Michigan State University is awarded a grant from the Faculty Early Career Development program (CAREER) to develop new technologies for genome-scale comparative noncoding RNA (ncRNA) identification. ncRNAs, which are not translated into protein but function directly as RNA, play diverse and important roles in many biochemical processes. Annotating ncRNAs in different organisms is thus highly important to modern biology. Among numerous efforts made for ncRNA detection, a few programs can be practically applied to whole genomes or large-scale databases. However, these genome-scale tools rely on conventional comparative sequence analysis, which cannot not effectively account for structural conservation in homologous ncRNAs and thus jeopardizes the sensitivity and accuracy of structured ncRNA search. In order to address the need of sensitive and fast large-scale ncRNA search, this project focuses on the development of novel and improved ncRNA detection algorithms that combine the efficiency of conventional sequence comparison tools and the structural features of ncRNAs. The specific objectives are: (1) fast known ncRNA identification algorithms and tools that can efficiently classify a large number of putative ncRNAs into corresponding ncRNA families, (2) highly efficient genome-scale sequence comparison algorithms for ncRNA homology search, and (3) a novel ncRNA structure modeling and comparison method.
The research goals of this project and the training needs of computational biology are integrated with the following educational objectives and plans. 1) Improve the awareness of computational biology as an important research area among students in biology and engineering. A new computational biology course for both senior undergraduates and graduates has been designed and is offered every fall. 2) Improve cross-disciplinary research training experiences for graduate and undergraduate students through MSU's Quantitative Biology Initiative (QBI) dual-major degree program. 3) Encourage retention and recruitment of underrepresented groups in computational biology related majors. The PI will continue to attend the K-12 women students outreach through Women in Engineering Summer Program every year, and help undergraduate women students through Women In Computing organization at MSU.
