Raza‐Ur Rahman

Singletrome: A method to analyze and enhance the transcriptome with long noncoding RNAs for single cell analysis

Singletrome enhances scRNA-seq analysis by integrating lncRNA annotations, improving mapping specificity and enabling lncRNA-based cell type clustering and disease prediction.

Spatial transcriptomics of healthy and fibrotic human liver at single-cell resolution

The paper uses spatial transcriptomics to map cell types and their spatial organization in healthy and fibrotic human liver, identifying changes in hepatocyte populations during fibrosis.

Single cell transcriptomic landscapes of human liver organoids stratify models of non-alcoholic fatty liver disease

The paper evaluates three NAFLD liver organoid models using single-cell transcriptomics, finding TGF-β1 induces fibrosis while OA reduces fibrotic signatures.

SEA: The Small RNA Expression Atlas

SEA provides a web tool for querying and analyzing small RNA expression across ten organisms, including differential expression and classification comparisons.

Oasis2.0: improved online analysis of small RNA-seq data

Oasis2.0 improves small RNA-seq analysis by enhancing detection, classification, and visualization of small RNAs across organisms and identifying cross-species miRNAs and viral/bacterial sRNAs.

The Landscape Of Human Mutually Exclusive Splicing

The paper estimates the extent and biological role of mutually exclusive splicing in humans by identifying and validating over 855 MXEs, including novel exons, and links them to disease pathology.