Y. Zhu

THiRST: Computer Vision Empowered Three-dimensional High-Resolution Spatial Transcriptomics Analytics

THiRST reconstructs 3D spatial transcriptomic data from serial 2D sections, improving cross-section consistency and enabling 3D gene expression analysis.

Explainable Multimodal Prognostic Modeling Uncovers New Clinically Relevant Pathological Features in a Multi-Institutional Pancreatic Neuroendocrine Tumor Cohort

This paper develops a multimodal prognostic model for pancreatic neuroendocrine tumors using clinicopathologic data and histology images, finding that stromal features are as prognostic as tumor cells.

Dynamic Regulation of Innate Lymphoid Cell Development During Ontogeny

This study investigates the developmental changes in innate lymphoid cell (ILC) subsets using scRNA-seq and differentiation assays, revealing distinct regulatory programs in fetal and adult stages.

Epigenetic reader ZMYND11 noncanonical function restricts HNRNPA1-mediated stress granule formation and oncogenic activity

This study identifies a noncanonical function of ZMYND11 as an arginine-methylated HNRNPA1 reader that suppresses stress granule formation and tumor progression.

A deep phenotyping study in mouse and iPSC models to understand the role of oligodendroglia in optic neuropathy in Wolfram syndrome

This study investigates the role of oligodendroglia in Wolfram syndrome using mouse models and iPSC-derived cells, finding preserved oligodendroglia function and suggesting alternative targets for treatment.

Stable isotopes and nanoSIMS single-cell imaging reveals soil plastisphere colonizers able to assimilate sulfamethoxazole

This study uses stable isotopes and nanoSIMS to show soil bacteria on plastics can assimilate sulfamethoxazole, revealing their role in soil ecosystems.

Human vascular organoids with a mosaic AKT1 mutation recapitulate Proteus syndrome

This paper creates a vascular organoid model with an AKT1 mutation to study Proteus syndrome and finds AKT inhibitors reverse vascular malformations.

Discovery of SARS-CoV-2 papain-like protease (PLpro) inhibitors with efficacy in a murine infection model

This study identifies potent SARS-CoV-2 PLpro inhibitors using machine learning, showing efficacy in a mouse model of COVID-19.

Transcriptomic interplay between Acinetobacter baumannii, human macrophage and polymyxin

This study uses dual RNA-sequencing to analyze transcriptomic changes in Acinetobacter baumannii and human macrophages under polymyxin B treatment, revealing key stress response mechanisms and potential therapeutic targets.

Deciphering the co-evolutionary dynamics of L2 β-lactamases via Deep learning

This paper uses deep learning to analyze the co-evolutionary dynamics of L2 β-lactamases and their functional mechanisms.

Revisiting the invasion paradox: resistance-richness relationship is driven by augmentation and displacement trends

The paper uses mathematical simulations to show colonization resistance does not have a monotonic relationship with species richness, but instead depends on augmentation and displacement trends.

A comprehensive landscape of the zinc-regulated human proteome

This study maps zinc-regulated cysteine sites in the human proteome, identifies cancer dependencies, and reveals a mechanism of zinc-induced cytotoxicity in lung cancers.

An Efficient and Safe Trans-complementation System for MPXV Mimicking Authentic Viral Infection

This paper develops a safe trans-complementation system for MPXV that mimics authentic infection, enabling research in lower biosafety labs without live virus.

Potential clinical value and influence of conductivity in conductive cardiac patches for reducing post-MI arrythmia risks

This study evaluates the clinical value of conductive cardiac patches by testing different conductivities and shows that higher conductivity reduces arrhythmia risks in post-MI hearts.

Electron-bifurcation and fluoride efflux systems in Acetobacterium spp. drive defluorination of perfluorinated unsaturated carboxylic acids

This study identifies electron-bifurcation and fluoride efflux systems in Acetobacterium spp. that enable reductive defluorination of PFAS, supported by biochemical and structural evidence.

The 3D ultrastructural morphology of a marine ammonia-oxidizing archaeon

This study uses cryo-ET and STEM-EDS to reveal the ultrastructural morphology and elemental composition of Nitrosopumilus maritimus SCM1, identifying two types of storage granules.

Regulation of blood pressure by METTL3 via RUNX1b-eNOS pathway in endothelial cells

This study shows METTL3 reduces blood pressure by stabilizing RUNX1b mRNA via m6A modification, increasing eNOS expression in endothelial cells.

The Arabidopsis PPR protein EMB1006 interacts with both EMB1270 and CFM2 to facilitate plastid clpP1 intron2 splicing

Machine Learning Elucidates Design Features of Plasmid DNA Lipid Nanoparticles for Cell Type-Preferential Transfection

This study uses machine learning to identify LNP composition parameters that enhance transfection efficiency across cell types and modulate cell type-preferentiality.

Filter-aided expansion proteomics

The paper introduces FAXP, a method combining hydrogel expansion and mass spectrometry for high-resolution proteomics of FFPE tissues, showing improved resolution and efficiency over existing methods.

Utility of T1 mapping and T2 mapping for non-invasive assessment of liver fibrosis: preclinical results

This study evaluates T1 and T2 mapping for assessing liver fibrosis in mice, finding they correlate with fibrosis stages and collagen/protein markers.

Nanoscale cellular organization of viral RNA and proteins in SARS-CoV-2 replication organelles

This study uses super-resolution microscopy to reveal the nanoscale organization of SARS-CoV-2 replication organelles, showing distinct vgRNA and dsRNA clusters and changes over infection stages.

A global survey of small RNA interactors identifies KhpA and KhpB as major RNA-binding proteins in Fusobacterium nucleatum

The paper identifies KhpA and KhpB as major RNA-binding proteins in Fusobacterium nucleatum through mass spectrometry analysis of sRNA interactors.

Identification and functional analysis of eRNA markers for hepatocellular carcinoma based on high-throughput data

This study identifies three eRNA biomarkers for hepatocellular carcinoma (HCC) and shows their involvement in cancer progression, prognosis, and potential as therapeutic targets.

Phase-changing citrate macromolecule combats oxidative pancreatic islet damage, enables islet engraftment and function in the omentum

PPCN, a thermoresponsive antioxidant polymer, supports islet viability and function in nonhuman primates when used for omentum transplantation.

CSTA: A Biomarker Regulating Esophageal Stricture Epithelial Barrier, Potential Medication Target

The paper identifies CSTA as a biomarker for esophageal epithelial barrier function and shows FK506 can rescue CSTA-knockdown effects in strictures.

Cryo-EM structures of human SID-1 transmembrane family proteins and implications for their low-pH-dependent RNA transport activity

The paper presents cryo-EM structures of human SIDT1 and SIDT2, revealing their dimeric architecture and demonstrating low-pH-dependent RNA binding and oligomerization.

Structure of Native Chromatin Fibres Revealed by Cryo-ET in situ

This study reveals the 3D structure of native chromatin fibres in human T-lymphoblasts using cryo-ET, showing a relaxed, variable zigzag organization of nucleosomes.

Local two-photon excitation reveals the mechanism of mitochondrial Ca2+ release

This study uses two-photon excitation to reveal that mitochondrial Ca2+ release is driven by ATP synthesis and the electron transport chain, not Ca2+ entry.

In situ structural insights into the excitation contraction coupling mechanism of skeletal muscle

This study reveals the nanometre-resolution structure of the RyR1-DHPR supercomplex in skeletal muscle triads, showing their unique arrangement and physical coupling mechanism for excitation-contraction coupling.