Jun Chen

The cleaved C-terminal domain of GmERS1-1 modulates cell cycle via GmACR1

This study identifies a proteolytic processing mechanism of the soybean ethylene receptor GmERS1-1 that modulates cell cycle progression via interaction with GmACR1 and GmCDK7.

Kintsugi decides, gene by gene, where spatial transcriptomics borrows information

Kintsugi improves spatial transcriptomics by letting data decide how much to borrow from neighbors and genes, showing it can identify epithelial programs and distinguish fibroblastic foci by composition rather than RNA amount.

FlashDeconv reveals resolution horizons in atlas-scale spatial transcriptomics

Leverage-weighted sketching plus sparse spatial regularization deconvolves 1.6 million Visium HD bins in 153 seconds on commodity hardware, revealing tissue-specific resolution limits where cell-type co-localization can reverse sign.

Transthyretin Contributes to Hippocampal Blood-Brain Barrier Recovery Following Intestinal Inflammation, with Reduced Expression in Alzheimer's Disease

The paper investigates how intestinal inflammation affects the blood-brain barrier (BBB) and identifies transthyretin (TTR) as a key factor in BBB recovery, with reduced TTR expression linked to Alzheimer's disease.

FlashS reveals multiscale spatial gene programs at atlas scale

FlashS identifies spatially variable genes at atlas scale by using a frequency-domain kernel test, achieving high accuracy and efficiency across multiple datasets.

Spatial ligand-receptor gene annotations carry conditional heritability association across human tissues

The paper introduces EdgeMap to assess conditional heritability of ligand-receptor gene annotations in spatial transcriptomics data, finding higher edge z-scores in biologically matched tissues.

The contribution of recent and historical demographic histories to genomic diversity and conservation status in plant species

This study assesses conservation status in 101 plant species by analyzing demographic parameters and genomic diversity, finding that census size is the best predictor of extinction risk.

ChatSpatial: Schema-Enforced Agentic Orchestration for Reproducible and Cross-Platform Spatial Transcriptomics

ChatSpatial enables reproducible spatial transcriptomics analysis by using an LLM to select and orchestrate tools with schema enforcement, improving parameter validity and workflow consistency.

Systematic detection of abnormal samples reveals widespread mislabeling in metagenomic studies

The paper identifies and classifies abnormal samples in metagenomic studies, revealing widespread mislabeling as a common cause.

DAXX governs the silencing of LINE1 during spermatogenesis in mice

This study identifies DAXX as a regulator of LINE1 silencing during spermatogenesis in mice, showing its role in maintaining DNA methylation and preventing transposable element activation.

Identifying a next-generation antimalarial trioxolane in a landscape of artemisinin partial resistance

The paper describes the discovery of new antimalarial trioxolanes effective against artemisinin-resistant parasites and their potential as development candidates for malaria treatment.

Purifying selection purges harmful variants in the rarest pine

The paper investigates purifying selection in the rarest pine species, finding efficient purging of harmful variants despite extreme population size reduction.