Funding agency: National Science Foundation, Division of Biological Infrastructure
Award #: DBI-1564936
Amount: $300,000
PI: Ion I. Mandoiu
Period: 07/2016-06/2020

Abstract:

Microbial communities are an essential part of life on Earth. Natural communities comprised of up to thousands of interacting microbial species drive fundamental biochemical processes ranging from nutrient processing in our guts to sequestration of carbon in the Earth’s oceans. The study of microbiomes has been recently revolutionized by the use of advanced sequencing technologies. However, large-scale initiatives such as the Human Microbiome Project and the Earth Microbiome Project are generating Petabytes (10¹⁵ bytes) of sequencing data, greatly challenging existing analysis tools. The goal of this project is to develop transformative computational methods and implement software tools enabling the analysis of these large-scale datasets. Specific aims of the project include: (i) developing highly scalable algorithms for de novo assembly and quantification from multiple metatranscriptomic samples, (ii) developing highly accurate algorithms for estimation of metabolic pathway activity level and differential activity testing, and (iii) developing and validating prototype implementations of developed methods.

Publications

Presentations

Software Packages and Web-Based Tools

• IsoEM2: Inferring Alternative Splicing Isoform Frequencies from High-Throughput RNA-Seq Data
• IsoDE2: Bootstrapping-based differential gene expression analysis for RNA-Seq data with and without replicates
• SC1: Web-based single cell RNA-seq analysis pipeline
• SMART2: Multi-Sample Statistical Mitogenome Assembly with Repeats
• XPathway: tools for pathway activity comparison
• Galaxy deployment of IsoEM2/IsoDE2 and XPathway