Facility Researcher

Bioinformatics & Data Management

Transforming raw data into biological knowledge.

 

The facility transforms raw data into biological knowledge. We provide Systems Biology analysis of datasets generated in the Shared Resources (e.g., microarray, proteomics and Next-Gen sequencing data) for our investigators as well as comparison with and analysis of other available datasets. Three members of the Facility assist researchers with advanced bioinformatics and biostatistics analysis helping to put data into biological context across various disease areas to create testable hypotheses and understand biology of the process. The facility also assists in database development, data management for large projects and implementing specific bioinformatic tools and pipelines. 

The bulk of support includes connecting functional genomic data with pathways and networks, connecting gene/protein expression and disease state and consultations on statistical aspects of the research with our team statistician. We also provide Bioinformatics classes and training for the entire Cancer Center community. Both internal and external customers are charged per hour.
 

Examples of recent systems biology/network building projects:

  • Network Analysis of Co-Expressed Metabolic Genes
  • Tumor-suppressive mechanisms of transcription factor XX


Examples of recent database-related projects include:

  • bNAber, Database of Broadly Neutralizing HIV-1 Antibodies
  • PluriTest website
  • Center on Proteolytic Pathways PMAP website
  • Neuron PhosphoProteomics web resource

 

Assistance is provided in the following areas:

  • Systems Biology Support: Generating and Analyzing networks and pathways to produce testable hypotheses, to discover mechanisms of drug action and new drug targets.
  • 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: experiment design, power analysis, estimation of the minimum number of animals required etc.
  • Microarray and Proteomics Data Analysis, Integrative analysis of multi-omics data
  • Gene Family Analysis and Annotation: Human Genome Analysis
  • Grant Preparation Assistance
  • Website and Database Development
  • Bioinformatics Classes, tutorials and trainings

 

We have extensive hardware and software to solve your research problems, including R/Bioconductor, GeneSpring GX and NGS, GenomeStudio, GenePattern, Cytoscape, Ingenuity Pathway Analysis (IPA), Oncomine, NextBio, Thomson Reuters MetaCore, Broad Institute Genome Analysis ToolKit (GATK), and Partek tools. We actively use data from public databases (GEO, TCGA, UCSC Cancer Genome Browser, CCLE, and others) for biomarker discovery, survival analysis and predictive modeling. In 2014 we expanded our MetaCore license with subscribing to Oncology Module, which has hundreds of prebuilt cancer maps and to MetaDrug module, which predicts possible targets of small molecules and finds biological pathways affected by small molecules.

 

For a complete list of services, please call (858)646-1000 ext. 5336 or email us.
 

Bioinformatics Services Internal
Subsidized
Internal External
Non-Profit
External
For-Profit
Bioinformatics Custom Data Analysis/Application hour $38 $47.50 $51.30 $99.94
Statistics data Analysis hour $38 $47.50 $51.30 $99.94

Leadership

Facility Director
Scientific Director

Contact

 

  • Alexey Eroshkin, Ph.D.
    Bioinformatics Core Manager 
    (858)795-3100 ext. 5336 
    Email Alexey Eroshkin
    Dr. Eroshkin specializes in Microarray, Proteomics and Next-Generation sequencing (SNP, Exome sequencing, RNA-seq and Chip-seq) data analysis - from raw data to biological interpretation (e.g., finding affected pathways, causal mutations). He also provides assistance with pipeline development, biomarker discovery, predictive modeling of disease stage as well as with igene functional annotation, analysis of protein structure-activity relationships, genome mining for new genes, multiple alignments and phylogenetic analysis. As Director of the Core, he is evaluating new tools, planning new projects and allocating resources. 
  • Andrew P. Hodges, Ph.D.
    Bioinformatics Scientist
    (858)646-3100 ext. 4058 
    Email Andrew Hodges 
    Dr. Hodges implements existing and novel systems biology and machine learning approaches for target and drug discovery in cancer and other diseases. He provides pathway analysis and functional annotation, statistical simulations and synthetic network design, and heterogeneous dataset integration all applied to fundamental and translational research. Andrew incorporates advanced technologies (R/Bioconductor, Cytoscape, NextBio, GenePattern, AracNe/MI, BN+1, etc.) for validating existing and generating new hypotheses. He will be assisting researchers with database mining, network analyses, and selection of the most promising biomarkers and drug targets.
  • Xiayu (Stacy) Huang, Ph.D.
    Biostatistician
    (858)646-3100 ext. 3916 
    Email Xiayu (Stacy) Huang
    Dr. Huang is in charge of statistical data analysis, e.g., calculation of the optimum number of animals needed for your experiments, survival analysis, including data downloaded from The Cancer Genome Atlas (TCGA), clinical data analysis, statistical data mining, statistics support for grants and manuscripts, etc. Stacy also performs genomic and proteomic data analysis (via GeneSpring, Bioconductor, GenePattern, Cytoscape and related software) including data QC, normalization, getting differentially expressed gene/protein lists, heatmaps, downstream pathway analysis. 

 

Please call (858)795-5336 or use the button below to send us an email.
 

Contact the Facility

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