Bioinformatics Shared Resources

Sanford Burnham Prebys Medical Discovery Institute


Here you can learn about our group, find information on the bioinformatics services we provide, and see the broad array of resources available to Sanford-Burnham researchers. Customers from other non-profit and commercial organizations are welcome. We can assist you in any of the following areas:

  • Next-Generation Sequencing Data Analysis: From Reads to Biology (RNA-Seq, ChiP-Seq, DNA-seq, CLIP-seq, scRNAseq, exome sequencing, SNP detection and more) 
  • Cancer driver gene discovery using VIPER algorithm from Califano group and other machine learning techniques
  • Next-Gen Sequencing, metabolomics and proteomics data integration and analysis aiming to generate testable hypotheses
  • Pathway/Network building and analysis using your 'omics data, public datasets, your gene list or no data at all   
  • Systems Biology Support and Pathway Analysis via Ingenuity IPA, MetaCore, NextBio, Oncomine and TRANSFAC
  • Biostatistics
  • Bioinformatics Classes 
  • Website and Database Development (visit - database of broadly neutralizing HIV-1 antibodies, 
  • Informatics Guidance
  • Grant Preparation Assistance
  • Pre-computed models of cancer progression in 23 major cancer types are now available for community at our Regulattice portal​ (Username: demo; Password: demo1).
  • Sample Surfer ( or (intranet)) is a program designed to select samples (from a large gene expression data set) that are similar to a given gene signature.

​Contact us by phone (858-795-5336858-795-5336), email ( or in person (bld.10 rm 2405, 2406). The link to the Core internal web site is here. Follow one of the links below to get started:

Complete job request on iLAB (you will need to login into iLAB)

  • ​​Learn about the BSR's services and prices.

About the BSR

  • Learn about the BSR's mission, personnel, and services.


  • Read about basic procedures and explore the hardware and software tools available at the Burnham Institute.

Events & Courses

  • See listings of upcoming seminars and course announcements.

Every Sanford-Burnham researcher has access to the following Systems Biology tools:


NextBio is the search engine that enables scientists to easily traverse incredible volumes of biological data to form novel hypotheses, validate findings and test ideas. Researchers and clinicians can enter a gene, protein, disease, or tissue of interest into a search box and receive ranked answers to their queries based on an unparalleled knowledge trove of biomedical information. Moreover, users can instantly correlate metadata signatures generated from their research with the results of thousands high throughput studies.  You can register and start using NextBio from dedicated, secured domain at to formulate, validate and share answers to complex questions across different assay platforms, organisms and research domains to advance scientific and clinical discovery. 

IPA is a web-based application that helps to analyze experimental data in the context of biological pathways and functions, search for genes, phenotypes and diseases, and create create/modify experimental models.  IPA contains manually curated findings from full-text scientific articles. Go to and contact customer support with request to create new account for you. Here is anothr sign up link for IPA account: do not need to ask Alexey Eroshkin for Institutional License Key anymore. Click on "Sign up" and fill the form. Once you fill out this form, you will receive an email with your private IPA account. 

GeneGo’s MetaCore/MetaDrug Discovery Platform provides software and databases for genomics and cheminformatics analysis in the context of manually curated pathways derived from full-text articles. Researchers can batch upload their experimental data and share with colleagues. They can then use this data for pathway analysis and ontological enrichment and have a downloadable report with publication quality images. The system provides in depth coverage of diseases, covering human, mouse, rat, dog, worm, yeast, fly, chicken and chimpanzee. To have access to the system please email your request to and you will receive your access keys. Here is the link to the portal: