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Bioinformatics Services

The BBSR bioinformaticians provide assistance in experimental design, feasibility assessment, power analysis, sample size calculation, data analysis and interpretation, as well as grant application and manuscript preparation. The resource offers pre-processing and sequencing analyses, knowledge-based and public database analyses, and advanced statistical analyses. To detect and prevent data quality issues that may impact later data analysis, BBSR bioinformaticians employ various quality control strategies, including quality assessment of sequencing data, sample outlier detection, and batch effect determination. BBSR bioinformaticians assist in projects involving large-scale experimental data sets that are available through research community efforts such as GEO, TCGA, CCLE, and ENCODE database compendia. With the fast development of researches in genomics and bioinformatics, to ensure that bioinformatics analysis by BBSR provides accurate, robust, and advanced genomic information, BBSR bioinformaticians routinely review and update their knowledge bases, analysis methodologies and pipelines.



  • Write-up of statistical and bioinformatics considerations for grants and protocols
  • Data analysis of clinical trials, community-based participatory research studies, population studies, and laboratory experiments
  • Write-up of statistical/bioinformatics methods and collaboration on results for manuscripts, abstracts, presentations, and reports to oversight committees and funding agencies
  • Support for data management and data sharing
  •  Participation in SCCC educational activities through seminars, lectures, or journal club on study design, data collection, and data science methods for clinical trial, community-based participatory research studies, population-based studies, and laboratory studies.

Bioinformatics Services

  • Experiment design for high-throughput genomic studies
  • Next-Generation Sequencing data analysis including whole transcriptome/single-cell RNA-Seq, ChIP-Seq, ATAC-Seq, exome/Whole Genome Sequencing, 16S rRNA, and other NGS technologies
  • Pathway/Gene Set Enrichment Analysis and gene network analysis
  • Functional metagenomics analysis
  • Biomarker discovery and prediction modeling for clinical outcomes
  • LINCS data pre-processing and pathway integrative analysis.
  • Drug sensitivity and genomic association analysis
  • Genomic data integration using public database such as TCGA, CPTAC, GEO, ENCODE, etc.
  • Integration analysis of genomic data across multiple platforms
  • Genomic data visualization
  • Bioinformatics new methodology and algorithm development
  • Bioinformatics software development including Bioconductor/R package and web-based software


  • R tools & Bioconductor packages
  • Ingenuity Pathway Analysis
  • Cytoscape
  • NCBI Toolkits, fastqc, STAR aligner, rMATS, and other sequence analysis tools
  • Multiple Dell 16-core Intel Xeon/Linux X86_64 work stations
  • Pegasus supercomputing cluster


  • BioMart
  • Molecular Signatures Database (MSigDB)
  • Gene Ontology (GO)
  • Greengenes 16S rRNA database

To request support from the BBSR, complete the Investigator Request for Statistical and Bioinformatics Request Form and submit by clicking the “Submit” button on the form or email the form to