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BIDMC Genomics, Proteomics, Bioinformatics and Systems Biology Center

Director: Bhasin, Manoj, Ph.D.; Libermann, Towia, Ph.D.

Location: 1st Floor, Room 107, 3rd floor, Room 380E, Simon C. Fireman Research North Building, 99 Brookline Ave, Boston, MA 02115

Core Summary:

The BIDMC Genomics, Proteomics, Bioinformatics and Systems Biology Center provides all of the tools of modern functional genomics and proteomics combined with in depth bioinformatics and systems biology analysis, for academic and corporate clients alike. Equipped with State-of-the-Art technologies for high throughput transcriptional profiling, genotyping, protein quantitation, protein profiling and identification, real-time PCR and robotics and various systems biology tools. The BIDMC Genomics, Proteomics, Bioinformatics and Systems Biology center is a core proteomics facility for the Dana-Farber/Harvard Cancer Center.

New Services:

• In-house developed workflows and algorithms for analysis of next-generation sequencing data including RNA-Seq, ChIP-Seq, Epigenetics-Seq and DNA seq
• Comprehensive workflow for analysis of Microbiome sequencing data
• Integrated systems biology analysis of transcriptome, miRNA, epigenome, metabolomics and proteomics data
• Coming soon on in-house development pipelines: MALDI Tissue imaging and targeted quantitative proteomics.

  • Beth Israel Deaconess Medical Center
Personnel/Contact Information:

Director: Bhasin, Manoj, Ph.D.
Phone: (617) 667-0009 / Fax: (617) 667-0011

Director: Libermann, Towia, Ph.D.
Phone: (617) 667-0760

Facilities and Equipment:

Location of Core: 1st Floor, Room 107, 3rd floor, Room 380E, Simon C. Fireman Research North Building, 99 Brookline Ave, Boston, MA 02115

Major Equipment:

  • ABI 4800 Plus MALDI-TOF/TOF analyzer
  • Affymetrix Expression Console
  • Affymetrix GeneChip High Throughput Array Station
  • Affymetrix GeneChip Operating Software SDK
  • Affymetrix GeneTitan High Throughput Array Plate Scanner
  • Agilent 1100/1200 HPLC
  • Agilent 2000 autosampler
  • Agilent fraction collector
  • Amersham Lucidea arrayer
  • Beckman Coulter Biomek FX laboratory automation workstation
  • Bioconductor
  • BioMicro Systems MAUI automatic hybridization station
  • CLC Bio Software
  • Cytoscape
  • GeneChip Fluidics Station 450
  • GeneChip Hybridization Oven 640
  • GeneChip Scanner 3000 7G
  • GeneGo
  • Gene Set Enrichment Analysis
  • Ingenuity IPA
  • JMP Genomics
  • m2iRNA
  • Mascot
  • Partek Genomics Suite
  • Perkin Elmer ScanArray Express HT Laser Scanner
  • ProteinPilot
  • R
  • SAS
  • ScanArray Express HT
  • SpectraMax 190 microplate reader
  • SPSS
  • StepOnePlus Real-Time PCR
  • SYBYL 8.0
  • Synergy Mx Monochromator-Based Multi-Mode Microplate Reader
  • UltiMate Plus nanoLC
  • Affymetrix Human and Mouse Gene 2.0 ST Arrays and 2.1 ST Arrayplates

    We are now introducing the Human and Mouse Gene 2.0 ST Arrays and 2.1 ST Arrayplates for comprehensive whole-transcript expression analysis. These arrays measure both messenger (mRNA) and long intergenic non-coding RNA transcripts (lincRNA). These whole-transcript array designs provide a complete expression profile of mRNA as well as the intermediary lincRNA transcripts that impact the mRNA expression profile. There is ample evidence that differential expression of lincRNAs plays an important role in the genesis and progression of disease and that aberrant expression of these molecules have also been linked to cancer. Recent advancements in transcriptome profiling provided evidence of the association of lincRNAs in a diverse range of cellular functions:

    1. Regulation of mRNA transcription
    2. Regulation of mRNA post-transcriptional modifications
    3. Occlusion/recruitment of transcription factor binding
    4. Activation and transportation of transcription factors
    5. Interaction with accessory proteins
    6. Guide protein complexes to locations in the genome

  • Bioinformatics and Systems Biology analyses offered

    • Experimental design assistance for OMICS studies
    • Analysis of high throughput sequencing, microarray, proteomic and metabolomics data.
    • RNA-Seq analysis (mRNA expression/alternate splicing/isoforms/novel transcripts or gene/ Gene fusion/ detection of RNA editing)
    • Variation discovery/allele analysis (CNV/SNP) from Exome or DNA-Seq data
    • Analysis of epigenomics, ChIP-Seq and DNA Methylation data
    • Comprehensive workflow for analysis of Microbiome sequencing data
    • Integrated analysis of transcriptome, miRNA, epigenome and proteomics data
    • Functional Genomics analysis of data including pathway and functional enrichment analysis
    • Systems biology analysis of data to identify potential therapeutic targets or biomarkers.
    • Development of predictors using Bayesian, SVM, ANN, and KNN Algorithms for diagnosis and prognosis of disease.
    • Target design for enrichment and deep sequencing
    • Antigenicity and subcellular localization prediction
    • Data and text mining from Public databases and literature
    • Personalized consulting
    • Customized data analysis and interpretation

  • Gene expression profiling service

  • Next Generation Sequencing Service

    We are now offering full service for your next generation sequencing needs including in depth bioinformatics and systems biology analysis.

  • Proteomics analysis service

    The Proteomics Core will provide a comprehensive array of services pertaining to the design, performance and analysis of proteomic studies. The core not only offers the ability to implement and validate previously developed proteomic methods to profile proteins in biological fluids and tissues, to quantitate proteins, to identify proteins and posttranslational modifications, and to study protein-protein interactions, but also the capability to modify or develop entirely new assays when warranted.

    A consultative service provided by key members of the core will be available to investigators to assess the rationale and feasibility for undertaking specific projects, designing proteomic studies, process and protocol development, proteomic data analysis, and the interpretation of results.

  • Real-time PCR service

    Real-time PCR provides a highly accurate means of quantitating RNA or DNA in solution. It is often used as a validation technique for microarray data. The Genomics Center provides RTPCR services, including primer design and assay optimization if necessary. Online ordering is not available at this time. To order a real-time PCR experiment, please download the order form and fax it to us.

Departmental Web Link(s):

Last updated: 2015-11-19T14:32:12.296-06:00