III-CXT-Small: Graphs to Diversity: extracting genomic variation from sequence graphs

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Recent advances in genome sequencing technologies have enabled thesequencing of bacteria directly from the environment, providing abroader outlook on the diversity of bacteria than ever beforepossible. Recent studies of environmental samples have revealedcomplex communities containing many previously unknown species, anduncovered a large amount of genetic variation and diversity even amongclosely related strains. Characterizing this genomic variation iscritical in studies of microbial ecology and evolution, yet currentlyavailable computational tools, originally developed for the study ofsingle organisms, are ill-suited for this task.This proposal aims to develop the theoretical and computationalinfrastructure for the study of genomic variation within mixtures oforganisms. The proposed research relies on both theoretical andempirical analyses of the structure of genome assembly graphs in orderto characterize graph signatures that are correlated with intra- andinter- species polymorphisms. A particular focus is placed onunderstanding and using the information provided by next generationsequencing technologies as well as other high-throughput experimentaltechniques. The proposed work provides critical analysis toolsto help biologists explore the genetic variation within theenvironment.Additional information about this project is available athttp://www.cbcb.umd.edu/research/Genomic_Variation.shtml.