Yichao Cai

A unified framework for quantitative splicing and transcript prediction

This paper introduces SpliceAI2, a deep learning model that improves identification and quantification of splice-altering variants and their effects on transcripts and disease.

Super-silencer perturbation by EZH2 and REST inhibition leads to large loss of chromatin interactions and reduction in cancer growth

The paper demonstrates that disrupting super-silencers via EZH2 and REST inhibition reduces chromatin interactions and cancer growth.

Super-silencers regulated by chromatin interactions control apoptotic genes

The paper identifies 'super-silencers' formed by chromatin interactions that regulate apoptotic genes and shows that combining GSK343 and X5050 disrupts these silencers to induce antitumor effects.

Chromatin Interaction Neural Network (ChINN): A machine learning-based method for predicting chromatin interactions from DNA sequences

ChINN predicts chromatin interactions from DNA sequences, showing good performance across samples and identifying sequence features associated with interactions in CLL patient data.

H3K27me3-rich genomic regions can function as silencers to repress gene expression via chromatin interactions

The paper identifies H3K27me3-rich regions as silencers that repress gene expression through chromatin interactions and shows their functional impact on cell identity and tumor growth.

Predicting chromatin interactions between open chromatin regions from DNA sequences

This paper introduces CHINN, a method predicting chromatin interactions from DNA sequences, showing good performance across samples and detecting differences in CLL samples.