The Southeast Resource Center for Integrated Metabolomics (SECIM) integrates existing strengths to create a comprehensive resource for basic and clinical scientists to obtain state-of-the-art metabolomics data and analyses. Bioinformatics (Core 4) is directed by Prof. Lauren Mclntyre, with assistance from the SECIM Program Coordinator, Dr. Eric Milgram, who will be responsible for developing the SECIM pipeline and implementing QA/QC on all analytical platforms in collaboration with technical core leaders. This core will provide robust and automated analysis tools in a Galaxy interface that will allow users to interactively analyze processed SECIM analytical data. This interface will be organized into a series of workflows that will be available through an Analysis Dashboard, which will provide basic statistical tools and automatic data reformatting. One ofthe primary goals ofthe Bioinformatics Core is to provide the foundation (e.g., data processing, normalization, scaling, reformatting, etc.) that is needed by most studies, freeing them to devote their efforts to answering specific scientific questions. Prof. Peihua Qiu, UF Chair of Biostatistics, will be a critical interface between the Bioinformatics Core and outside projects with biostatistics components. The Bioinformatics Core will also work with select exemplar projects to develop novel analytical approaches. The projects will be chosen for their potential for impact and overall importance to the field. Examples will include projects such as efficient correlation of LC-MS and NMR data, which will be conducted in collaboration with the SECIM technical cores and the Nicholson group at Imperial College London;and new approaches to isotopic ratio outlier analysis (IROA) that expand the capabilities beyond 2-group studies and integrate 13C NMR for efficient biomarker identification in collaboration with SECIM consultant Dr. Chris Beecher. As these advanced tools are developed, they will be deployed on the Galaxy interface and made available to SECIM users and other academic investigators. Finally, the Bioinformatics Core will provide a critical interface to the Promotion and Outreach Core by helping to identify the needs of individual projects that utilize SECIM and to develop instructional modules that will be offered through our annual Metabolomics Workshops

Public Health Relevance

The major goal of metabolomics is the measurement and characterization of metabolites from living organisms, including people. Small molecule metabolites are sensitive to disease, treatment, and many environmental factors, and they can be used as indicators of disease in diagnosis or as markers to assess the outcome of treatment.

Agency
National Institute of Health (NIH)
Institute
National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)
Type
Resource-Related Research Projects--Cooperative Agreements (U24)
Project #
1U24DK097209-01A1
Application #
8694158
Study Section
Special Emphasis Panel (ZRG1-BST-F (50))
Project Start
Project End
Budget Start
2013-09-11
Budget End
2014-08-31
Support Year
1
Fiscal Year
2013
Total Cost
$297,418
Indirect Cost
$98,032
Name
University of Florida
Department
Type
DUNS #
969663814
City
Gainesville
State
FL
Country
United States
Zip Code
32611
Ardente, A J; Garrett, T J; Wells, R S et al. (2016) A Targeted Metabolomics Assay to Measure Eight Purines in the Diet of Common Bottlenose Dolphins, Tursiops truncatus. J Chromatogr Sep Tech 7:
Chouinard, Christopher D; Wei, Michael S; Beekman, Christopher R et al. (2016) Ion Mobility in Clinical Analysis: Current Progress and Future Perspectives. Clin Chem 62:124-33
Patterson, Rainey E; Kalavalapalli, Srilaxmi; Williams, Caroline M et al. (2016) Lipotoxicity in steatohepatitis occurs despite an increase in tricarboxylic acid cycle activity. Am J Physiol Endocrinol Metab 310:E484-94
Qiu, Yunping; Moir, Robyn; Willis, Ian et al. (2016) Isotopic Ratio Outlier Analysis of the S. cerevisiae Metabolome Using Accurate Mass Gas Chromatography/Time-of-Flight Mass Spectrometry: A New Method for Discovery. Anal Chem 88:2747-54
Liu, Haiyan; Tayyari, Fariba; Edison, Arthur S et al. (2016) NMR-based metabolomics reveals urinary metabolome modifications in female Sprague-Dawley rats by cranberry procyanidins. J Nutr Biochem 34:136-45
Markley, John L; Brüschweiler, Rafael; Edison, Arthur S et al. (2016) The future of NMR-based metabolomics. Curr Opin Biotechnol 43:34-40
Koethe, John R; Jenkins, Cathy A; Petucci, Christopher et al. (2016) Superior Glucose Tolerance and Metabolomic Profiles, Independent of Adiposity, in HIV-Infected Women Compared With Men on Antiretroviral Therapy. Medicine (Baltimore) 95:e3634
Bingol, Kerem; Bruschweiler-Li, Lei; Li, Dawei et al. (2016) Emerging new strategies for successful metabolite identification in metabolomics. Bioanalysis 8:557-73
Zhang, Bo; Xie, Mouzhe; Bruschweiler-Li, Lei et al. (2016) Nanoparticle-Assisted Removal of Protein in Human Serum for Metabolomics Studies. Anal Chem 88:1003-7
Antharam, Vijay C; McEwen, Daniel C; Garrett, Timothy J et al. (2016) An Integrated Metabolomic and Microbiome Analysis Identified Specific Gut Microbiota Associated with Fecal Cholesterol and Coprostanol in Clostridium difficile Infection. PLoS One 11:e0148824

Showing the most recent 10 out of 32 publications