Kassambara A, Rème T, Jourdan M, Fest T, Hose D, Tarte K, Klein B. GenomicScape: An Easy-to-Use Web Tool for Gene Expression Data Analysis. Application to Investigate the Molecular Events in the Differentiation of B Cells into Plasma Cells. PLoS Computational Biology. 2015. Download the PDF
Summary of the Study
DNA microarrays have significantly advanced our understanding of biological processes and diseases. Despite an abundance of public transcriptomic data, user-friendly analysis tools are lacking. This study presents GenomicScape, a free web-based platform that enables:
- Mining datasets from various microarray platforms
- Identifying differentially expressed genes between cell populations
- Performing clustering and pathway analysis
- Exporting expression profiles, tables, and figures
Using GenomicScape, we constructed a molecular atlas of B cell differentiation using transcriptomic profiles of:
Naïve B cells, centroblasts, centrocytes, memory B cells, preplasmablasts, plasmablasts, early plasma cells, and bone marrow plasma cells.
The platform outputs genes and pathways associated with each stage and provides interactive clustering tools. Researchers can also upload their own datasets for exploration.
In this study, Alboukadel Kassambara was responsible for the design and full-stack development of the GenomicScape web application, including the integration of R with a PHP/MySQL framework. He standardized and uploaded the transcriptomic datasets, implemented interactive analysis tools, and contributed to making the platform accessible for real-time gene expression analysis in B cell and plasma cell differentiation.
Citation
Publication: In PLoS Computational Biology
Date: January 29, 2015
Type: Journal Article
PDF: Download the PDF
Scientific Contributions
Here are more scientific abstracts authored or co-authored by Alboukadel Kassambara. These contributions span computational biology, bioinformatics, biostatistics, machine learning, and multi-omics, with a focus on immuno-oncology and translational research.
