Bioinformatics Core

Members
Publications
Open Positions

The Bioinformatics Core provides bioinformatics consultation, training, and resource development to Memorial Sloan-Kettering Cancer Center investigators and supports the high-performance computing resources of the Computational Biology Center.

 

Sequence Data (Next-gen and Sanger) Processing and Analysis

Core personnel have developed processing and analysis pipelines for high-throughput next-gen (SOLiD and 454) and Sanger sequence data. The input to this pipeline is raw Roche 454 and ABI SOLiD reads from the Genomics Core Lab, or Sanger sequence traces from internal or external sources, and output is 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 reads and samples. Charges for standard Sanger analyses are $0.10/trace. Additional custom analyses or changes to the pipeline may incur additional consult charges. Please contact Nicholas Socci at for additional details.

CGH Array Normalization and Segmentation

Core personnel have developed a CGH array (Agilent and Affymetrix) normalization and segmentation pipeline. The input to this pipeline is raw Agilent CGH array or Affymetrix SNP 6.0 array data from the Genomics Core Lab, and the output is genomic segments annotated with copy-number data. Charges for this standard analysis on GCL data have already been incorporated into GCL pricing. If data is from outside Memorial Sloan-Kettering, please contact the core for pricing. Additional custom analyses can be performed, but additional consult charges will result. Please contact Nicholas Socci at for more details.

Scientific Consultations

Members of the Bioinformatics Core provide consultation services (both large and small) on a variety of topics including the following: microarray data (gene expression and aCGH) analysis, automated functional and pathway analyses of high-throughput data, and protein and nucleotide sequence analysis. Core members have participated in numerous internal and external proposals, and have also reviewed bioinformatics analysis methods and results. Consultations are provided to Memorial Sloan-Kettering investigators at a cost of $120/hour for any work exceeding an hour. Cost estimates are given before work begins. Please contact Raya Khanin at for more information.

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

Core personnel configure, maintain, and administer high-performance computing resources for investigators in the Computational Biology Center and other SKI investigators who need access to significant Linux compute and storage resources. Please contact Joanne Edington at for systems availability, access, and pricing.

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).

For more information, please contact Nicholas Socci at or review our staff contact information. Many of our activities have resulted in publications and bioinformatics resources.

Nicholas Socci
(Core Facility Head)

Location

11th floor of the Zuckerman Research Center

Walk-in Clinics

Open to the Tri-Institutional community; offered by the Bioinformatics Core and the and the Integrated Genomics Operation (IGO).

cBioPortal Clinic (Genomics Core Lab)
1st and 3rd Monday of the month, 2:00 – 3:00 PM
ZRC CyberLibrary Team Room (Left on entering lobby from East 69th Street)

Programming Clinic (Bioinformatics Core)
Every Tuesday, 2:00 to 3:00 PM
ZRC CyberLibrary Team Room (Left on entering lobby from East 69th Street)

Bioinformatics Clinic (Bioinformatics Core)
Every Wednesday, 2:00 to 3:00 PM
RRL Medical Library Team Room (Left on entering lobby from East 67th Street)

Recommended Links

Computational Biology Center
Tri-Institutional Workshops
Tri-Institutional Programs