Regulatory RNA genes pervade bacteria. Our understanding of these noncoding genes has increased dramatically in recent years, thanks, in part, to advances in high-throughput sequencing technology. High-throughput sequencing technology enables, among other things, experiments that produce massive amounts of data about RNA transcripts in bacteria. However, processing the large resulting data sets from high-throughput sequencing experiments can be a bottleneck in biological and medical research studies, partly because existing methods are insufficient for analyzing these data sets from bacteria. This project aims to develop new algorithms for correcting errors in the large sets of data generated from bacterial high-throughput sequencing experiments. Further, a computational system will be designed for managing and analyzing the sequencing data, with the aim of systematically annotating evinced transcripts. Finally, since many RNA genes in bacteria act as regulators of other transcripts, novel methods will be developed to identify the interactions between these noncoding RNAs and their regulatory targets. The methods developed will be applied and evaluated in several different bacterial systems.

Public Health Relevance

High-throughput sequencing experiments can provide information about gene expression in human pathogens during infection, but existing computational methods for processing the information are insufficient. In this project, computational tools and methods will be developed for analyzing high-throughput sequencing data, and these new methods will be evaluated on data collected from various bacterial organisms, including Escherichia coli, Neisseria gonorrhoeae, and Pseudomonas aeruginosa. More broadly, the computational infrastructure developed in this project will serve as a resource to biological and medical researchers studying myriad bacteria that are human pathogens.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Academic Research Enhancement Awards (AREA) (R15)
Project #
2R15GM102755-02A1
Application #
9301711
Study Section
Prokaryotic Cell and Molecular Biology Study Section (PCMB)
Program Officer
Sledjeski, Darren D
Project Start
2017-05-01
Project End
2020-04-30
Budget Start
2017-05-01
Budget End
2020-04-30
Support Year
2
Fiscal Year
2017
Total Cost
Indirect Cost
Name
Wellesley College
Department
Biostatistics & Other Math Sci
Type
Schools of Arts and Sciences
DUNS #
076572965
City
Wellesley
State
MA
Country
United States
Zip Code
02481
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