Bioinformatics Core R&D |
Publications  |
The core develops and prototypes biomedical datasets, databases and software tools that will benefit the entire MSKCC research community. Currently, these include the following:
- Mapback: a functional analysis tool that maps protein amino acid residue coordinates (from the RefSeq reference sequence set) to coding DNA sequence (CDS) coordinates and chromosomal coordinates for both hg18 and hg19 human genome builds. Known somatic mutations (from COSMIC) are also integrated. Human Ensembl and UniProt protein reference sequence sets have also been mapped, and mouse (mm9) data are also available. Released to MSKCC on December 20, 2007.
- Mutagrator: a functional analysis tool that displays COSMIC somatic mutations in human tyrosine kinases in the context of the TK domain. Released to MKSCC on May 7, 2007. We are currently working on Mutagrator2, which extends the tool to all RefSeq protein sequences.
- Pathlite [MSK only]: web resource providing institution-wide access to paraffin and frozen archives. Released to MSKCC on June 21, 2006.
- CancerGenes: searchable database of genes related to the development or maintenance of cancer. Released on March 22, 2006.
- Study Tracker [registration required]: a web tool for tracking subjects and samples in multi-institutional studies. Developed in collaboration with the Sarcoma Program. Released to MSKCC on September 18, 2005.
- Database and Reagent Registry [MSK only]: a repository for clinical databases and tissue/sample banks in the hospital developed in collaboration with Office of Clinical Research. Released to MSKCC on June 8, 2004.
