Bioinformatics & Data Management (La Jolla)

Overview

The facility transforms raw data into biological knowledge. It provides Systems Biology analysis of datasets generated in the Shared Resources (e.g., microarray, proteomics and Next-Gen sequencing data) or by Sanford-Burnham investigators, as well as comparison with and analysis of other available databases. Four PhD-level members of the Facility assist researchers with advanced bioinformatics and biostatistics analysis helping to generate testable hypotheses and understand biology of the process under study. The facility also assists in data management for large projects, and in implementing specific bioinformatic tools and pipelines e.g., Animal Informatics, microarray data management tool caArray, proteomics database LabKey, and clinical samples LIMS caTissue).

We will work with you to ensure you have a better understanding of your data and their biological interpretation. The bulk of support includes connecting functional genomic data with pathways and networks, consultations on statistical aspects of the research with our team statistician, and connections between gene/protein expression and disease state. We also provide Bioinformatics classes and training for the entire Cancer Center community. Both internal and external customers are charged per hour (see prices here).

Examples of recent projects include:
Tech - Shared Resources: ServicesQuickJump-Contacts and Prices

Services

Assistance is provided in the following areas:

  • Next-Generation Sequencing Data Analysis: From Reads to Biology (RNA-Seq, ChiP-Seq, DNA-seq, exome sequencing, targeted resequencing, SNP and indel detection and more)
  • Biostatistics
  • Systems Biology Support and Pathway Analysis (utilizing GeneGO, IPA and NextBio)
  • Microarray and Proteomics Data Analysis
  • Integrative analysis of multi-omics data
  • Gene Family Analysis and Annotation
  • Human Genome Analysis
  • Grant Preparation Assistance
  • Informatics Guidance
  • Website and Database Development
  • Bioinformatics Classes
  • Additional informatics assistance is available from the Lake Nona Bioinformatics Core

Equipment and Resources

We have the necessary hardware and software to solve your research problem. Microarray and proteomics data analysis is supported with multiple software including R, GeneSpring, GenomeStudio, BioConductor and GenePattern. Further commercial pathway analysis includes Ingenuity Pathway Analysis (IPA), NextBio and GeneGo’s MetaCore. For analysis of next generation DNA sequence data there are two powerful 5 node Linux clusters. Next-Gen data analysis tools include Avadis NGS, BioScope, Broad Institute Genome Analysis ToolKit (GATK), SOLiD Alignment Browser (SAB), SOLiD Analysis Tools (SAT), and Partek tools. BioScope software provides a command line and simple web interface for running application-specific sequence analysis tools. These tools allow configurable workflows for resequencing and whole transcriptome analysis and ChIP-seq analysis.

Contact

Alexey Eroshkin, Ph.D., Bioinformatics Specialist and Core Director

Microarray, Proteomics and Next-Generation sequencing (SNP, Exomes, RNA-seq and Chip-seq) data analysis from raw data to biological interpretation (e.g., finding affected pathways, causal mutations). Biomarker discovery and predictive modeling of disease stage. Identification of protease substrates (www.proteolysis.org), protein functional annotation, analysis of protein structure-activity relationships, genome mining for new genes, multiple alignments and phylogenetic analysis. As Director of the core, I am also evaluating new tools, planning new projects and allocating resources.


Roy Williams, Ph.D., Bioinformatics Specialist

Data analysis (microarray and proteomics) and genome annotation. Questions about methods for analyzing systems biology data and how to view it in a suitable biological context. Have worked with Affymetrix, GeneSpring, MatLab, R, Bioconductor and related software extensively over the last six years.


Xiayu (Stacy) Huang, Ph.D., Biostatistician

Statistical data analysis, e.g., calculation of the optimum number of animals needed for the experiment, Microarray and proteomics data analysis (via GeneSpring, Bioconductor, GenePattern and related software).

Price List
Bioinformatics Custom Data Analysis/Applicationhour$35.0043.754792.05z500
Statistics data analysishour$35.0043.754792.05z900
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