Bioinformatics tools, custom databases, experimental designs, data acquisition/archival/access methods and data analysis/interpretation methods have had and will continue to have great impact on the RCE progress and will be the deliverables of a bioinformatics program. It should be noted that new bioinformatics technologies are anticipated to be developed and they will be necessary to integrate and analyze the many diverse types of data, and ideas for these tools will come from the biological scientists working in the projects and cores as well as bioinformaticists in our core, but bioinformaticists will develop the solution. We also leverage the existing commercial and non-commercial systems (tools, databases, development environments) to speed the bioinformatics solution development, for maximum data exchange compatibility issues, such as security, and for robustness. In the previous grant period, we created numerous tools and databases, which have had tens of thousands of users, have analyzed over 25 large array-based datasets and have reported this work in 13 publications.
The Specific Aims for this core are: 1) To develop applied computational biology resources-codes databases and interpretations of data-to facilitate advances in the understanding and characterization of Category A-C pathogens, validate the performance of the codes/databases either collaboratively or via wet lab testing/checking a sampling of results and to provide computational support for project investigators;2) To apply our computer codes (new and pathogen adapted) to pre-compute a variety of data for Category A-C pathogens, including ORF amplification primers (PCR, qPCR), DMA chip oligonucleotide probes for re-sequencing and expression, a collection of text-based literature and its extracted and associated biomedical objects: 3) To construct a pathogen-specific, internet accessible, www-based bioinformatics tool set and data warehouse of utilities and make them available to facilitate intra- and inter- institutional collaborations among project and core personnel and others in the biothreat and emerging pathogen research community;4) To provide an experimental design data analysis and interpretation collaborative service to RCE researchers, especially as it appears to data intensive studies such as pathogen or host expression, proteomics or genomics, and 5) To continue to expand and maintain computer servers to support this effort.

Public Health Relevance

There is a need for bioinformatics support at all levels and times for projects in the Regional Centers of Excellence (RCE) to maximize the efficiency and speed of the research and to make the results of the RCE research available to scientists and others, making it possible exploit those findings to advance anti-biothreat work

Agency
National Institute of Health (NIH)
Institute
National Institute of Allergy and Infectious Diseases (NIAID)
Type
Specialized Center--Cooperative Agreements (U54)
Project #
2U54AI057156-06
Application #
7676466
Study Section
Special Emphasis Panel (ZAI1-DDS-M (J2))
Project Start
2009-04-15
Project End
2014-02-28
Budget Start
2009-04-15
Budget End
2010-02-28
Support Year
6
Fiscal Year
2009
Total Cost
$433,175
Indirect Cost
Name
University of Texas Medical Br Galveston
Department
Type
DUNS #
800771149
City
Galveston
State
TX
Country
United States
Zip Code
77555
Pandey, Aseem; Lin, Furong; Cabello, Ana L et al. (2018) Activation of Host IRE1?-Dependent Signaling Axis Contributes the Intracellular Parasitism of Brucella melitensis. Front Cell Infect Microbiol 8:103
Russell-Lodrigue, Kasi E; Killeen, Stephanie Z; Ficht, Thomas A et al. (2018) Mucosal bacterial dissemination in a rhesus macaque model of experimental brucellosis. J Med Primatol 47:75-77
Matz, L M; Kamdar, K Y; Holder, M E et al. (2018) Challenges of Francisella classification exemplified by an atypical clinical isolate. Diagn Microbiol Infect Dis 90:241-247
Langsjoen, Rose M; Haller, Sherry L; Roy, Chad J et al. (2018) Chikungunya Virus Strains Show Lineage-Specific Variations in Virulence and Cross-Protective Ability in Murine and Nonhuman Primate Models. MBio 9:
Raja, B; Goux, H J; Marapadaga, A et al. (2017) Development of a panel of recombinase polymerase amplification assays for detection of common bacterial urinary tract infection pathogens. J Appl Microbiol 123:544-555
Nunes, Marcio R T; Contreras-Gutierrez, María Angélica; Guzman, Hilda et al. (2017) Genetic characterization, molecular epidemiology, and phylogenetic relationships of insect-specific viruses in the taxon Negevirus. Virology 504:152-167
Rossetti, Carlos A; Drake, Kenneth L; Lawhon, Sara D et al. (2017) Systems Biology Analysis of Temporal In vivo Brucella melitensis and Bovine Transcriptomes Predicts host:Pathogen Protein-Protein Interactions. Front Microbiol 8:1275
Paterson, Andrew S; Raja, Balakrishnan; Mandadi, Vinay et al. (2017) A low-cost smartphone-based platform for highly sensitive point-of-care testing with persistent luminescent phosphors. Lab Chip 17:1051-1059
Park, Arnold; Yun, Tatyana; Vigant, Frederic et al. (2016) Nipah Virus C Protein Recruits Tsg101 to Promote the Efficient Release of Virus in an ESCRT-Dependent Pathway. PLoS Pathog 12:e1005659
Pandey, Aseem; Cabello, Ana; Akoolo, Lavoisier et al. (2016) The Case for Live Attenuated Vaccines against the Neglected Zoonotic Diseases Brucellosis and Bovine Tuberculosis. PLoS Negl Trop Dis 10:e0004572

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