Huanming Yang

Chromatin state shapes site-specific A-to-I RNA editing

The paper identifies chromatin state regulators that influence A-to-I RNA editing frequency across species and tissues.

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.

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.

Multimodal AI Decodes Extreme Environment Functional Dark Matter Beyond Homology

The paper develops ACCESS, a multimodal graph neural network to annotate functional dark matter proteins from extreme environments beyond homology-based methods.

A Benchmark of Evo2 Genomic AI Models for Efficient and Practical Deployment

This paper benchmarks the Evo2 genomic AI model in cancer genomics, showing FP8 precision on H800 GPUs improves inference speed and accuracy, while larger models perform worse on non-FP8 hardware.

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.

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.

Himalayan whole-genome sequences provide insight into population formation and adaptation

The paper presents whole-genome sequences from 16 Himalayan populations to study population structure, adaptation, and genetic history, revealing early population divergence, shared adaptive haplotypes, and recent gene flow.

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.

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.

An interpretable integration model improving disease-free survival prediction for gastric cancer based on CT images and clinical parameters

This paper proposes a model integrating deep features, radiomics features, and clinical parameters to improve gastric cancer disease-free survival prediction, achieving a 3%-5% C-index and 10% AUC improvement.

Dissecting aneuploidy phenotypes by constructing Sc2.0 chromosome VII and SCRaMbLEing synthetic disomic yeast

The paper constructs a synthetic disomic yeast using SCRaMbLE and a newly synthesized chromosome to study aneuploidy phenotypes, finding that both copy number and specific chromosomal regions affect fitness.

Single-cell transcriptional profiling reveals cellular and molecular divergence in human maternal-fetal interface

The paper uses single-cell transcriptomics to analyze cellular and molecular differences across maternal-fetal sections of the placenta, identifying key cell types and regulatory factors involved in placental development and preeclampsia.

Chord: Identifying Doublets in Single-Cell RNA Sequencing Data by an Ensemble Machine Learning Algorithm

Chord improves doublet detection in scRNA-seq by combining multiple methods, showing higher accuracy and stability across different datasets.

Integrating convolution and self-attention improves language model of human genome for interpreting non-coding regions at base-resolution

LOGO is a lightweight language model for interpreting non-coding regions of the human genome, achieving improved performance in promoter identification and enhancer-promoter interaction prediction.

Towards Practical and Robust DNA-based Data Archiving Using "Yin-Yang Codec" System

This paper introduces a DNA-based data archiving system called Yin-Yang Codec, which achieves high recovery rates and physical information density in both in vitro and in vivo storage.

Plasma cell-free DNA promise disease monitoring and tissue injury assessment of COVID-19

This study analyzes cell-free DNA in COVID-19 patients to show its potential for disease monitoring and tissue injury assessment.

Mendelian randomization analyses support causal relationships between blood metabolites and the gut microbiome

This study uses Mendelian randomization to identify causal relationships between gut microbiome composition and blood metabolites in a Chinese cohort.

Metagenome-genome-wide association studies reveal human genetic impact on the oral microbiome

This study identifies genetic loci associated with the oral microbiome using metagenome-genome-wide association studies in over 1,915 individuals.

Cell free extrachromosomal circular DNA is common in human urine

This study identifies and characterizes over one million urinary cell free eccDNAs in healthy adults, revealing their genomic distribution, sequence features, and potential role of direct repeats in their biogenesis.

Diversity, function and evolution of marine invertebrate genomes

The paper compiles and analyzes 190 marine invertebrate genomes to explore their diversity, function, and evolutionary relationships.

Diversity, function and evolution of aquatic vertebrate genomes

The paper analyzes 630 aquatic vertebrate genomes to create a compendium, revealing TE diversity and gene family evolution related to the water-to-land transition.

Spatiotemporal transcriptome at single-cell resolution reveals key radial glial cell population in axolotl telencephalon development and regeneration

The paper uses Stereo-seq to map single-cell transcriptomes of axolotl telencephalon during development and regeneration, identifying a key radial glial cell subtype involved in early wound healing.

A Chinese host genetic study discovered type I interferons and causality of cholesterol levels and WBC counts on COVID-19 severity

This study identifies cholesterol levels and WBC counts as causal factors for COVID-19 severity through GWAS and MR analysis, and highlights type I interferon pathways in disease mechanisms.

stLFRsv: a germline SV analysis pipeline using co-barcoded reads

stLFRsv detects structural variations using co-barcoded long reads, achieving 74.2% precision and 22.3% recall for deletions in HG002/NA24385.

M-GWAS for the gut microbiome in Chinese adults illuminates on complex diseases

This paper performs M-GWAS on a Chinese cohort to identify genetic contributions to the gut microbiome and its associations with complex diseases.

Genome Diversity in Ukraine

This study provides genome-wide data for the Ukrainian population, identifying novel genetic variants and highlighting its unique genetic diversity.

Initial Whole Genome Sequencing and Analysis of the Host Genetic Contribution to COVID-19 Severity and Susceptibility

This study analyzes whole-genome sequencing data from 332 Chinese COVID-19 patients to identify genetic variants associated with disease severity and susceptibility.