Ahmed Mohamed

hoodscanR identifies and analyzes cell neighborhoods in spatial transcriptomics data, revealing transcriptional differences in tumor cells across neighborhoods.

mastR identifies markers from bulk RNA-seq data using a permutation test and signal-to-noise ratio approach, outperforming existing methods in benchmark tests.

vissE identifies and visualizes higher-order molecular phenotypes from functional enrichment analysis by summarizing redundancies into biological themes.

standR is a Bioconductor package that improves the analysis of Nanostring GeoMx DSP spatial transcriptomic data by addressing technical variability and enhancing statistical power.

This study integrates proteomic and transcriptomic data from human T-cells to show time-dependent metabolic reprogramming and divergence in gene expression during activation.

This study performs lipidomics and proteomics on plasma cells from multiple myeloma patients to identify metabolic changes associated with relapse.

RaftProt V2 improves a database of lipid raft-associated proteins by enhancing search capabilities, visualization, and integration of datasets across cell/tissue types and UniRef/Gene levels.