Bioinformatics and Systems Biology

The Bioinformatics and Systems Biology shared resource offers computational tools, expertise, and services for analysis of single cell and other high-throughput omics data at Winship Cancer Institute of Emory University.

The Bioinformatics and Systems Biology shared resource provides expertise and infrastructure in designing, analyses and simulation of high-throughput omics data to answer underlying biological questions.

We provide support for designing and analysis of single cell genomics, proteomics, assay for transposase-accessible chromatin sequencing (ATAC-Seq) and immune repertoire analysis. We also 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, we place a special emphasis on implementing and developing systems biology frameworks and models for integrative analysis of genomic, epigenomics, proteomic, metabolomic, imaging and clinical data to identify key molecules driving pathophysiology. We also have a unique service to predict the antigenic regions (T-epitope, B –epitopes) from the gene and protein sequences to predict potential subunit vaccine candidates.

Capabilities and Services

Services include:

  • Single cell omics data analysis from various platforms
  • Mass cytometry (CyTOF) data analysis
  • Analysis of high throughput sequencing, proteomic and metabolomics data
  • RNA sequencing analysis (mRNA expression quantification & differential analysis, alternate splicing/isoform analysis, novel transcripts discovery, detection of gene fusion or RNA editing)
  • Variation discovery/allele analysis (CNV/SNP) from exome or DNA sequencing data
  • Analysis of epigenomics and DNA methylation data
  • Analysis of microbiome sequencing data
  • ChIP sequencing 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, Support Vector Machine (SVM), Artificial Neural Networks (ANN) and K-Nearest Neighbor (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

Application Tools

We offer bioinformatics application tools developed for cancer research and intended to equip investigators with tools to enable efficient data mining for formulating a specific research question to then engage resources and others on how best to address it.

Service Request

For assistance, please submit request online with all required funding and project information via the PPMS service request system.

Contact Us

Khanjan "Kuki" Gandhi, MS, MBA, Sr. Bioinformatics Analyst
Bioinformatics and Systems Biology Shared Resource
Health Sciences Research Building
1760 Haygood Drive NE, 4th Floor, Atlanta, GA 30322

Phone: (404) 778-0675 | Email

Publication Acknowledgement Policy

The National Cancer Institute requires that publications acknowledge the Winship Cancer Institute Cancer Center Support Grant (CCSG), and it is tracking compliance. If a Winship Cancer Institute CCSG-supported Shared Resource provided data, designed the study, performed analyses, provided results used in your publication, and/or provided any systems or services that were used for the work that resulted in your publication, please include the following statement in the acknowledgment section of your publication(s):

Research reported in this publication was supported in part by the Biostatistics and Systems Biology shared resource of Winship Cancer Institute of Emory University and NIH/NCI under award number P30CA138292. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.

Photo of  Manoj Bhasin, PhD, MS
Manoj Bhasin, PhD, MS

Manoj Bhasin, PhD, MS

Scientific Director, Bioinformatics and Systems Biology Shared Resource
Winship Cancer Institute of Emory University

Dr. Bhasin is performing a large scale analysis of cancer gene-expression data to determine the true biological differences in different cancers, predicting biomarkers and developing cancer prediction models.

Photo of  Bhakti Dwivedi, PhD, MS
Bhakti Dwivedi, PhD, MS

Bhakti Dwivedi, PhD, MS

Associate Bioinformatics Scientist, Bioinformatics and Systems Biology Shared Resource
Winship Cancer Institute of Emory University

Dr. Dwivedi's quantitative areas of expertise include bioinformatics study/data analysis plan, bioinformatics software tool development, pathways/network analysis, phylogenetic analysis, metagenomics, cancer microbiome analysis, and external data validation.

Photo of  Khanjan "Kuki" Gandhi, MS, MBA
Khanjan "Kuki" Gandhi, MS, MBA

Khanjan "Kuki" Gandhi, MS, MBA

Senior Bioinformatics Analyst, Bioinformatics and Systems Biology Shared Resource
Winship Cancer Institute of Emory University

Ms. Gandhi provides bioinformatics support in study design, data analysis, interpretation and assessment of clinical relevance of several biological data types including next generation sequencing (NGS) data.

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