Gene Wei-Ming Yeo

Genome-Wide Interrogation of SARS-CoV-2 RNA-Protein Interactions Uncovers Hidden Regulatory Sites

This study maps SARS-CoV-2 protein-RNA interactions using eCLIP, revealing new regulatory sites for viral replication and translation.

Tau is an m6A-associated RNA binding protein that causes RNA dysregulation in disease

The paper identifies tau as an m6A-associated RNA binding protein that causes RNA dysregulation in MAPT coding-variant patients and V337M iNeurons.

Dosage-sensitive RBFOX2 autoregulation promotes cardiomyocyte differentiation by maturing the transcriptome

This study shows that RBFOX2 autoregulation is critical for cardiomyocyte differentiation by maturing the transcriptome, and its disruption leads to congenital heart disease.

SpatialTRACE predicts anatomical axes and regions in spatial transcriptomics and microscopy

SpatialTRACE extends anatomical annotations from a few structures to tissue-wide maps using graph and image-based models in spatial transcriptomics and microscopy.

Flipper: An advanced framework for identifyingdifferential RNA binding behavior with eCLIP data

Flipper identifies differential RNA binding behavior using eCLIP data with improved normalization and separation of expression/splicing effects from true binding changes.

ESCAPE: assigning site-specific activity to covalent ligands in cells by prime editing

ESCAPE identifies covalent ligand-protein interactions by using prime editing to disrupt cysteine residues and assesses their impact on cellular phenotypes.

Structural and mechanistic analysis of covalent ligands targeting the RNA-binding protein NONO

This paper reports covalent ligands targeting the RNA-binding protein NONO, showing they stabilize mRNA interactions, remodel transcriptomes, and suppress cancer cell growth with high specificity.

Dual-targeting snRNA gene therapy rescues STMN2 and UNC13A splicing in TDP-43 proteinopathies

This study develops a gene therapy strategy using snRNAs to correct mis-splicing of STMN2 and UNC13A in TDP-43 proteinopathies, showing restoration of protein levels and axonal regeneration in motor neurons.

SPRINT-MS: A high-throughput platform for identifying protein-protein interactions using pooled IP-MS and sparse signal recovery.

SPRINT-MS identifies protein-protein interactions using pooled IP-MS and sparse signal recovery, achieving high throughput and efficiency comparable to individual IP-MS experiments.

KIF5A binds RNA to orchestrate synaptic mRNA localization and stress granules in ALS

This study shows KIF5A binds RNA to regulate synaptic mRNA localization and stress granules, with ALS mutations disrupting synaptic homeostasis.

A splice-switching antisense oligonucleotide approach for pediatric genetic epilepsies

This study identifies splice-switching antisense oligonucleotides that correct splicing defects in SCN8A, reducing seizures and improving survival in a mouse model of genetic epilepsy.

Imaging Cellular Metabolic Rewiring with SuMMIT-SRS

The paper introduces SuMMIT-SRS, a multiplexed metabolic imaging technique, and demonstrates its application in various cell types to study metabolic rewiring.

Human AUTS2 regulates neurodevelopmental pathways via dual DNA/RNA binding.

This study identifies AUTS2's dual DNA/RNA binding in human neural progenitors and shows its role in regulating Wnt pathway genes, linking its disruption to neurodevelopmental disorders.

Small nuclear RNAs enhance protein-free RNA-programmable base conversion on mammalian coding transcripts

This study shows that guided A>I snRNAs improve RNA base conversion efficiency and reduce off-target effects compared to ADAR-recruiting circular RNAs in human cells.

RNA folding drives species-dependent host mRNA partitioning in Ebola virus condensates

The paper investigates how RNA folding influences host mRNA partitioning into Ebola virus condensates under different conditions and identifies implications for viral-host co-evolution.

RNA triggers chronic stress during neuronal aging

This study identifies mitochondrial-derived double-stranded RNA as a source of RNA stress in aged neurons, which activates the ISR through PKR and contributes to neurodegeneration.

Rational Generation of Monoclonal Antibodies and Intrabodies Selective for Pathogenic TDP-43

This paper generates monoclonal antibodies and intrabodies that selectively target misfolded TDP-43 aggregates in disease, showing they inhibit transmission and promote degradation in cell models.

Human CCR4 deadenylase homolog Angel1 is a Non-Stop mRNA Decay factor

The paper identifies Angel1 as a key factor in non-stop mRNA decay by showing its role in destabilizing mRNAs lacking stop codons.

Integrative CRISPR Screens and RNA-Omics Discover an Essential Role for PUF60-3' Splice Site Interactions in Cancer Progression

The paper identifies PUF60's role in cancer progression by combining CRISPR screens and RNA-omics, showing its splicing activity supports TNBC proliferation and is a potential therapeutic target.

Short 5' UTRs serve as a marker for viral mRNA translation inhibition by the IFIT2-IFIT3 antiviral complex

The paper shows that short 5' UTRs in viral mRNAs are recognized by the IFIT2-IFIT3 complex, leading to translation inhibition and antiviral activity.

Functional Diversity of Memory CD8 T Cells is Spatiotemporally Imprinted

The paper investigates how spatial location influences the functional diversity of memory CD8 T cells by analyzing their transcriptomes in the small intestine.

LARP6 regulates the mRNA translation of fibrogenic genes in liver fibrosis

This study shows LARP6 regulates fibrogenic gene translation in liver fibrosis by interacting with collagen mRNAs and reducing fibrosis in human HSCs.

Stress Granules Underlie Acute Myeloid Leukemia Stem Cell Survival and Stress Adaptation

This study identifies stress granules as critical for AML stem cell survival and stress adaptation, revealing their role in gene regulation and potential as therapeutic targets.

Localized synthesis of molecular chaperones sustains neuronal proteostasis

The paper shows that neuronal stress response involves localized synthesis of HSPA8 mRNA in dendrites to maintain proteostasis and prevent neurodegeneration.

The YTHDF proteins shape the brain gene signatures of Alzheimer's disease

This study identifies YTHDF proteins as key regulators of Alzheimer's disease brain gene signatures through m6A-dependent and independent mechanisms.

Large-scale map of RNA binding protein interactomes across the mRNA life-cycle

The paper constructs an RNA-aware RBP-centric PPI map across the mRNA life-cycle, revealing 20,359 novel interactions and showing 73% are RNA-dependent.

Bento: A toolkit for subcellular analysis of spatial transcriptomics data

Bento enables subcellular analysis of spatial transcriptomics data by defining domains, annotating localization patterns, and quantifying gene colocalization, demonstrating its use on multiple datasets.

Transcriptome Regulation by PARP13 in Basal and Antiviral States in Human Cells

This study investigates PARP13's role in transcriptome regulation during basal and antiviral states, finding it shifts target localization but not binding preferences and supports ISGylation-related gene expression.

Expanded palette of RNA base editors for comprehensive RBP-RNA interactome studies

The paper identifies optimal RNA base editors for RBP-RNA interaction studies by evaluating over thirty rBEs using PRINTER framework.

Xiphoid nucleus of the midline thalamus controls cold-induced food seeking

The paper identifies the xiphoid nucleus in the midline thalamus as a key region controlling cold-induced food seeking through neural activity and connectivity studies in mice.