Integrating metabolomics data with genomics information
The Genomics Integration core's mission is to provide services, consult with biologists and clinicians, and demonstrate use of integrating large genomics datasets with metabolomics studies as a key piece in solving complex problems in biology and medicine.
The core is strategically advised by Prof. Frederic Chedin, a specialist in epigenomics who is leveraging expertise in biochemistry, cell biology, molecular biology, and genomics, through the use of methods such as ChIP-seq, MethylC-seq, and RNA-seq.
The core is overseen by Dr. Dinesh Barupal who coordinates efforts across the four laboratories involved in the core. WCMC staff in the core are statistician Sili Fan and Dr Kwanjeera Wanichthanarak who devised and implement a new resource, the GRINN database that provides an R package specifically designed to integrate multi-omic data sets by leveraging domain knowledge from major publically available databases. The developed package supports calculation of a wide variety of biological networks including: metabolite-protein-gene, metabolite-protein, metabolite-pathway, protein-gene, protein-pathway and gene-pathway combinations. The biochemical networks can be further incorporated with outputs from correlation analyses to help estimate relationships in absence of domain knowledge and integrate unknown species. Resulting networks can be exported in a variety of common data formats and further extended using external network analysis and visualization tools.
The core specifically aims to nurture projects by interdisciplinary teams focused on high impact goals in nutrition, epidemiology, cancer metabolism, internal medicine, pediatrics, and clinical immunology. The core leads by advancing computational methods in informing metabolomic studies by genomic data, but the core also aims at showcasing the power of genomic data integration in specific demonstration projects, and by consulting and forming teams to submit pilot projects. The submission date for pilot grants next year is around March 15, 2017. Please, think about how your existing cohort study and or your genomic experiments could be enriched with metabolomics data, and contact us before submitting your pilot projects!
Genomic, proteomic and bioinformatic services
We offer fee-based services in genomics, proteomics and bioinformatics. We are looking forward to consult with you, which other types of data might be important for your study, from physiological endpoints to genomic interactions, and how such data may be integrated with metabolic information to gain meaningful insights into biological processes.
Sequencing and gene expression services are also offered at the UC Davis Genome Center and its DNA technologies & Gene Expression Analysis services core. Please see the Genome Center's sample submission page or contact the Genome Center's core manager Dr Ryan Kim at firstname.lastname@example.org for details. The core focuses on Next-Gen Sequencing (NGS) and genotyping, using mainly Illumina, PacBio, and Fluidigm platforms. The Genome Center's core exploits ultra high throughput sequencing and Illumina expression arrays. Workshops in these technologies are offered as an important part of the facility operations. The core also offers access to microarray scanners, liquid handlers, and nucleic acid analyzers to facilitate your experiments.
The UC Davis Genome Center also offers comprehensive proteomics services. Using two high-end microcapillary LC-QExactive mass spectrometers, the core has particular emphasis on label free quantitative proteomic profiling, the analysis of macromolecular complexes, the post-translational modification of their constituents and standard protein identification from complex protein mixtures. Core personnel can also provide amino acid analysis using one of three Hitachi amino acid analyzers and N-terminal sequencing using one of two N-terminal sequencers if needed. Please visit the proteomics service website or contact the Genome Center's proteomics core manager Dr. Brett Phinney at email@example.com for details.
Thirdly, the UC Davis Genome Center further provides ample expertise in bioinformatics and statistics through its bioinformatics services core. This core focuses on data analysis for RNA-Seq differential expression, genomic variant discovery (SNPs, indels and translocations), genome and transcriptome assembly, development of custom scientific software and technology infrastructure and data analysis for various next-generation sequencing technologies, such as Illumina and PacBio RS. For detailed information, please contact Dr. Joseph Fass at firstname.lastname@example.org.
Lastly, our Metabolomics Central Service Core provides services in univariate and multivariate statistical analysis of data sets, pathway analysis and mapping, partial correlation and network analysis. We collaborate in turning your metabolomic data into biologically significant discoveries! Please, contact our Principal Statistician for further information, Dr. Dmitry Grapov at email@example.com .
All these services are available by approved recharge rates as fee-for-service units for internal and external academic researchers as well as for industry partners.
Mouse Metabolic Phenotyping Center
UC Davis is the only institution in the U.S. to host both an NIH metabolomic center and an NIH mouse metabolic phenotyping center. The West Coast Metabolomics Center closely collaborates and partners with the UC Davis Mouse Metabolic Phenotyping Center to leverage information from different streams of data, comprising services from its Metabolism and Endocrinology Core, the Body Composition Themoregulation Food Intake Behavior Core, and the Cardiovascular Biology and Pathology Core. Importantly, the UC Davis mouse metabolic phenotyping center also hosts mouse colonies, and can create genomic knock-out mice on demand, in addition to the variety of gene knockout mice that are already available.
Please see these specific services offered for mouse biology researchers !