Bioinformatics Shared Resource

Co-Director
 
 

Citing the P30 Cancer Center Support Grant (CCSG)

Bioinformatics involves the analysis of high throughput sequence and molecular data for study of cancer genomes. The Bioinformatics Shared Resource (BISR) provides comprehensive analysis of genomic and proteomic data to UACC members in support of their research. This contribution can result in short- or long-term projects, ranging from one day to many months, depending on the nature and extent of the support required.

The Shared Resource provides all levels of support from experimental design to analysis and publication of these data and development of grant applications. BISR staff works with researchers to select the data analysis approach that would help answer the research question. The resource assists in providing information about cancer data resources and utilization of bioinformatics pipelines and analytical tools for research projects. BISR also provides cohort identification in public clinically annotated molecular data for hypothesis generation. The goal is to provide assistance with data analysis that will lead to testable hypotheses and fundamentally important discoveries in cancer research.

The BISR specializes in the biological interpretation of data that may lead to a new understanding of cancer biology and the discovery of new diagnostic markers, risk genetic markers, and drug targets. The staff is well prepared to perform all of these types of analysis.

The Bioinformatics Shared Resource at The University of Arizona provides support in the following areas:

  • Analysis of genome data (e.g. gene expression, non-coding RNAs, CGH, next gen sequence analysis), proteomics, and other types of molecular data sets of cancer cells and tissues
  • Analysis of cancer molecular and clinical annotated datasets from public resources. NIH-TCGA (Cancer Genome Atlas) project, Cosmic (Catalogue of somatic mutations in Cancer), CCLE (Cancer Cell Line Encyclopedia), NIH LINCS project (Library of Network-based Cellular Signatures), NCBI GEO datasets and any other public resource.
  • Application of broad range of statistical and computational approaches for integrative analysis of molecular data with clinical parameters and correlating molecular profiles to patient attributes and outcome.
  • Support for pathway analysis, data visualization, systems biology analysis, analysis of genetic vulnerabilities for drug targeting and predictive patterns for outcome.
  • Assist in generation of preliminary data for development of grant applications and supporting bioinformatics data for publications.
  • Bioinformatics support for Cancer Center projects and other Shared Resources in the form of molecular databases, genome databases, and data sharing tools.

Who we are

The Bioinformatics Shared Resource was founded in 2002 to provide bioinformatics, genomics, and proteomics support to The University of Arizona Cancer Center researchers so that they can fully utilize the power of the human genome project in their research. The Shared Resosurce collects, stores, and makes available a variety of molecular and genetic data on cancer genomes. It uses established computational tools but also develops new tools as needed for analysis of all genome-related data. A variety of computer-related services for informatics support of research projects is also provided. Through these various levels of support, the Bioinformatics Shared Resource provides an integrated approach that assists researchers in their quest for new biological information about cancer cells and tissues and thus aids in finding new drug targets and preventative methods. Some examples of the types of services we offer are given below.

The Bioinformatics group includes the following staff members

  • Ritu Pandey, PhD, Co-Director of Bioinformatics Shared Resource at The University of Arizona Cancer Center.  Dr. Pandey specializes in management and analysis of high throughput molecular data.

Location

  • All the Informatics and Bioinformatic team members are currently  located on the first floor of the Levy building in and around rooms 1930
    • Ritu Pandey     Room 1932  Phone: (520) 626-0391

      Mailing Address: 
                          
                           The University of Arizona Cancer Center
                           1515 N. Campbell Ave.
                           PO Box 245024
                           Tucson, AZ  85724-5024

BSR Project Pricing, Turnaround Time & Consulting

Interaction with Cancer Center Members:

The service offered is expertise in data analysis and management. If staff can assist a cancer researcher on a temporary consulting basis, then the Shared Resource will charge for the time spent on a project. The Shared Resource staff welcomes the opportunity to participate in laboratory meetings, research discussions and writing papers and grant applications. Staff can perform a free preliminary data analysis to support the feasibility of an application and can also add experience and expertise in data management and analysis, thereby helping to increase the fundability of many research grant applications. 

Expertise

Areas of expertise include both computational biology - biological sequence analysis, protein structure analysis, genome analysis, advanced computational analysis of large data sets such as gene expression, single nucleotide polymorphism (SNPs) and proteomics data and basic biological studies - population and molecular genetics, molecular and cell biology, biochemistry, and evolutionary biology. The goal is to provide assistance with data analysis that will lead to testable hypotheses and fundamentally important discoveries in cancer research. Staff specializes in the biological interpretation of data, leading to a new understanding of cancer biology, and the discovery of new diagnostic markers, risk genetic markers (haplotypes), patterns in data, and drug targets. The staff is well prepared to perform all of these types of analysis.

FUTURE ROLE FOR THE BIOINFORMATICS SHARED RESOURCE AS A RESOURCE FOR CANCER GENOME AND POPULATION GENETIC DATA.

The Bioinformatics Shared Resource will continue to aid The University of Arizona Cancer Center investigators with access to genome and proteome data, data analysis, and integration of large data sets data with clinical and biological information for specific research projects. It will keep abreast of new data sets, analytical tools and generate new computational tools and methods, as needed. 

Some of our Past Informatics Initiatives at the Cancer Center

These are some of the tools that were developed by the group or adopted and deployed to support Cancer Center programs, Shared Resources and the researchers. 

  • Protbase — This is a web based lab data management system for Proteomics Shared Resource. This system offers users to submit sample request, track their experiment, download/view results and share their experiments. Further more, it offers facility core staff to track experiments request and lab usage for proteomics services, upload results and bill the researchers for services offered. 
  • Genomics Core database — A storing and tracking system for microarray data for the Genomics Shared Resource. 
  • UACC PubDB —  A web based system for storing and tracking publications by University of Arizona Cancer Center members, programs and shared services.
  • Pathway Miner — A web based system for biological interpretation of results from microarray experiments.