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)
Institute
National Institute of Allergy and Infectious Diseases (NIAID)
Type
Research Program--Cooperative Agreements (U19)
Project #
2U19AI084044-06
Application #
8769304
Study Section
Special Emphasis Panel (ZAI1)
Project Start
Project End
Budget Start
2014-09-01
Budget End
2015-08-31
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
Palmer, Allison; Criss, Alison K (2018) Gonococcal Defenses against Antimicrobial Activities of Neutrophils. Trends Microbiol 26:1022-1034
Schroeder, Holly A; Nunn, Kenetta L; Schaefer, Alison et al. (2018) Herpes simplex virus-binding IgG traps HSV in human cervicovaginal mucus across the menstrual cycle and diverse vaginal microbial composition. Mucosal Immunol 11:1477-1486
Ragland, Stephanie A; Humbert, Mar?a V; Christodoulides, Myron et al. (2018) Neisseria gonorrhoeae employs two protein inhibitors to evade killing by human lysozyme. PLoS Pathog 14:e1007080
van Houdt, Robin; Ma, Bing; Bruisten, Sylvia M et al. (2018) Lactobacillus iners-dominated vaginal microbiota is associated with increased susceptibility to Chlamydia trachomatis infection in Dutch women: a case-control study. Sex Transm Infect 94:117-123
Cornejo, Omar E; Hickey, Roxana J; Suzuki, Haruo et al. (2018) Focusing the diversity of Gardnerella vaginalis through the lens of ecotypes. Evol Appl 11:312-324
Tyssen, David; Wang, Ying-Ying; Hayward, Joshua A et al. (2018) Anti-HIV-1 Activity of Lactic Acid in Human Cervicovaginal Fluid. mSphere 3:
Tachedjian, Gilda; O'Hanlon, Deirdre E; Ravel, Jacques (2018) The implausible ""in vivo"" role of hydrogen peroxide as an antimicrobial factor produced by vaginal microbiota. Microbiome 6:29
Noyes, Noelle; Cho, Kyu-Chul; Ravel, Jacques et al. (2018) Associations between sexual habits, menstrual hygiene practices, demographics and the vaginal microbiome as revealed by Bayesian network analysis. PLoS One 13:e0191625
Wang, Liuyang; Pittman, Kelly J; Barker, Jeffrey R et al. (2018) An Atlas of Genetic Variation Linking Pathogen-Induced Cellular Traits to Human Disease. Cell Host Microbe 24:308-323.e6
Bradford, L Latéy; Ravel, Jacques (2017) The vaginal mycobiome: A contemporary perspective on fungi in women's health and diseases. Virulence 8:342-351

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