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

基因组测序技术的最新进展使直接从环境中对细菌进行测序成为可能，为细菌的多样性提供了比以往任何时候都更广阔的前景。最近对环境样品的研究揭示了复杂的群落包含许多以前未知的物种，并发现了大量的遗传变异和多样性，甚至是密切相关的菌株。描述这种基因组变异在微生物生态学和进化的研究中是至关重要的，然而目前可用的计算工具，最初是为研究单一生物而开发的，并不适合这项任务。本提案旨在为研究混合生物中的基因组变异发展理论和计算基础设施。 该研究基于对基因组组装图结构的理论和实验分析，以表征与种内和种间多态性相关的图签名。 一个特别的重点放在理解和使用下一代测序技术以及其他高通量实验技术提供的信息。 这项工作提供了重要的分析工具，帮助生物学家探索环境中的遗传变异。www.cbcb.umd.edu/research/Genomic_Variation.shtml

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.