Nicholas Socci (Core Facility Head)



Visit the Bioinformatics Core’s Intranet site

More »

The Bioinformatics Core is located in the Zuckerman Research Center. It 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.

Walk-in Clinics Offered

The following clinics are offered by the Bioinformatics Core and the Integrated Genomics Operation (IGO)

cBioPortal Clinic (IGO)
1st and 3rd Monday of the month, 2:00 to 3:30 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)

These programs are open to the Tri-Institutional community.

Sequence Data Processing and Analysis

Core personnel have developed processing and analysis pipelines for high-throughput next-generation sequencing data. These programs can compute reference-mapped sequence (secondary analysis), as well as tertiary analyses tailored to the experimental question(s), such as SNP detection, RNA-seq, and CHiPseq. Charges for standard next-gen analyses are based on numbers of reads and samples. Additional custom analyses or changes to the pipeline may incur additional consult charges.

CGH Array Normalization and Segmentation

We 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.

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 $160/hour for any work exceeding an hour. Cost estimates are given before work begins.

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).

High-Performance Computing Systems Access

Our High Performance Computing Group provides the MSKCC research community with access to high performance computing (HPC) resources including machines (computer hardware), analytical tools, storage space, and technical support for solving data-intensive research problems. For more information, visit the High Performance Computing Group’s page.


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).