Sinan U. Umu

MirMachine 2 annotates microRNAs across thousands of animal genomes, revealing methodological biases in apparent microRNA absence.

Easydecon efficiently maps cell types to high-definition spatial transcriptomic data by combining hotspot detection and similarity-based refinement.

The paper uses single-cell spatial transcriptomics to identify coordinated cellular programs in MSS colorectal cancer that correlate with prognosis.

MirGeneDB 3.0 updates the microRNA gene database with expanded species coverage, refined nomenclature, and improved covariance models for phylogenetic analysis.

The paper introduces MirMachine, a tool that uses trained covariance models to annotate microRNA complements in genomes, enabling annotation of large and extinct genomes and assessing genome assembly completeness.

Cellsnake provides a user-friendly, reproducible workflow for scRNA-seq analysis, addressing installation and learning curve issues for non-expert users.

This paper evaluates factors predicting bioinformatic software accuracy and finds that sustained development, not citations or journal impact, is most indicative of accuracy.

The paper analyzes APOBEC3-induced mutations and integration patterns in HPV16 and HPV18 cervical samples across different disease stages to identify genomic factors associated with cancer progression.

The paper identifies associations between common traits and circulating ncRNA expression, highlighting the need to adjust for age, sex, and other factors in ncRNA biomarker analyses.

The paper profiles circulating RNAs in human serum using RNA-seq and identifies potential biomarkers by analyzing biological and technical variation.