Jianwen Que

Comparative single cell analysis of wound and cancer identifies the metabolic dialogues between tumor initiating stem cells and macrophages

This study compares single-cell RNA sequencing data from wound healing and cancer to identify metabolic differences between tumor-associated macrophages and wound-associated macrophages, highlighting SOX2High stem cells as key regulators.

ILC2s navigate tissue redistribution during infection using stage-specific S1P receptors

This study shows that ILC2s use different S1P receptors at distinct stages to migrate during infection, highlighting a shared vascular network for lymphocyte movement.

Decoding the MYC locus reveals a druggable ultraconserved RNA element

The paper maps the functional fitness landscape of the MYC locus, identifies an ultraconserved RNA element critical for MYC function, and shows it can be targeted to kill MYC-addicted cancer cells.

Genotype-to-phenotype mapping of somatic clonal mosaicism via single-cell co-capture of DNA mutations and mRNA transcripts

The paper develops scG2P to jointly capture DNA mutations and mRNA transcripts in single cells, revealing clonal architectures and phenotypes in aged esophageal tissue.

STAT3 regulates basal cell identity and morphogenesis during early esophageal development

This study shows STAT3 is essential for esophageal progenitor cell development and epithelial morphogenesis in humans, but not in mice.

Training Data Diversity Enhances the Basecalling of Novel RNA Modification-Induced Nanopore Sequencing Readouts

This study shows that diverse training data improves basecalling accuracy for novel RNA modifications in nanopore sequencing.

Specialized Pericyte Subtypes in the Pulmonary Capillary

The paper identifies two specialized pericyte subtypes in pulmonary capillaries using Higd1b as a marker and shows their distinct functions and responses to hypoxia.

SOX2-induced IL-1alpha-mediated immune suppression drives epithelial dysplasia malignant transformation

This study identifies a SOX2-CCL2-IL1 pathway that drives immune suppression in precancerous epithelial dysplasia, promoting malignant transformation.

An Iterative Approach to Polish the Nanopore Sequencing Basecalling for Therapeutic RNA Quality Control

This paper introduces an iterative method to improve nanopore sequencing basecalling accuracy for therapeutic RNA quality control, enabling precise analysis of modified RNAs.

Human Vascularized Macrophage-Islet Organoids to Model Immune-Mediated Pancreatic β cell Pyroptosis upon Viral Infection

The paper develops vascularized macrophage-islet organoids to study immune-mediated β cell pyroptosis during viral infection and identifies TNFSF12-TNFRSF12A as a key mechanism.

Adapting Nanopore Sequencing Basecalling Models for Modification Detection via Incremental Learning and Anomaly Detection

This paper adapts nanopore sequencing basecalling models for modification detection using incremental learning and anomaly detection, achieving single-molecule and single-nucleotide resolution across multiple species and modification types.

Crk mediates Csk-Hippo signaling independently of Yap tyrosine phosphorylation to induce cell extrusion

A Spatiotemporal and Machine-Learning Platform Accelerates the Manufacturing of hPSC-derived Esophageal Mucosa

The paper develops a spatiotemporal multi-omics platform and machine-learning tool to manufacture hPSC-derived esophageal mucosa.

Conditional blastocyst complementation of a defective Foxa2 lineage efficiently promotes generation of the whole lung

The paper identifies the Foxa2 lineage's role in lung development and demonstrates that conditional complementation of this lineage can generate a whole lung in mice.

Wnt/Fgf crosstalk is required for the specification of tracheal basal progenitor cells

This study identifies the role of Wnt/Fgf crosstalk in tracheal basal progenitor cell specification through genetic ablation experiments in mouse models.