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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


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.





  • Data analysis services ( Data analysis service )

    • 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


  • Cytoscape ( Software )

    Cytoscape is an open source bioinformatics software platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data.

  • Gene Set Enrichment Analysis ( Software )

    Gene Set Enrichment Analysis (GSEA) is a computational method that determines whether an a priori defined set of genes shows statistically significant, concordant differences between two biological states.

  • GeneGo ( Software )

    Web-based systems biology analysis software.

  • GEXPAS ( Software )

    Web-based genomics software. It also works with the following types of files: cel, dat, text, CSV, Excel.

  • Ingenuity IPA ( Software )

    "IPA is software that helps researchers model, analyze, and understand the complex biological and chemical systems at the core of life science research.

    IPA helps you understand biology at multiple levels by integrating data from a variety of experimental platforms and providing insight into the molecular and chemical interactions, cellular phenotypes, and disease processes of your system. Even if you don’t have experimental data, you can use IPA to intelligently search the Ingenuity®Knowledge Base for information on genes, proteins, chemicals, drugs, and molecular relationships to build biological models or get up to speed in a relevant area of research. IPA provides the right biological context to facilitate informed decision-making, advance research project design, and generate new testable hypotheses."

  • JMP Genomics ( Software )

    "Whether you’re working with large data sets from next-gen sequencing studies or microarrays, JMP Genomics provides the tools you need to analyze rare and common variants, detect differential expression patterns, discover reliable biomarker profiles, and incorporate pathway information into your analysis workflows. In addition, our latest release extends the software’s capabilities for creating and manipulating genetic linkage maps, and then utilizing these maps in downstream QTL mapping for important agronomic crops.

    The unique pedigree of JMP Genomics combines dynamically interactive JMP graphics and robust SAS® Analytics, so you can see and explore your data from every angle, understand it and share analysis results with colleagues.

    JMP Genomics automatically organizes results into tabbed reports and lets you customize your view of analysis options. With capabilities for integration with R, Excel and other tools, JMP Genomics becomes your analytic hub."

  • m2iRNA ( Software )

    Custom software that will analyze correlations between mRNA and microRNA species.

  • Mascot ( Software )

    "Mascot is a powerful search engine which uses mass spectrometry data to identify proteins from primary sequence databases. While a number of similar programs available, Mascot is unique in that it integrates all of the proven methods of searching. These different search methods can be categorised as follows:

    * Peptide Mass Fingerprint in which the only experimental data are peptide mass values.

    * Sequence Query in which peptide mass data are combined with amino acid sequence and composition information. A super-set of a sequence tag query.

    * MS/MS Ion Search using uninterpreted MS/MS data from one or more peptides."

  • MATLAB ( Software )

    "MATLAB® is a high-level language and interactive environment that enables you to perform computationally intensive tasks faster than with traditional programming languages such as C, C++, and Fortran."

  • Partek Genomics Suite ( Software )

    "Partek® Genomics Suite™ is a comprehensive suite of advanced statistics and interactive data visualization specifically designed to reliably extract biological signals from noisy data. The software is unique in supporting all microarray and next generation sequencing technologies including gene expression and digital gene expression (DGE), exon/alternative splicing and RNA-Seq, copy number and association, ChIP-chip, ChIP-seq, and microRNA in a single software package allowing for analysis of multiple applications in one complete solution."

  • ProteinPilot ( Software )

    Proteomics software that analyzes protein expression data.

  • R/Bioconductor ( Software )

    "Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, more than 460 packages, and an active user community."

  • SAS ( Software )

    Statistical package.

  • SEQUEST ( Software )

    SEQUEST is a tandem mass spectrometry data analysis program used for protein identification. Sequest identifies collections of tandem mass spectra to peptide sequences that have been generated from databases of protein sequences.

  • SPSS ( Software )

    "IBM SPSS Statistics is a comprehensive, easy-to-use set of data and predictive analytics tools for business users, analysts and statistical programmers."

  • SYBYL 8.0 ( Software )

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Last updated: 2019-12-20T09:14:05.256-05:00

Copyright © 2016 by the President and Fellows of Harvard College
The eagle-i Consortium is supported by NIH Grant #5U24RR029825-02 / Copyright 2016