Rendong Yang

Analysis of isoform complexity in pan-transcriptome graphs with atroplex

This paper introduces atroplex, a framework for indexing and comparing isoform complexity across pan-transcriptomes, enabling cross-cohort structural analysis of alternative splicing.

OctopusV and TentacleSV: a one-stop toolkit for multi-sample, cross-platform structural variant comparison and analysis

OctopusV and TentacleSV provide a toolkit for multi-sample, cross-platform structural variant analysis, improving precision and consistency in cancer genomics and rare disease diagnostics.

A Comprehensive Benchmark of Tools for Efficient Genomic Interval Querying

The paper benchmarks genomic interval querying tools using simulated datasets, evaluating performance, memory usage, and precision across different tools and data structures.

A Genomic Language Model for Chimera Artifact Detection in Nanopore Direct RNA Sequencing

Deep-Chopper detects and removes adapter sequences from nanopore dRNA-seq reads, improving transcriptome analysis accuracy.

Radiation dermatitis in the hairless mouse model mimics human radiation dermatitis

This study establishes a hairless mouse model of radiation dermatitis that mimics human disease, showing severe skin injury and specific histopathological markers for preclinical research.

PxBLAT: An Efficient Python Binding Library for BLAT

PxBLAT provides a Python library for efficient BLAT integration, improving usability and performance in bioinformatics workflows.

ScanExitronLR: characterization and quantification of exitron splicing events in long-read RNA-seq data

ScanExitronLR identifies and quantifies exitron splicing events in long-read RNA-seq data, outperforming short-read tools on noisy data.

RAS Internal Tandem Duplication Disrupts GAP-binding to Activate Oncogenic Signaling

The paper identifies a novel NRAS internal tandem duplication in colorectal cancer that disrupts GAP-binding, leading to sustained RAS activation and oncogenic signaling.