Bioinformatics: Overview


Virtual Clinics

Members of the bioinformatics core are available to answer your questions on a wide range of bioinformatics and computer programming topics. The best way to reach us is by emailing [email protected]. In place of our usual weekly clinics, a Zoom call can be arranged as requested to connect you directly with a member of our team. Areas of expertise include:

  • Bioinformatics: computer-based comparison, organization and display of biological data, including online tools and repositories, sequence analysis and microarray analysis
  • General computer usage: programming, scripting (Python, Java, Perl, R), SQL, Matlab, Excel, Linux, graphing utilities, shell scripting, and cluster usage.

We look forward to hearing from you!

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.

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.

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).


These are a series of hands-on practical workshops on bioinformatics- and genomics-related topics. Workshops started in January 2004, and now occur at least twice a year, and cover topics such as sequence analysis, Unix, and R. These workshops are a collaborative effort between the Applied Bioinformatics Core at Weill Cornell Medicine and the Bioinformatics Core at Memorial Sloan Kettering and are open to all faculty, staff and fellows for a nominal fee, and are free for students. All workshop materials are available online at:

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.