eagle-i Harvard UniversityHarvard University
See it in Search

BIDMC Genomics, Proteomics, Bioinformatics and Systems Biology Center

Director: Libermann, Towia, Ph.D.

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

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, statistics, machine learning, and systems biology analysis, for academic and corporate clients alike. The Center has a particular emphasis on precision medicine and biomarker discovery. Equipped with State-of-the-Art technologies for high throughput proteomics, transcriptional profiling, genotyping, multiplex immunoassay protein validation, and real-time PCR and various systems biology tools. The Center provides all investigators access to comprehensive interdisciplinary, translational, and clinically-oriented facilities for high-sensitivity, high-resolution, and high-throughput multi-omics services. The Center allows investigators to use the most cost-effective, state-of-the-art proteomics and genomics strategies for extracting the most relevant information for each project. It provides assistance in study design, experimental execution, data analysis, and systems biology, while also serving as a forum for education, scientific interactions, and cross-fertilization in proteomics and genomics.
The BIDMC Genomics, Proteomics, Bioinformatics and Systems Biology Center is also the proteomics core facility for the Dana-Farber/Harvard Cancer Center.

New Services:

• SOMAscan (SomaLogic) is a high multiplex, high sensitivity aptamer-based immune-like protein and biomarker discovery platform that simultaneously quantifies 1,305 human proteins in all types of protein extracts from bodily fluids such as serum, plasma, urine, saliva, CSF, cyst fluid, and tissue, cells, lavage, animal models and exosomes.
• Integrated systems biology analysis of transcriptome, miRNA, epigenome, metabolomics and proteomics data
• In-house developed workflows and algorithms for analysis of proteomics data
• Machine learning and AI approaches for predictor model development

Affiliations:

People:

Resources:

Instruments

  • ABI 4800 Plus MALDI-TOF/TOF analyzer ( Mass spectrometer )

    Identifies and quantitates low-abundance proteins in complex biological samples, using iTRAQ Reagents. Handles up to 8 samples at a time (8-plex workflow).

  • Affymetrix GeneChip Fluidics Station 450 ( Microarray wash station )

    Lab contains two copies of this instrument.

    "The GeneChip® Fluidics Station 450 is used for the wash and stain operation of Affymetrix GeneChip® arrays. The instrument includes design advancements to provide improved ease of use and true walk-away freedom dramatically improving efficiency in your genetic analysis.

    The GeneChip Fluidics Station 450 is 110V- and 220V- compatible."

  • Affymetrix GeneChip Fluidics Station 450 ( Fluidics station )

    "The GeneChip® Fluidics Station 450 is used for the wash and stain operation of Affymetrix GeneChip® arrays. The instrument includes design advancements to provide improved ease of use and true walk-away freedom dramatically improving efficiency in your genetic analysis."

  • Affymetrix GeneChip Hybridization Oven 640 ( Hybridization oven )

    Lab contains two copies of this instrument. To be used for hybridization after the plate comes out of the array station. Supports 96-well plate.

  • Affymetrix GeneChip Hybridization Oven 640 ( Hybridization oven )

    "The GeneChip® Hybridization Oven 640 automates your hybridization process for GeneChip brand probe arrays. The oven provides precise temperature control to ensure successful hybridization, and cartridge rotation to provide continuous mixing. Up to 64 arrays can be processed at one time. The digital speed control display provides you with the option of selecting specific rotation speeds and to visually monitor the speed during the cycle."

  • Affymetrix GeneChip Scanner 3000 7G ( Array scanner )

    "The GeneChip® Scanner 3000 7G is an extension of the GeneChip® Scanner 3000 (GCS 3000) series that allows you to scan next-generation higher-density arrays, including SNP arrays with up to 900,000 SNPs, tiling arrays for transcription and all-exon arrays for whole-genome analysis.

    The GCS 3000 7G combines space-saving and other design improvements with speed, superior performance and lower scanner-to-scanner variation to dramatically improve throughput and efficiency in your genetic analysis. The GCS 3000 7G also provides enhanced auto-focus and more consistent scanner-to-scanner biological performance to improve data integrity and data sharing between researchers."

  • Affymetrix GeneChip Scanner 3000 7G ( Gene chip scanner )

    "The GeneChip® Scanner 3000 7G is an extension of the GeneChip® Scanner 3000 (GCS 3000) series that allows you to scan next-generation higher-density arrays, including SNP arrays with up to 900,000 SNPs, tiling arrays for transcription and all-exon arrays for whole-genome analysis.

    The GCS 3000 7G combines space-saving and other design improvements with speed, superior performance and lower scanner-to-scanner variation to dramatically improve throughput and efficiency in your genetic analysis. The GCS 3000 7G also provides enhanced auto-focus and more consistent scanner-to-scanner biological performance to improve data integrity and data sharing between researchers."

  • Affymetrix GeneTitan High Throughput Array Plate Scanner ( Genotype analysis platform )

    "Affymetrix GeneTitan Instrument for fully automated 16, 24 and 96 well Affymetrix ArrayPlate whole genome expression arrays The BIDMC Genomics and Proteomics Center has upgraded the Affymetrix capabilities further by acquiring the fully automated GeneTitan instrument that enables hybridization of 16, 24 or 96 samples per run in a 96 well plate format. Various expression arrays for human, mouse and rat are available for the GeneTitan. We offer all 16, 24 and 96 well Affymetrix ArrayPlate whole genome expression arrays at highly competitive prices (significantly lower price per sample than any regular Affymetrix cartridge array) and expand the line of arrays to gene 1.1 ST and U219 ArrayPlates."

