Xun Xu

Chromosome-level genome assembly of Helichrysum odoratissimum, a medicinal plant from Southern Africa

This paper presents a chromosome-level genome assembly for Helichrysum odoratissimum to support genetic and functional studies.

Spatiotemporal transcriptome atlas of human embryos after gastrulation

The paper creates a spatiotemporal transcriptome atlas of human embryos after gastrulation, revealing organ-specific regulons and regulatory networks during development.

RegFormer: A Single-Cell Foundation Model Powered by Gene Regulatory Hierarchies

RegFormer improves single-cell RNA sequencing analysis by integrating gene regulatory networks with Mamba-based modeling, outperforming existing models in clustering, integration, and annotation.

Complete Genomes of Cultivated Gut Bacteria Reveal Mobile Genetic Element-Driven Functional Diversity with Therapeutic Implications

The paper presents a comprehensive compendium of fully circularized human gut bacterial genomes and reveals how mobile genetic elements drive functional diversity with therapeutic implications.

Cell Type Architecture and Positional Gene Gradients in an Adult Animal at Subcellular Resolution

This study reconstructs 3D spatial transcriptomic models of planarians to map cell type distribution and positional gene regulation, identifying candidate genes involved in regeneration.

Single-Cell Genomics Elucidates Molecular Variations and Regulatory Mechanisms in Circulating Immune Cells

The paper introduces CIMA, a multi-omics atlas of human immune cells, identifying regulatory mechanisms and genetic associations across sex, age, and genetic factors.

FEDRANN: effective long-read overlap detection based on dimensionality reduction and approximate nearest neighbors

FEDRANN improves long-read overlap detection using dimensionality reduction and approximate nearest neighbors, outperforming existing methods on real data.

4D Single-Cell Spatial Transcriptomics Reveals Dynamic Morphogenetic Gradients and Regenerative Domains in Planarians

This study constructs a 4D spatiotemporal transcriptomic map of planarian regeneration using Stereo-seq, identifying dynamic gradients and an injury-induced regenerative zone.

Ultrahigh-Throughput Forster Resonance Energy Transfer-Activated Droplet Sorting for Terminator Polymerase Engineering

This paper introduces a dual-channel FRET-based droplet sorting system to enhance terminator polymerase engineering, achieving 30-fold enrichment of active variants in a single round.

A Population-scale Single-cell Spatial Transcriptomic Atlas of the Human Cortex

This study creates a single-cell spatial transcriptomic atlas of the human cortex, revealing gene expression patterns, aging effects, and disease associations across layers and species.

Efficient reliability analysis of spatially resolved transcriptomics at varying resolutions using SpaSEG

SpaSEG is a convolutional neural network model for analyzing spatially resolved transcriptomics data, showing superior reliability and efficiency in detecting spatial patterns and intercellular interactions.

Spatiotemporal transcriptomic maps of mouse intracerebral hemorrhage at single-cell resolution

This study creates spatiotemporal transcriptomic maps of mouse brain after ICH to understand cellular responses and identify therapeutic targets.

Genomic evolution reshapes cell type diversification in the amniote brain

The paper creates a single-cell atlas of amniote brains to study cell type diversification and identifies species-specific gene expression patterns and novel cell subtypes.

Efficiently Constructing Complete Genomes with CycloneSEQ to Fill Gaps in Bacterial Draft Assemblies

The paper evaluates CycloneSEQ long-read sequencing for improving bacterial genome assemblies, showing it can produce complete circular genomes when combined with short-read data.

StereoMM: A Graph Fusion Model for Integrating Spatial Transcriptomic Data and Pathological Images

StereoMM integrates spatial transcriptomic data and histological images to improve spatial domain recognition and tumor heterogeneity analysis in cancer tissues.

Stereopy: modeling comparative and spatiotemporal cellular heterogeneity via multi-sample spatial transcriptomics

Stereopy provides a framework for analyzing multi-sample spatial transcriptomics data to model comparative and spatiotemporal cellular heterogeneity through three key algorithms.

SpaGRN: investigating spatially informed regulatory paths for spatially resolved transcriptomics data

SpaGRN predicts spatially informed gene regulatory networks from spatial transcriptomics data, revealing spatiotemporal regulatory patterns in Drosophila development.

Structural variants contribute to the gut microbiome, blood metabolic traits and their causal relationships

This study identifies 138,859 structural variants in 2,002 individuals, finding 30 associations with gut microbes and 48 with blood metabolites, including causal relationships between microbiome and metabolites.

Multimodal brain cell atlas across the adult macaque lifespan

The paper constructs a multimodal brain cell atlas of adult macaques across their lifespan, revealing aging-related molecular changes and identifying aging hotspots and regulatory loci.

Spatial transcriptomics elucidates the central role of cerebral vasculatures in the progression of Japanese encephalitis

This study uses spatial transcriptomics to show that cerebral vasculatures, particularly meninges, drive inflammation and tissue damage in Japanese encephalitis by forming a feedback loop involving immune cells and cell death mechanisms.

Spatiotemporal transcriptomic profiling reveals the dynamic immunological landscape of alveolar echinococcosis

This study uses spatiotemporal transcriptomics to analyze immune dynamics in E. multilocularis infected mouse liver, identifying key immune cell roles and shifts in immune strategy during infection.

Inferring cell trajectories of spatial transcriptomics via optimal transport analysis

spaTrack infers spatial cell trajectories using optimal transport, revealing spatiotemporal dynamics in regeneration and tumor development.

A near-complete genome assembly of the bearded dragon Pogona vitticeps provides insights into the origin of Pogona sex chromosomes

The paper constructs a near-complete genome assembly for the bearded dragon Pogona vitticeps and characterizes the Z sex chromosome, identifying key genes involved in sex determination.

Unraveling the impact of host genetics and factors on the urinary microbiome in a young population

This study characterizes the urinary microbiome in 1579 Chinese individuals, identifying host factors and genetic associations that influence microbial composition and urotype classification.

Revolutionizing large-scale DNA synthesis with microchip-based massive in parallel synthesis system

This paper introduces a microchip-based DNA synthesis system that significantly improves DNA product concentration and simplifies downstream processes for large-scale gene synthesis.

Comparative spatiotemporal single cell transcriptomes reveal rewiring of pre-existing regulations during emergence of Kranz anatomy in C4 grasses

The paper uses single cell transcriptomes to study how regulatory networks change during the development of Kranz anatomy in C4 grasses.

Genetic studies of gestational diabetes mellitus in 21,813 Chinese women

This study identifies four genome-wide significant SNPs associated with GDM in Chinese women and develops an early prediction model using clinical and genetic indicators.

Multi-trait genome-wide association study in 34,394 Chinese women reveals the genetic architecture of plasma metabolites during pregnancy

This study identifies 30 novel metabolite-gene associations in 34,394 Chinese pregnant women and finds pleiotropy and causal relationships between metabolites and diseases.

Genetic analysis of 104 pregnancy phenotypes in 39,194 Chinese women

This study performs a large-scale genetic analysis of 104 pregnancy phenotypes in 39,194 Chinese women, identifying 407 trait-locus associations and uncovering novel genetic insights into pregnancy-related traits.

Deciphering the Cell-Specific Transcript Heterogeneity and Alternative Splicing during the Early Embryonic Development of Zebrafish

The paper uses single-cell long-read transcriptome sequencing to study transcript diversity and alternative splicing in zebrafish embryos, identifying cell populations with distinct splicing regulations during early development.