Urminder Singh

The paper identifies thousands of human orphan genes from RNA-Seq data, validates them with single-cell RNA-seq, and provides a compendium for future research.

The paper compares twelve methods for inferring gene co-expression networks and identifying functional communities in yeast, finding that CLR followed by Generalized Modularity Density clustering performs best.

This study investigates how SARS-CoV-2 infection affects mitochondrial gene expression in different tissues and disease stages, finding targeted inhibition in some organs and upregulation in others.

The paper evaluates gene annotation pipelines for predicting orphan genes in genomes, finding that combining methods improves prediction accuracy, especially for Arabidopsis.

The paper re-mines RNA-Seq data to identify unannotated ORFs in yeast, revealing many likely protein-coding genes and providing a resource for further study.

The paper identifies miR-2392 as a miRNA involved in SARS-CoV-2 infection, showing its role in inflammation, glycolysis, and hypoxia, and develops a miRNA-based therapeutic targeting it.

pyrpipe is a Python package that simplifies RNA-Seq analysis by enabling reproducible, flexible, and customizable pipelines through object-oriented programming and integration with existing tools.

orfipy is a fast and flexible Python tool for extracting open reading frames from fasta sequences, offering customizable search options and multiple output formats.

The paper identifies differential expression of COVID-19-related genes between European Americans and African Americans using TCGA and GTEx data.

MetaOmGraph enables interactive exploratory analysis of large expression datasets, identifying novel biomarker genes in cancer and plant metabolomics.

The paper introduces phylostratr, an R package for phylostratigraphy, enabling automated and customizable analysis of gene evolutionary origins across species.

synder infers genomic orthologs by using synteny maps to trace features between genomes, demonstrated with Arabidopsis thaliana transcription factors.