  • Agilent 1100/1200 HPLC ( High performance liquid chromatography instrument )

  • Agilent 2000 autosampler ( Autosampler )

  • Agilent fraction collector ( Fraction collector )

  • Agilent SureScan scanner ( Array scanner )

    The SureScan Microarray Scanner is a laser induced fluorescence scanner designed to read microarrays printed on a standard 1 inch x 3 inch glass slides. It measures the fluorescence intensity of two dyes simultaneously from labeled sample nucleic acid bound to microarrays.

  • Applied Biosystems Stepone Plus 96well real-time PCR system ( Real-time PCR machine )

    96-well format with capability for 384-well format.

  • Beckman Coulter Biomek FX laboratory automation workstation ( Liquid handler )

    Handles both 8- and 96-well formats.

  • BioTek Synergy Mx Monochromator-Based Multi-Mode Microplate Reader ( Microplate reader )

    Reads from 200 to 900 nm (wavelength) without filters/.

  • ProteinSimple ELLA instrument ( ELISA microplate reader )

    The assay performance includes sub-picogram level sensitivity, 4+ logs of dynamic range and reproducibility.

Protocols

Reagents

  • CytoScan® HD Cytogenetics Solution ( Microarray )

    "The CytoScan HD Solution provides the broadest coverage, highest performance, and most genotype–able single nucleotide polymorphisms (SNPs) for detecting human chromosomal aberrations with high-density coverage of all OMIM and RefSeq genes. This single array includes more than 2.6 million copy number markers of which 750,000 are genotype–able SNPs and 1.9 million are non–polymorphic probes."

Services

  • Data Analysis and Bioinformatics Services ( Data analysis service )

    The core offers a full bioinformatics core for data management and analysis as well as new software development.
    The Bioinformatics Core provides investigators with access to phenotypically annotated proteomics and genomics data as well as a large set of analytic procedures (i.e. machine learning, AI, predictor model development, unsupervised and supervised learning techniques, statistical analysis tools, automated clustering and classification procedures, pathway analysis and generation tools, protein identification database tools, data-visualization tools, annotation tools) with which to explore the data sets for further hypothesis generation.

    • Analysis of high throughput sequencing, microarray, proteomic, lipidomics, and metabolomics data
    • Integrated analysis of transcriptome, miRNA, epigenome and proteomics data
    • Pathway and functional enrichment analysis
    • Systems biology analysis of data
    • Development of predictors using machine learning, AI, Bayesian, SVM, ANN, and KNN Algorithms for diagnosis and prognosis of disease
    • RNA-Seq and microarray 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
    • Data and text mining from Public databases and literature

  • Genomics service ( Material processing service )

    The Genomics Core offers Affymetrix genechip technologies, both cartridge based and 96 well high throughput as well as next generation sequencing.

  • Proteomic services ( Material analysis service )

    The Proteomics Core provides a comprehensive array of services pertaining to the design, performance and analysis of proteomic and genomic studies. The core not only offers the ability to implement and validate previously developed proteomic and genomic methods to profile proteins, DNA, and RNA in biological fluids and tissues, but also the capability to modify or develop entirely new assays when warranted.

    High multiplex, high sensitivity aptamer-based SOMAscan-1305 protein biomarker discovery

    Relative quantitation by µLC/MS/MS

    ITRAQ - 8-plex isobaric peptide tagging system that enables you to label all primary amines, regardless of peptide class

    Protein profiling of complex biological samples (serum, urine, CSF, biopsies tissue, cell extracts, lavage, saliva, exosomes, etc).

    Profiling by µLC/MS

    Multidimensional protein fractionation by µLC

Software

  • Affymetrix Expression Console ( Software )

    Genomics Software. "Affymetrix® Expression Console software supports Probe Set summarization and CHP file generation for both 3' Expression (GeneChip® Human Genome U133 Plus 2.0 Array) and Exon Arrays (GeneChip Human Exon 1.0 ST Array)."

  • Affymetrix GeneChip Operating Software SDK ( Software )

    "The Affymetrix® GCOS SDK is a set of application programming interfaces (API) used to access the Affymetrix GCOS system. The GCOS SDK is a very thoroughly documented collection of software libraries, application programming interfaces, and sample code that illustrate and enable the use of and integration with the Affymetrix GCOS by external programs."

  • 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."

  • 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." Systems biology analysis software. Uses Java.

  • 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." Systems biology analysis software.

  • 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 Pathways Analysis 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."

  • m2iRNA ( Software )

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

  • 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.

  • Python ( Software )

    programming language

  • R ( Software )

    "R is a free software environment for statistical computing and graphics."

  • XLSTAT ( Software )

    XLSTAT is a powerful yet flexible Excel data analysis add-on that allows users to analyze, customize and share results within Microsoft Excel. Over 220 standard to advanced statistical features available


Web Links:

Last updated: 2019-12-09T13:35:21.428-05:00

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