The Bioinformatics Shared Resources (BISR) has undergone substantial change since the previous CCSG renewal in response to the changing technologies and accompanying informatics demands that have emerged during this period. The BISR has evolved from a facility largely focused on the development and management of databases and data storage/retrieval from various analytical sources (largely custom NimbleGen and Affymetrix microarrays) to one that is focused on addressing the challenges of massivelyparallel sequencing. In its current configuration, the BISR brings together multiple units at the AECC and the College to focus on the bioinformatics needs of investigators that utilize a variety of high-throughput genomic and epigenomic platforms, in particular massively-parallel sequencing, in their research. The components of the Bioinformatics Shared Resource include: (1) High-performance computing which was developed to meet the storage and processing needs of investigators based upon the sizes and complexities of data sets generated. High-performance computing has dedicated systems administrators, supporting relational database services and specialized high-performance computing resources, (ii) Computational genomics, (iii) The novel Wasp System software developed to receive, process, and provide initial analyses and presentation of data. Wasp has been designed not only to meet the data management needs of massively parallel sequencing but has been built with the flexibility that will allow adaptation to other types of datasets as they emerge in the future. The Bioinformatics Shared Resource works with Clinical Research Informatics to ensure that molecular data are fully interoperable with those of other AECC shared facilities, creating a """"""""virtual database"""""""" integrating these disparate sources of information for analysis by biostatisticians and others. Clinical Research Informatics also addresses the increasing emphasis on clinical/translational studies by facilitating the development of effective, secure linkages with Montefiore Medical Center clinical data.

Public Health Relevance

The Bioinformatics Shared Resource focuses on informatics needed by investigators utilizing a variety of high-throughput genomic and epigenomic platforms (e.g., massively-parallel sequencing), and supports the translational research mission of the Albert Einstein Cancer Center (AECC). As an NCI-designated Cancer Center, AECC contributes to the national effort to reduce morbidity and mortality from cancer.

Agency
National Institute of Health (NIH)
Institute
National Cancer Institute (NCI)
Type
Center Core Grants (P30)
Project #
5P30CA013330-41
Application #
8753327
Study Section
Subcommittee B - Comprehensiveness (NCI)
Project Start
Project End
Budget Start
2014-07-01
Budget End
2015-06-30
Support Year
41
Fiscal Year
2014
Total Cost
Indirect Cost
Name
Albert Einstein College of Medicine
Department
Type
DUNS #
City
Bronx
State
NY
Country
United States
Zip Code
10461
Chen, Zigui; Schiffman, Mark; Herrero, Rolando et al. (2018) Classification and evolution of human papillomavirus genome variants: Alpha-5 (HPV26, 51, 69, 82), Alpha-6 (HPV30, 53, 56, 66), Alpha-11 (HPV34, 73), Alpha-13 (HPV54) and Alpha-3 (HPV61). Virology 516:86-101
Dulyaninova, Natalya G; Ruiz, Penelope D; Gamble, Matthew J et al. (2018) S100A4 regulates macrophage invasion by distinct myosin-dependent and myosin-independent mechanisms. Mol Biol Cell 29:632-642
Kunnath-Velayudhan, Shajo; Porcelli, Steven A (2018) Isolation of intact RNA from murine CD4+ T cells after intracellular cytokine staining and fluorescence-activated cell sorting. J Immunol Methods 456:77-80
Heo, Moonseong; Kim, Namhee; Rinke, Michael L et al. (2018) Sample size determinations for stepped-wedge clinical trials from a three-level data hierarchy perspective. Stat Methods Med Res 27:480-489
Sparano, Joseph A (2018) Prognostic gene expression assays in breast cancer: are two better than one? NPJ Breast Cancer 4:11
Zamurrad, Sumaira; Hatch, Hayden A M; Drelon, Coralie et al. (2018) A Drosophila Model of Intellectual Disability Caused by Mutations in the Histone Demethylase KDM5. Cell Rep 22:2359-2369
Nadaradjane, Celine; Yang, Chia-Ping Huang; Rodriguez-Gabin, Alicia et al. (2018) Improved Dose-Response Relationship of (+)-Discodermolide-Taxol Hybrid Congeners. J Nat Prod 81:607-615
Centini, Ryan; Tsang, Mark; Iwata, Terri et al. (2018) Loss of Fnip1 alters kidney developmental transcriptional program and synergizes with TSC1 loss to promote mTORC1 activation and renal cyst formation. PLoS One 13:e0197973
Celestrin, Kevin; Díaz-Balzac, Carlos A; Tang, Leo T H et al. (2018) Four specific immunoglobulin domains in UNC-52/Perlecan function with NID-1/Nidogen during dendrite morphogenesis in Caenorhabditis elegans. Development 145:
Tiwari, Sangeeta; van Tonder, Andries J; Vilchèze, Catherine et al. (2018) Arginine-deprivation-induced oxidative damage sterilizes Mycobacterium tuberculosis. Proc Natl Acad Sci U S A 115:9779-9784

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