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.
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.
|Arabyan, Narine; Huang, Bihua C; Weimer, Bart C (2017) Draft Genome Sequences of Salmonella Lysozyme Gene Knockout Mutants. Genome Announc 5:|
|Zhang, Jie; Light, Alan R; Hoppel, Charles L et al. (2017) Acylcarnitines as markers of exercise-associated fuel partitioning, xenometabolism, and potential signals to muscle afferent neurons. Exp Physiol 102:48-69|
|Flitter, Becca A; Hvorecny, Kelli L; Ono, Emiko et al. (2017) Pseudomonas aeruginosa sabotages the generation of host proresolving lipid mediators. Proc Natl Acad Sci U S A 114:136-141|
|Wan, Debin; Yang, Jun; Barnych, Bogdan et al. (2017) A new sensitive LC/MS/MS analysis of vitamin D metabolites using a click derivatization reagent, 2-nitrosopyridine. J Lipid Res 58:798-808|
|Fong, Louise Y; Jing, Ruiyan; Smalley, Karl J et al. (2017) Integration of metabolomics, transcriptomics, and microRNA expression profiling reveals a miR-143-HK2-glucose network underlying zinc-deficiency-associated esophageal neoplasia. Oncotarget 8:81910-81925|
|Jonscher, Karen R; Stewart, Michael S; Alfonso-Garcia, Alba et al. (2017) Early PQQ supplementation has persistent long-term protective effects on developmental programming of hepatic lipotoxicity and inflammation in obese mice. FASEB J 31:1434-1448|
|Barnych, Bogdan; Rand, Amy A; Cajka, Tomas et al. (2017) Synthesis of cyclooxygenase metabolites of 8,9-epoxyeicosatrienoic acid (EET): 11- and 15-hydroxy 8,9-EETs. Org Biomol Chem 15:4308-4313|
|Tu, Lan N; Showalter, Megan R; Cajka, Tomas et al. (2017) Metabolomic characteristics of cholesterol-induced non-obese nonalcoholic fatty liver disease in mice. Sci Rep 7:6120|
|Blaženovi?, Ivana; Kind, Tobias; Torbašinovi?, Hrvoje et al. (2017) Comprehensive comparison of in silico MS/MS fragmentation tools of the CASMI contest: database boosting is needed to achieve 93% accuracy. J Cheminform 9:32|
|Agrawal, Karan; Waller, Justin D; Pedersen, Theresa L et al. (2017) Effects of stimulation technique, anatomical region, and time on human sweat lipid mediator profiles. Prostaglandins Other Lipid Mediat :|
Showing the most recent 10 out of 148 publications