Xiaojian Shao

Systematic benchmarking reveals pseudo-bulk biases and provides practical fixes for accurate RNA deconvolution.

The paper constructs a standardized BAL scRNA-seq atlas using BAL-EA, a novel annotation framework, revealing disease-associated shifts in COPD and validating findings in COVID-19 datasets.

The paper identifies altered sperm DNA methylation in overweight men linked to transposable element regulation and potential impacts on offspring neurodevelopmental risks.

CART-GPT predicts CAR-T therapy efficacy and neurotoxicity risk using a transformer model trained on 1.12 million single-cell RNA-seq profiles with clinical outcomes.

The paper develops a non-linear ODE model of skeletal muscle regeneration using scRNA-seq data to capture cell population dynamics and regulatory interactions.

The paper identifies differentially methylated regions in children after liver transplant that are associated with rejection, highlighting immune-related pathways and potential therapeutic targets.

This study examines the association between p,p-DDE exposure and sperm epigenome alterations in Greenlandic Inuit and South African VhaVenda men, identifying potential impacts on future generations.

The paper extends a SARS-CoV-2-human protein-protein interaction network using a probabilistic database and identifies dense subgraphs to generate novel hypotheses about virus-targeting genes, proteins, and diseases.

GenPipes provides a scalable framework for genomic analyses, offering pre-built pipelines and flexibility for custom workflows.