


2. (Material and Methods in) Symul, L., Jeganathan, P., Costello, E., France, et al. (2021+). Sub-communities of the vaginal ecosystem in pregnant and non-pregnant women. bioRxiv.