The Bioinformatics Core provides computational and statistical support to the MSK research community. The core offers a wide array of services from standardized state-of-the-art pipelines based on published best practices to customized research-level analysis for novel assays and data types.
BIC works with teams that have varying levels of computing experience from assisting trained bioinformatics personnel to providing full support for labs without dedicated computational support. We also provide consultation, tutoring, and courses to help train MSK researchers in computational methods.
We provide support in additional areas including data wrangling, generating publication quality graphics for manuscripts, and providing support throughout the grant writing process. The core researches the latest developments in the field of Bioinformatics to develop and deploy state-of-the-art methods.
Sequence Data Processing and Analysis
Core personnel have developed processing and analysis pipelines for a number of next-generation sequencing assays: RNAseq, Targeted Sequencing (IMPACT, Whole Exome), Whole Genome Copy number, ChIPSeq/ATACSeq, BiSulfite Methylation amount others. Output is provided for various levels of processing: reference-mapped sequence (secondary analysis), as well as tertiary analyses tailored to the experimental question(s), such as SNP detection, RNA-seq, and CHiP-seq. Charges for standard next-gen analyses [MSK only] are based on numbers of samples for low level analysis or complexity of experimental design for higher level analysis. Additional custom analyses or changes to the pipeline may incur additional consult charges. Please contact Nicholas Socci (soccin@mskcc.org) for additional details.
Software and Database Development
Core personnel have developed databases and web tools for the benefit of the entire Memorial Sloan-Kettering research community. Examples include a multi-institutional study tracker (in collaboration with the Soft Tissue Sarcoma Program Project and the Office of Clinical Research), a de-identified database of pathology diagnostic reports (in collaboration with the Department of Pathology), a tissue microarray database (in collaboration with the Pathology Core), a gene expression and CGH microarray normalization and analysis pipeline (in collaboration with the Genomics Core Lab), a high-throughput mutation detection pipeline (in collaboration with the Genomics Core Lab and the Beene Translational Oncology Core), and various online sequence and microarray analysis tools (in collaboration with numerous Memorial Sloan-Kettering investigators). Please contact Manda Wilson at for more information.
High-Performance Computing Systems Access
Please visit http://hpc.mskcc.org/ for more information.
Training
Hands-on practical workshops on various bioinformatics and genomics topics are provided to all Tri-Institutional and Clinical Translational Science Center faculty, staff and students. These workshops occur at least twice a year, and are a collaborative effort between Weill Cornell Medical Center (the Institute for Computational Biomedicine and the Microarray Facility) and Memorial Sloan-Kettering (Bioinformatics Core and Genomics Core Lab).
Support
The Bioinformatics Core has been supported in the past, in part by a generous grant from the Bristol-Myers Squibb Foundation. In addition, it derives support from institutional funding sources, including the Tri-Institutional Research Program and the NCI Cancer Centers Program. The Bioinformatics Core also participates in the development and adoption of NCI’s Cancer Biomedical Informatics Grid (caBIG) and is a participant in the Soft Tissue Sarcoma Program Project (PI: Sam Singer), the Soft Tissue Sarcoma SPORE (PI: Sam Singer), the Lung Adenocarcinoma Program Project (PI: Mark Kris), the Clinical Translational Science Center (PI: Julianne Imperato-McGinley), and the Stand Up To Cancer Dream Team grant targeting the PI3K Pathway in Women’s Cancers (PIs: Charles Sawyers, of Memorial Sloan-Kettering, Lew Cantley, of Harvard Medical School and Beth Israel Deaconess Medical Center, and Gordon Mills, of M.D. Anderson Cancer Center).
MSKCC Facilities and Other Resources
The Memorial Sloan Kettering Cancer Center (MSKCC) Bioinformatics Core Facility occupies approximate 1,200 square feet of computer lab space on the 4th of the Zuckerman Research Center (417 East 68th Street New York, NY 10065). The building is located in the heart of New York’s biomedical research district (Weill Cornell Medical Center, Rockefeller University, The Hospital for Special Surgery are within 5 blocks), facilitating interactions with scientific experts in genomics and clinical medicine. The facility, lead by Dr. Nicholas Socci (PI on subaward), is comprised of 8 bioinformatician engineers, research scientists and software developers. It contains all resources necessary to ensure successful operation, including desk space for each staff member, computers, conference rooms and access to a High Performance Compute resource. Read more.
For more information, please contact Nicholas Socci at soccin@mskcc.org. Many of our activities have resulted in publications and bioinformatics resources,
