Q. Yu

A deep learning-based toolkit for 3D nuclei segmentation and quantitative analysis in cellular and tissue context

The paper introduces computational tools for 3D nuclei segmentation and analysis, showing variations in nuclear-to-cell volume ratios across tissues.

Hepatic Macrophage Migration Inhibitory Factor Promotes Pancreatic Cancer Liver Metastasis in NAFLD

This study shows that hepatic MIF promotes PDAC liver metastasis in NAFLD by enhancing cancer stemness and immune suppression through the MIF-CD44 axis.

Neisseria gonorrhoeae induces local secretion of IL-10 at the human cervix to promote asymptomatic colonization

This study shows Neisseria gonorrhoeae induces IL-10 secretion at the cervix via CEACAMs to prevent epithelial shedding and inflammation, enabling asymptomatic colonization.

De novo pyrimidine biosynthesis inhibition synergizes with BCL-XL targeting in pancreatic cancer

This study identifies that combining DHODH inhibition with BCL-XL targeting synergistically induces apoptosis in pancreatic cancer, offering a new combination therapy strategy.

NK Cell Exhaustion in Wilson's Disease Revealed by Single-cell RNA Sequencing Predicts the Prognosis of Cholecystitis

This study uses single-cell RNA sequencing to show NK cell exhaustion in Wilson's disease is linked to worse cholecystitis outcomes.

Lineage frequency time series reveal elevated levels of genetic drift in SARS-CoV-2 transmission in England

This paper develops a method to estimate genetic drift in SARS-CoV-2 transmission using lineage frequency time series and applies it to genomic data from England, finding consistently higher genetic drift than expected.

Human transmembrane protein 68 links triacylglycerol synthesis to membrane lipid homeostasis

This study identifies TMEM68 as a triacylglycerol synthase that regulates lipid metabolism and membrane lipid composition in neuro- and glioblastoma cells.

Adaptive Functions of Structural Variants in Human Brain Development

This study identifies human-specific structural variants in rhesus macaques, showing their impact on human brain development through gene expression changes.

Inserting Pre-Analytical Chromatographic Priming Runs Significantly Improves Targeted Pathway Proteomics With Sample Multiplexing

The paper introduces GoDigViewer to optimize GoDig assays by implementing chromatographic priming runs, significantly improving peptide-level quantification success rates in targeted pathway proteomics.

PerturBase: a comprehensive database for single-cell perturbation data analysis and visualization

PerturBase is a database that compiles and visualizes single-cell perturbation data from multiple studies, enabling analysis of genetic and chemical perturbations across millions of cells.

Posttranscriptional tuning of gene expression over a large dynamic range in synthetic tobacco chloroplast operons

The paper investigates how different UTRs and tRNA elements affect gene expression in synthetic tobacco chloroplast operons, showing a wide range of expression levels controlled by PPR10.

An integrated transcriptomic cell atlas of human endoderm-derived organoids

This paper creates a human endoderm organoid cell atlas by integrating single-cell transcriptomes from multiple organoid types to compare cell states with primary tissues and disease models.

Quantitative dynamics of intracellular NMN by genetically encoded biosensor

This study develops a genetically encoded biosensor to measure intracellular NMN dynamics in live cells and identifies Slc25a45 as a potential mitochondrial NMN transporter.

Enterocytozoon hepatopenaei Proliferate in Procambarus clarkii: A Warning for Crayfish and Shrimp Aquaculture

This study shows that crayfish (Procambarus clarkii) can harbor and transmit the microsporidian parasite Enterocytozoon hepatopenaei, posing a risk to shrimp farming.

CD8 T-cell dysfunction is linked with CAR T-cell failure and can be mitigated by a non-alpha IL-2 agonist, pegenzileukin

The paper identifies dysfunctional CD8 CAR T-cells in rrLBCL tumors and shows that pegenzileukin mitigates this dysfunction, improving CAR T-cell responses.

Rediversification Following Ecotype Isolation Reveals Hidden Adaptive Potential

The paper shows that two-ecotype microbial communities can rediversify into two ecotypes after isolation, with similar patterns despite evolutionary time, but with differences in growth traits and transcriptional states.

Arabidopsis ORP2A positively regulates glucose signaling by interacting with AtRGS1 and promoting AtRGS1 degradation

Genetically Encoded RNA-based Bioluminescence Resonance Energy Transfer (BRET) Sensors

This paper introduces genetically encoded RNA-based BRET sensors for real-time target detection in living cells, using a luciferase donor and RNA-based acceptor.

Effect and mechanism of black soybean peptides alleviating oxidative damage in the celiac disease cell model

This study investigates how black soybean peptides alleviate oxidative damage caused by alpha gliadin peptide in a celiac disease cell model.

Half-calcified Calmodulin Promotes Basal Activity and Inactivation of the Calcium Channel CaV1.2.

The paper identifies a half-calcified calmodulin species that promotes CaV1.2 channel activity and inactivation by interacting with specific residues in the IQ motif.

FBXO11 deficiency in mice impairs lung development and aggravates cigarette smoke-induced airway fibrosis

This study shows that FBXO11 deficiency in mice leads to impaired lung development and worsens cigarette smoke-induced airway fibrosis by promoting epithelial-mesenchymal transition.

Ratiometric NAD+ sensors reveal subcellular NAD+ modulators

The paper introduces NAD+ sensors to measure subcellular and clinical NAD+ dynamics, revealing NAD+ redistribution effects of -GPC in live cells.

Spatiotemporal landscape of SARS-CoV-2 pulmonary infection reveals Slamf9+Spp1+ macrophages promoting viral clearance and inflammation resolution

This study identifies Slamf9+Spp1+ macrophages in hamsters that promote SARS-CoV-2 clearance and inflammation resolution through spatial transcriptomics and scRNA-seq.

Early Endosome Capture Proteomics and its Application to Amyloid Precursor Protein Intramembrane Processing by β and γ-Secretases

This paper develops a method to isolate early endosomes and uses it to study amyloid precursor protein processing by β and γ-secretases in these compartments.

Global Spatial Transcriptome of Macaque Brain at Single-Cell Resolution

The paper creates a 3-D cell type atlas of the monkey brain using single-cell spatial transcriptomics and identifies molecular markers for neocortical layers and subregions.

Reconstructing cell interactions and state trajectories in pancreatic cancer stromal tumoroids

This study develops a stromal tumoroid model of pancreatic cancer to investigate cell interactions and state changes, identifying key factors like SDC1 and PPARG that influence cancer cell behavior and therapy response.

A chromosome-level phased Citrus sinensis genome facilitates understanding Huanglongbing tolerance mechanisms at the allelic level in an irradiation induced mutant

The paper presents a chromosome-level phased genome of Valencia sweet orange, enabling allelic-level analysis of Huanglongbing tolerance in mutants.

On-tissue spatial proteomics integrating MALDI-MS imaging with shotgun proteomics reveals soy consumption-induced biomarkers in a fragile X syndrome mouse model

Maturation of human intestinal epithelium from pluripotency in vitro

This study develops an in vitro protocol to generate mature human intestinal epithelium from pluripotent stem cells using NRG1 and single-cell transcriptomics.

Molecular mechanism of the anti-lung cancer effect of Jin Ning Fang based on network pharmacology and experimental verification

This paper identifies the molecular mechanism of Jin Ning Fang's anti-lung cancer effect using network pharmacology and experimental validation, revealing key targets and compounds involved.