Chaolin Zhang

Oncogenic NOVA1 expression dysregulates alternative splicing in breast cancer

This study shows that NOVA1 overexpression in breast cancer disrupts alternative splicing, particularly in genes related to cell communication and cytoskeleton, and is linked to worse outcomes in Luminal A tumors.

Exon inclusion signatures enable accurate estimation of splicing factor activity

The paper estimates splicing factor activity from exon inclusion changes, identifying cancer-related splicing programs and their association with patient survival and cancer hallmarks.

A neuron type-specific microexon in Ank3/ankyrin-G modulates calcium activity and neuronal excitability

The paper identifies a neuron type-specific microexon in Ank3/ankyrin-G that modulates calcium activity and neuronal excitability through alternative splicing.

Primate-specific adaptation of Ku protects transcriptomic integrity by suppressing Alu-mediated alternative splicing

This study shows that primate-specific Ku adaptation suppresses Alu-mediated alternative splicing, maintaining transcriptomic integrity and linking Ku function to brain development and disease.

Ku suppresses RNA-mediated innate immune responses in human cells to accommodate primate-specific Alu expansion.

The paper shows Ku suppresses RNA-mediated innate immune responses in human cells, enabling primate-specific Alu element expansion by reducing dsRNA-induced inflammation.

Reference-informed prediction of alternative splicing and splicing-altering mutations from sequences

DeltaSplice predicts splicing-altering mutations and alternative splicing from genomic sequences, outperforming existing methods and identifying disease-related variants in neurodevelopmental disorders.

Reverse engineering neuron type-specific and type-orthogonal splicing-regulatory networks using single-cell transcriptomes

The paper uses single-cell transcriptomes to reverse engineer splicing-regulatory networks specific to and orthogonal of neuron types, identifying key RNA-binding proteins and regulatory modules.

Deep screening of proximal and distal splicing-regulatory elements in a native sequence context

The paper develops SpliceRUSH, a high-throughput screening method to map splicing-regulatory elements in their native sequence context, identifying both known and novel SREs in the SMN2 gene.

Vascular-Derived SPARC and SerpinE1 Regulate Interneuron Tangential Migration and Accelerate Functional Maturation of Human Stem Cell-Derived Interneurons

Complexity and graded regulation of neuronal cell type-specific alternative splicing revealed by single-cell RNA sequencing

The paper uses scRNA-seq to analyze alternative splicing regulation across neuronal cell types, revealing distinct splicing programs and RBPs involved in graded regulation.

Deep-learning enables proteome-scale identification of phase-separated protein candidates from immunofluorescence images

The paper uses deep learning to identify phase-separated protein candidates from immunofluorescence images by classifying spherical droplet structures.

Modeling RNA-binding protein specificity in vivo by precisely registering protein-RNA crosslink sites

The paper develops a computational method, mCross, to model RBP binding specificity using precise crosslink site registration and validates it with ENCODE eCLIP data.

Dazl regulates germ cell survival through a network of polyA proximal mRNA interactions

This study identifies Dazl's role in germ cell survival by mapping its RNA interactions and showing its regulation of genes critical for proliferation and survival.

LIN28 selectively modulates a subclass of let-7 microRNAs

The paper identifies a GAU motif recognized by LIN28's CSD domain, which enhances let-7 microRNA suppression in Class I precursors, contributing to development and cancer.

Precise temporal regulation of alternative splicing during neural development

The paper identifies early- and late-switch exons in neural development and shows they are regulated by RNA-binding proteins, with some neuronal subtypes lacking these regulators and retaining an immature splicing program.

A cell type-specific expression signature predicts haploinsufficient autism-susceptibility genes

The paper uses cell-type specific expression profiles to prioritize autism-susceptibility genes by identifying a signature associated with haploinsufficient genes in specific neuronal cell types.