Cho-Yi Chen

The paper introduces netZoo, an open-source software suite for analyzing biological networks, demonstrating its use on cancer cell line data to identify drug resistance and cancer development factors.

The paper identifies DE genes and pathways in brain tissues associated with cerebrovascular diseases using GTEx data and mixed models.

The paper develops a preprocessing and normalization pipeline for large-scale RNA-Seq data, addressing batch and tissue effects in heterogeneous datasets.

This study analyzes gene regulation across 38 tissues to show that transcription factor-target connections are more tissue-specific than genes, and that tissue-specific genes are not highly targeted in their networks but occupy bottleneck positions.

The paper compares gene expression and regulatory patterns between cell lines and their source tissues, finding reduced expression levels and altered transcription factor regulation in cell lines.

The paper identifies sexual dimorphism in gene expression and regulatory networks across 31 human tissues using GTEx data, showing that many genes and networks are sex-specific.