The Bioinformatics Shared Resource continuously develops new and efficient approaches to data analysis as a response to emerging research needs. Facility functions include: statistical analyses and computational modeling for all types of high-throughput data; advanced bioinformatics tools for integrative cancer biology; and data management. Routine data analyses include large scale information datasets (omics data) generated by high-throughput technologies, which address the following areas:
- Gene expression (RNA-seq, single cell RNA-see, smRNA-seq, Nanostring)
- Gene regulation (ChIP-seq, Cut & Run, ATAC-seq, epigenetic profiling, Hi-ChIP, HiC)
- Genome and transcriptome sequencing (alternate splicing, RNA editing, gene fusion, SNP and INDEL mutation detection, CNV)
- Biomarkers (discovering markers in mRNA ,miRNA and protein expression data)
- Proteomic analyses (mass spectrometry-based spectra, LCMS, DIGE, RPPA, etc.)
- Pathway and network analysis
- Integration of multi-platform data
- Other customized data analysis projects
- High-throughput data analysis:
- Next generation sequencing data analysis
- Single cell RNA-seq
- Hybridization platforms (Nanostring, microarrays)
- Low-density PCR arrays (mi-RNA, pathways, custom)
- Proteomics and metabolomics data
- Enrichment Analysis (Ingenuity, DAVID)
- Comprehensive analysis of complex projects that require multi-platform data integration
- Consultation and support of experimental design and customized bioinformatics services
- Statistical consultation and predictive model building
- Computational support for data management, high performance computing, and custom programming
- Centralized computation resources, including data management and collaboration tools, sequence databases, homology algorithms, and other sequence manipulation tools
- Web-based application/database development and management
- Training: Genome Browser, Ingenuity, DAVID
- Grant and publication support: results, methods, figures
- Advanced biological models and illustrations
For pricing information, visit iLab or contact the managing director.
This facility is supported in part by a Cancer Center Support Grant (CCSG) awarded by the National Cancer Institute (NCI) to the Ellen and Ronald Caplan Cancer Center.
The Wistar Institute
Andrew Kossenkov, Ph.D.
Priyankara Wickramasinghe, Ph.D.
Toshitha Kannan, M.S.
Qin Liu, M.D., Ph.D., Professor
David Speicher, Ph.D., Professor