The Bioinformatics Core was created to provide and build bioinformatics services and infrastructure for the MSKCC research community. The services of the core include scientific consultations, high performance computing and high capacity data storage support, training via clinics and workshops, custom programming on both small and large scale software projects, and pipelines for data analysis. The Core has grown to 13 full time staff members including PhD level research scientists and a professional staff of engineers, programmers and systems administrators. The Core provides all levels of bioinformatics support from small scale script writing to long term analytic support. As new technologies emerge, such as next-generation sequencing, the Core's focus and services have grown to meet them. The broad range of services and collaborative work provided by the Bioinformatics Core has supported the research of 66 investigators in the past year. During the past grant period the work of the Core has contributed to 365 publications of researchers from 8 research programs. For example, the Core supported Drs. Sawyers, Gerald, and Sander in the analysis of genomic datasets generated by the MSKCC Genomics Core from 214 primary and metastatic prostate cancer samples that were obtained from the MSKCC Pathology Core. The Core developed the informatics pipeline for analysis of exon resequencing data, generated plots of copy number alterations from array CGH data, and conducted preliminary analyses of the mRNA transcriptome and microRNA expression data from arrays run by the Genomics Core. This work led to the first comprehensive integrated genomic analysis of prostate cancer and has served as a key source of information for the field since its publication in 2010.

National Institute of Health (NIH)
National Cancer Institute (NCI)
Center Core Grants (P30)
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Subcommittee I - Transistion to Independence (NCI)
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Sloan-Kettering Institute for Cancer Research
New York
United States
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Pak, Linda M; Gonen, Mithat; Seier, Kenneth et al. (2018) Can physician gestalt predict survival in patients with resectable pancreatic adenocarcinoma? Abdom Radiol (NY) 43:2113-2118
Thomas, Rozario; Marks, Daniel Henry; Chin, Yvette et al. (2018) Whole chromosome loss and associated breakage-fusion-bridge cycles transform mouse tetraploid cells. EMBO J 37:201-218
Shoag, Jonathan; Liu, Deli; Blattner, Mirjam et al. (2018) SPOP mutation drives prostate neoplasia without stabilizing oncogenic transcription factor ERG. J Clin Invest 128:381-386
Abreu, Carla M; Prakash, Rohit; Romanienko, Peter J et al. (2018) Shu complex SWS1-SWSAP1 promotes early steps in mouse meiotic recombination. Nat Commun 9:3961
Katsoulakis, Evangelia; Leeman, Jonathan E; Lok, Benjamin H et al. (2018) Long-term outcomes in oral cavity squamous cell carcinoma with adjuvant and salvage radiotherapy after surgery. Laryngoscope 128:2539-2545
Huicochea Castellanos, Sandra; Corrias, Giuseppe; Ulaner, Gary A et al. (2018) Detection of recurrent pancreatic cancer: value of second-opinion interpretations of cross-sectional images by subspecialized radiologists. Abdom Radiol (NY) :
Hoseini, Sayed Shahabuddin; Guo, Hongfen; Wu, Zhihao et al. (2018) A potent tetravalent T-cell-engaging bispecific antibody against CD33 in acute myeloid leukemia. Blood Adv 2:1250-1258
Attiyeh, Marc A; Fernández-Del Castillo, Carlos; Al Efishat, Mohammad et al. (2018) Development and Validation of a Multi-institutional Preoperative Nomogram for Predicting Grade of Dysplasia in Intraductal Papillary Mucinous Neoplasms (IPMNs) of the Pancreas: A Report from The Pancreatic Surgery Consortium. Ann Surg 267:157-163
Tollinche, Luis; Tan, KaySee; Han, Austin et al. (2018) Analyzing Volatile Anesthetic Consumption by Auditing Fresh Gas Flow: An Observational Study at an Academic Hospital. Int J Anesth Anesth 5:
Tadros, Audree B; Wen, Hannah Y; Morrow, Monica (2018) Breast Cancers of Special Histologic Subtypes Are Biologically Diverse. Ann Surg Oncol 25:3158-3164

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