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Bioinformatics and Systems Biology

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Boston, Massachusetts, US

About Bioinformatics and Systems Biology

The analysis of high-throughput genomics, proteomics, metabolomics and epigenomics data is the most critical step in systematically understanding pathophysiology of a disease as well as identifying potential biomarkers. The analysis of OMICS data often presents a challenge to translational and basic science... Show more »

The analysis of high-throughput genomics, proteomics, metabolomics and epigenomics data is the most critical step in systematically understanding pathophysiology of a disease as well as identifying potential biomarkers. The analysis of OMICS data often presents a challenge to translational and basic science researchers. 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 support 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 identifying key molecules driving pathophysiology. In addition to analyses support, core also provides resources for data management and high performance computing.

Recent Publications

  • Jaíra Ferreira de Vasconcellos, Angelo Brunelli Albertoni Laranjeira, Paulo C Leal, Manoj K Bhasin, Priscila Pini Zenatti, Ricardo J Nunes, Rosendo A Yunes, Alexandre E Nowill, Towia A Libermann, Luiz Fernando Zerbini, José Andrés Yunes, SB225002 Induces Cell Death and Cell Cycle Arrest in Acute Lymphoblastic Leukemia Cells through the Activation of GLIPR1, PloS one 10 (8), e0134783
  • RC Starling, J Stehlik, DA Baran, B Armstrong, JR Stone, D Ikle, Y Morrison, ND Bridges, P Putheti, TB Strom, M Bhasin, I Guleria, A Chandraker, M Sayegh, KP Daly, DM Briscoe, PS Heeger, Multicenter Analysis of Immune Biomarkers and Heart Transplant Outcomes: Results of the Clinical Trials in Organ Transplantation‐05 Study, American Journal of Transplantation 2015/8/1
  • Khurram Owais, Thomas Huang, Feroze Mahmood, Jeffery Hubbard, Rabya Saraf, Amit Bardia, Kamal R Khabbaz, Yunping Li, Manoj Bhasin, Ashraf A Sabe, Frank Sellke, Robina Matyal, Cardiopulmonary Bypass Decreases Activation of the Signal Transducer and Activator of Transcription 3 (STAT3) Pathway in Diabetic Human Myocardium, The Annals of thoracic surgery 2015/7/28
  • Liang Zhang, Xiaoen Wang, Andrea J Bullock, Marcella Callea, Harleen Shah, Jiaxi Song, Kelli Moreno, Barbara Visentin, Douglas Deutschman, David C Alsop, Michael B Atkins, James W Mier, Sabina Signoretti, Manoj Bhasin, Roger A Sabbadini, Rupal S Bhatt, Anti-S1P Antibody as a Novel Therapeutic Strategy for VEGFR TKI-Resistant Renal Cancer, Clinical Cancer Research 21 (8), 1925-1934
  • Andrej Jedinak, Adam Curatolo, David Zurakowski, Simon Dillon, Manoj K Bhasin, Towia A Libermann, Roopali Roy, Monisha Sachdev, Kevin R Loughlin, Marsha A Moses, Novel non-invasive biomarkers that distinguish between benign prostate hyperplasia and prostate cancer, BMC cancer 15 (1), 259
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Certifications & Qualifications

GCP

Our Services (53)


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Biomarker Discovery

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Biomarker Analysis

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Gene expression profiling

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Affymetrix Microarray

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Affymetrix photolithographic microarray manufacture process allows for interrogation of a transcripts with a single array. Oligos are synthesized chemically directly on the chip surface by a highly reproducible method, allowing for consistency of quality not available on traditional cDNA arrays. The BIDMC Genomics Center offers... Show more »

Affymetrix photolithographic microarray manufacture process allows for interrogation of a transcripts with a single array. Oligos are synthesized chemically directly on the chip surface by a highly reproducible method, allowing for consistency of quality not available on traditional cDNA arrays. The BIDMC Genomics Center offers Affymetrix experiments, from RNA isolation to data analyis as a service.

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RNA-Seq Data Analysis

Price on request
  • mRNA expression/alternate splicing/isoforms/novel transcripts or gene/ Gene fusion/ detection of RNA editing
  • Single cell mRNA-Seq data analysis from various platforms
  • Integrated analysis of transcriptome, miRNA, epigenome and proteomics data
  • mRNA expression/alternate splicing/isoforms/novel transcripts or gene/ Gene fusion/ detection of RNA editing
  • Single cell mRNA-Seq data analysis from various platforms
  • Integrated analysis of transcriptome, miRNA, epigenome and proteomics data
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Affymetrix RNA Microarray

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Systems Biology

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Systems biology analysis of data to identify potential therapeutic targets or biomarkers

Systems biology analysis of data to identify potential therapeutic targets or biomarkers

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Affymetrix High Throughput (HT) Microarray

Price on request

More cost effective, efficient, reproducible, precise, and more sensitive than GeneChip cartridge arrays.

Up to 96 samples on one run with as little as 50ng of RNA or picograms with LCM.

The new GeneChip HT Array Plate Scanner designed to scan and create high-resolution images of GeneChip HT Array Plates at an... Show more »

More cost effective, efficient, reproducible, precise, and more sensitive than GeneChip cartridge arrays.

