The Genomics Integration Core will advance metabolomics by making improvements in tools for interpreting and using metabolic data, specifically in the context of biochemical pathways and networks, but also by integrating data generated from genomics research, such as results from SNP genotyping, microbial genomics, or transcript and protein expression studies, into metabolomics studies. The core will be pivotal for conducting regional pilot and feasibility projects and critical for the success of the training and educational mission of the Promotion and Outreach Core. The Genomics Integration Core will be comprised of four different laboratories: the Weimer metagenomics laboratory, the Karp pathway informatics research group, the Pollard statistical genomics research group and the Lin and Perroud bioinformatics services core within the UC Davis Genome Center. The core will be responsible for both advancing the content of diverse metabolomics databases and tools and integrating the use of those tools and tools from other disciplines, particularly genomics, into metabolic studies such as pathway mapping. Newly developed tools will be employed in the Genome Center's bioinformatics service core as determined in coordination with the WC3MRC's Central Service Core. Specifically, the Genomics Integration Core will provide comprehensive bioinformatics and statistical tools for interpreting metabolomic data. The Core will collaborate with regional scientists on study design, data analysis and genomic interpretation of metabolomic data. The core will test and compare existing tools for linking genomic and metabolomic data, such as pathway mapping. Specifically, scientists in this core will work to advance genomics and pathway tools for metabolomic studies. The Genomics Integration Core will focus on advancing a range of existing tools in order to connect genomic pathways and disease phenotype data. Gene-enzyme annotations in the HumanCyc pathway database, integration of text-mining results into Cytoscape representations of metabolic networks, extension of current pathway enrichment approaches to include full metabolomic network statistics, development of tools for visualizing metabolite-centric network graphs with genomic information on demand, or other appropriate technologies will be explored in these efforts. The Genomics Integration Core will develop and test improvements in such tools and validate their utility and user friendliness by collaborating with regional scientists in clinical and preclinical research projects. Finally, this core will provide training and education in conjunction with the Promotion and Outreach Core.

Public Health Relevance

Sequencing of the human genome has opened new avenues for understanding health and the progression of diseases. We now begin to learn which parts of the genome enable metabolic responses in humans, and which parts of metabolism may be contributed by gut microbiota living in symbiosis. Integration of pathway modeling will enable a far better understanding and treatment of human diseases.

National Institute of Health (NIH)
Resource-Related Research Projects--Cooperative Agreements (U24)
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University of California Davis
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Guerrero, Andres; Lerno, Larry; Barile, Daniela et al. (2015) Top-down analysis of highly post-translationally modified peptides by Fourier transform ion cyclotron resonance mass spectrometry. J Am Soc Mass Spectrom 26:453-9
Ma, Yan; Kind, Tobias; Yang, Dawei et al. (2014) MS2Analyzer: A software for small molecule substructure annotations from accurate tandem mass spectra. Anal Chem 86:10724-31
Noto, Antonio; Fanos, Vassilios; Barberini, Luigi et al. (2014) The urinary metabolomics profile of an Italian autistic children population and their unaffected siblings. J Matern Fetal Neonatal Med 27 Suppl 2:46-52
Schuchardt, Jan Philipp; Schneider, Inga; Willenberg, Ina et al. (2014) Increase of EPA-derived hydroxy, epoxy and dihydroxy fatty acid levels in human plasma after a single dose of long-chain omega-3 PUFA. Prostaglandins Other Lipid Mediat 109-111:23-31
Schuster, Gertrud U; Bratt, Jennifer M; Jiang, Xiaowen et al. (2014) Dietary long-chain omega-3 fatty acids do not diminish eosinophilic pulmonary inflammation in mice. Am J Respir Cell Mol Biol 50:626-36
Snowden, Stuart G; Grapov, Dmitry; Settergren, Magnus et al. (2014) High-dose simvastatin exhibits enhanced lipid-lowering effects relative to simvastatin/ezetimibe combination therapy. Circ Cardiovasc Genet 7:955-64
Ulu, Arzu; Stephen Lee, Kin Sing; Miyabe, Christina et al. (2014) An omega-3 epoxide of docosahexaenoic acid lowers blood pressure in angiotensin-II-dependent hypertension. J Cardiovasc Pharmacol 64:87-99
Ono, Emiko; Dutile, Stefanie; Kazani, Shamsah et al. (2014) Lipoxin generation is related to soluble epoxide hydrolase activity in severe asthma. Am J Respir Crit Care Med 190:886-97
Campbell, Caitlin; Grapov, Dmitry; Fiehn, Oliver et al. (2014) Improved metabolic health alters host metabolism in parallel with changes in systemic xeno-metabolites of gut origin. PLoS One 9:e84260
Cajka, Tomas; Fiehn, Oliver (2014) Comprehensive analysis of lipids in biological systems by liquid chromatography-mass spectrometry. Trends Analyt Chem 61:192-206

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