The Genomics Core, based at the University of Maryland, Baltimore (UMB), will perform genomic and transcriptomic sequencing and analysis in support of individual projects and the overall Program. The Core will be co-directed by Drs. Garry Myers and Jacques Ravel. The co-directors will be responsible for communicating with key personnel of the Clinical Core C and project PIs to facilitate data sharing, analysis and dissemination in coordination with the Program Manager. Over the duration of the Program and using the samples collected under Core C and provided by Projects 1-3, the Genomics Core will: (1) sequence and assemble whole genome sequences (and population genomes) of Chlamydia trachomatis and/or Neisseria gonorrhoeae;(2) sequence and map transcriptomes, including metatranscriptomes, miRNAseq transcriptomes of participants' serum and transcriptomes of both Chlamydia and the host cell using the innovative heterogenous RNA-Seq (hRNA-Seq) approach developed by the co-directors;(3) analyze sequence data acquired by the Genomics Core in close collaboration with individual project PIs using bioinformatics tools and systems biology approaches;(4) disseminate all data and resources generated by Projects 1-3 and Cores B-C through the Open Science Data Framework (OSDF), an innovative and scalable platform to store data of different types along with their metadata and create relationships between the different datasets.

Agency
National Institute of Health (NIH)
Type
Research Program--Cooperative Agreements (U19)
Project #
2U19AI084044-06
Application #
8769304
Study Section
Special Emphasis Panel (ZAI1)
Project Start
Project End
Budget Start
Budget End
Support Year
6
Fiscal Year
2014
Total Cost
Indirect Cost
Name
University of Maryland Baltimore
Department
Type
DUNS #
City
Baltimore
State
MD
Country
United States
Zip Code
21201
Ravel, Jacques; Brotman, Rebecca M (2016) Translating the vaginal microbiome: gaps and challenges. Genome Med 8:35
France, Michael T; Mendes-Soares, Helena; Forney, Larry J (2016) Genomic Comparisons of Lactobacillus crispatus and Lactobacillus iners Reveal Potential Ecological Drivers of Community Composition in the Vagina. Appl Environ Microbiol 82:7063-7073
Pittman, Kelly J; Glover, Luke C; Wang, Liuyang et al. (2016) The Legacy of Past Pandemics: Common Human Mutations That Protect against Infectious Disease. PLoS Pathog 12:e1005680
Robinson, Courtney K; Brotman, Rebecca M; Ravel, Jacques (2016) Intricacies of assessing the human microbiome in epidemiologic studies. Ann Epidemiol 26:311-21
Dareng, E O; Ma, B; Famooto, A O et al. (2016) Prevalent high-risk HPV infection and vaginal microbiota in Nigerian women. Epidemiol Infect 144:123-37
Nunn, Kenetta L; Forney, Larry J (2016) Unraveling the Dynamics of the Human Vaginal Microbiome. Yale J Biol Med 89:331-337
Neuendorf, Elizabeth; Gajer, Pawel; Bowlin, Anne K et al. (2015) Chlamydia caviae infection alters abundance but not composition of the guinea pig vaginal microbiota. Pathog Dis 73:
Wang, Liuyang; Oehlers, Stefan H; Espenschied, Scott T et al. (2015) CPAG: software for leveraging pleiotropy in GWAS to reveal similarity between human traits links plasma fatty acids and intestinal inflammation. Genome Biol 16:190
Breshears, Laura M; Edwards, Vonetta L; Ravel, Jacques et al. (2015) Lactobacillus crispatus inhibits growth of Gardnerella vaginalis and Neisseria gonorrhoeae on a porcine vaginal mucosa model. BMC Microbiol 15:276
Nunn, Kenetta L; Wang, Ying-Ying; Harit, Dimple et al. (2015) Enhanced Trapping of HIV-1 by Human Cervicovaginal Mucus Is Associated with Lactobacillus crispatus-Dominant Microbiota. MBio 6:e01084-15

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