Up to 96 samples on one run with as little as 50ng of RNA or picograms with LCM.

The new GeneChip HT Array Plate Scanner designed to scan and create high-resolution images of GeneChip HT Array Plates at an unprecedented rate, price, and reproducibility with less starting material.

Delivers the highest quality and quantity of genomic information. The high throughput scanner provides researchers with the ability to complete large projects run on 24-array or 96-array Affymetrix HT Array Plates (including human, mouse and rat). Our new HT scanner accelerates the pace of discovery, taking less than three minutes to auto-focus and scan each array.

Fully automated robotics
Up to 96 samples per run
Quick turn around

HT Array Plates
The scanner supports the following GeneChip® HT Array Plates, available in 24- and 96-array versions:

GeneChip® HT HG-U133+ PM Array Plate
GeneChip® HT MG-430 PM Array Plate
GeneChip® HT RG-230 PM Array Plate
HT Human Genome U133A/U133B
HT Mouse Genome 430A/430B
HT Rat Focus

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Proteomics Data Analysis

Price on request

Customized data analysis and interpretation

Customized data analysis and interpretation

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Affymetrix microRNA (miRNA) Microarray

Price on request

Affymetrix photolithographic microarray manufacture process allows for interrogation of a transcripts with a single array. Oligos are synthesized chemically directly on the chip surface by a highly reproducible method, allowing for consistency of quality not available on traditional cDNA arrays. The BIDMC Genomics Center offers... Show more »

Affymetrix photolithographic microarray manufacture process allows for interrogation of a transcripts with a single array. Oligos are synthesized chemically directly on the chip surface by a highly reproducible method, allowing for consistency of quality not available on traditional cDNA arrays. The BIDMC Genomics Center offers Affymetrix experiments, from RNA isolation to data analyis as a service.

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Genomics Data Analysis

Price on request
  • Functional Genomics analysis of data including pathway and functional enrichment analysis
  • Customized data analysis and interpretation
  • Functional Genomics analysis of data including pathway and functional enrichment analysis
  • Customized data analysis and interpretation
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Bioinformatics

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Microbiomics Data Analysis

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Comprehensive workflow for analysis of Microbiome sequencing data

Comprehensive workflow for analysis of Microbiome sequencing data

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Metabolomics Data Analysis

Price on request
  • Analysis of high throughput sequencing, microarray, proteomic and metabolomics data
  • Customized data analysis and interpretation
  • Analysis of high throughput sequencing, microarray, proteomic and metabolomics data
  • Customized data analysis and interpretation
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Quantitative Proteomics

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8-plex iTRAQ quantitative proteomics service using two-dimensional peptide fractionation and mass spectrometric analysis on the AB Sciex 4800 MALDI-TOF/TOF mass spectrometer.

8-plex iTRAQ quantitative proteomics service using two-dimensional peptide fractionation and mass spectrometric analysis on the AB Sciex 4800 MALDI-TOF/TOF mass spectrometer.

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RNA Sequencing

Price on request

We provide RNA sequencing on Illumina HiSeq 2000 instruments

We provide RNA sequencing on Illumina HiSeq 2000 instruments

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SNP Discovery Sequencing

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Variation discovery/allele analysis (CNV/SNP) from Exome or DNA-Seq data

Variation discovery/allele analysis (CNV/SNP) from Exome or DNA-Seq data

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SNP Genotyping

Single Nucleotide Polymorphism Genotyping
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DNA Methylation Analysis

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Analysis of epigenomics, ChIP-Seq and DNA Methylation data

Analysis of epigenomics, ChIP-Seq and DNA Methylation data

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Data Mining

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Data and text mining from Public databases and literature

Data and text mining from Public databases and literature

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Whole Exome Sequencing (WES)

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We provide exome sequencing on Illumina HiSeq2000 instruments.

We provide exome sequencing on Illumina HiSeq2000 instruments.

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Predictive Modeling

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Development of predictors using Bayesian, SVM, ANN, and KNN Algorithms for diagnosis and prognosis of disease

Development of predictors using Bayesian, SVM, ANN, and KNN Algorithms for diagnosis and prognosis of disease

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qPCR

Quantitative PCR
Price on request

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.

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.

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Proteomics Consulting

Price on request

Experimental design assistance for OMICS studies

Experimental design assistance for OMICS studies

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Computational Modeling

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Proteomics

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Project Management

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Nucleic Acid Analysis

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Bioanalysis

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DNA Services

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Nucleic Acid Services

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Sequencing Data Analysis and Management

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Genotyping and Gene Expression Assays

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Targeted Gene Sequencing

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DNA Microarrays

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Biostatistics & Bioinformatics

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RNA Services

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Pharmacology & Toxicology

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Protein Sequencing

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DNA Sequencing

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RNA Microarray

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Exome Sequencing Services

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Data Services

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Epigenetic Studies

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Nucleic Acid Data Analysis

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Omics

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Omics Services

Omics Services

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Biology

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MicroRNA (miRNA) Microarray

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PCR

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Next Generation Sequencing (NGS)

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Biomarkers

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Assay Development

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Biochemistry & Molecular Biology

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RNA Microarray Platforms

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Manoj Bhasin

Director
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Towia Libermann

Associate Professor of Medicine

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