Zhong Wang

A Context-Aware 14-3-3 Binding Predictor Enabled by Data Augmentation, Multi-Scale Biological Features, and Protein Language Model Embeddings

The paper introduces CAMP-14-3-3, a framework that improves 14-3-3 binding prediction by integrating multi-scale biological features and protein language model embeddings, outperforming existing methods.

V-ATPase-Driven Lysosomal Activation Orchestrates MEK2-Induced Endothelial Reprogramming

This paper shows that MEK2 activation reprograms fibroblasts into endothelial-like cells by enhancing lysosomal activity through the V-ATPase-TFEB axis.

A ubiquitination-mediated degradation system to target phospho-14-3-3-binding-motif embedded proteins

This paper introduces a method to degrade phospho-14-3-3-binding-motif proteins using a ubiquitin-proteasome system, demonstrating its efficiency and specificity for studying these proteins.

SWI/SNF component BAF250a coordinates OCT4 and WNT signaling pathway to control cardiac lineage differentiation

This study shows BAF250a facilitates cardiac differentiation by enabling OCT4 and β-catenin interaction, affecting gene expression and cell cycle progression in human ESCs.

Bayesian cell-type deconvolution and gene expression inference reveals tumor-microenvironment interactions

The paper develops BayesPrism, a Bayesian method to infer cellular composition and gene expression from bulk RNA-seq using scRNA-seq as prior, revealing tumor-microenvironment interactions across multiple cancer types.

Identification of regulatory elements from nascent transcription using dREG

The paper introduces an improved dREG implementation for identifying transcription initiation regions using PRO-seq data, showing higher accuracy, resolution, and efficiency.

Chromatin run-on reveals the transcriptional etiology of glioblastoma multiforme

This study introduces ChRO-seq to map nascent transcription in glioblastoma and identifies enhancers and transcription factors driving GBM subtypes and clinical outcomes.

Natural Selection has Shaped Coding and Non-coding Transcription in Primate CD4+ T-cells

The paper compares nascent transcription in primates to identify evolutionary patterns in coding and non-coding transcription, finding that transcription factor binding sites and adaptive substitutions drive species-specific differences.

RTFBSDB: an integrated framework for transcription factor binding site analysis

The paper introduces rtfbsdb, a framework that integrates TF binding motifs and tools for genome scanning, with options to use RNA-seq or PRO-seq data for motif analysis.