Naim U. Rashid

Determination of permissive and restraining cancer-associated fibroblast (DeCAF) subtypes

The paper develops a classifier, DeCAF, to identify permissive and restraining cancer-associated fibroblast subtypes from bulk RNAseq data and validates its clinical relevance across multiple cancer types.

Sub-Cluster Identification through Semi-SupervisedOptimization of Rare-cell Silhouettes (SCISSORS) in Single-Cell Sequencing

SCISSORS identifies rare cell types in scRNA-seq data through semi-supervised reclustering and marker gene detection.

Kinome state is predictive of cell viability in pancreatic cancer tumor and stroma cell lines

The paper links kinome state with cell viability in PDAC tumor and stroma cell lines using regression and classification models, finding predictive relationships and key kinases driving viability responses.

Efficient Detection and Classification of Epigenomic Changes Under Multiple Conditions

The paper introduces a method to detect and classify differential epigenomic activity across multiple conditions, showing improved performance and speed compared to existing tools.

Model-based Feature Selection and Clustering of RNA-seq Data for Unsupervised Subtype Discovery

The paper introduces FSCseq, a model-based clustering method for RNA-seq data that selects informative genes, accounts for normalization factors, and identifies cancer subtypes.

Compression of quantification uncertainty for scRNA-seq counts

The paper introduces a method to compress quantification uncertainty in scRNA-seq data by storing mean and variance instead of full inferential replicates, improving computational efficiency without loss of performance.