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Bioinformatics & Systems Biology Core (BIDMC)

Director: Bhasin, Manoj, Ph.D.

Location: Research North Bldg., Room 380E, 99 Brookline Avenue, Boston, MA 02115

Core Summary:

The mission of Bioinformatics and Systems Biology core is to provide expertise and infrastructure in designing, analyses and simulation of high-throughput OMICS data to answer underlying biological questions. The core supports analysis of data from many next-generation sequencing assays, including transcriptional quantification (RNA-Seq), protein-nucleic acid interactions (ChIP-Seq), global methylation, genotyping or variant analysis through genome sequencing. To support cutting edge research, a special emphasis was made on implementing/developing systems biology frameworks and models for integrative analysis of genomic, epigenomics proteomic, metabolomic, imaging and clinical data to identify key molecules driving pathophysiology. The core has unique service to predict the Antigenic regions (T-epitope, B –epitopes) from the gene and protein sequences to predict potential subunit vaccine candidates.

Institutions:
  • Beth Israel Deaconess Medical Center
Personnel/Contact Information:

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

Member: General Inquiries
Phone: (617) 667-0009
Email

Facilities and Equipment:

Location of Core: Research North Bldg., Room 380E, 99 Brookline Avenue, Boston, MA 02115

Major Equipment:

  • Cytoscape
  • GeneGo
  • Gene Set Enrichment Analysis
  • GEXPAS
  • Ingenuity IPA
  • JMP Genomics
  • m2iRNA
  • Mascot
  • MATLAB
  • Partek Genomics Suite
  • ProteinPilot
  • R/Bioconductor
  • SAS
  • SEQUEST
  • SPSS
  • SYBYL 8.0
Services:
  • Data analysis services

    • 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 and DNA Methylation data
    • Analysis of Microbiome sequencing data
    • Single cell mRNA-Seq data analysis from various platforms.
    • Chip-Seq Data analysis
    • Integrated analysis of transcriptome, miRNA, epigenome and proteomics data
    • Pathway and functional enrichment analysis
    • Systems biology analysis of data
    • Development of predictors using Bayesian, SVM, ANN, and KNN Algorithms for diagnosis and prognosis of disease.
    • Target design for enrichment and deep sequencing
    • Antigenicity (T & B cell epitope prediction)
    • Prediction of immunotherapy Candidates
    • Data and text mining from Public databases and literature

    The core provides express analysis service (48hrs) for standard RNASEQ, Variant, ChiP-Seq, Proteomics and Metabolomics data at premium rates. For enquiry, please email mbhasin@bidmc.harvard.edu


Departmental Web Link(s):

Last updated: 2015-09-03T09:54:48.017-05:00