Shuhua Xu

Adaptive introgression in Tibetans spans focal and distributed architectures

This study identifies Neanderthal-derived adaptive variation in Tibetans, showing functional convergence in immune and metabolic pathways, beyond the well-known EPAS1 locus.

Unifying physical and molecular coordinate systems across modalities in spatial biology

The paper introduces MAPS, a platform for unifying physical and molecular coordinates across modalities in spatial biology, demonstrating its effectiveness on diverse datasets and applications.

scWeave: A deep learning model that bidirectionally translates between gene expression and chromatin structure at single cell resolution

scWeave translates between gene expression and chromatin structure at single-cell resolution using deep learning, improving cross-modality inference across multiple datasets.

ArchaicSeeker 3.0: A deep-learning framework for scalable, haplotype-resolved inference of archaic introgression

ArchaicSeeker 3.0 detects archaic introgression using deep learning, outperforming existing methods in precision, recall, and F1 score across diverse genomic contexts and population sizes.

Genomic Evidence for Males of Exceptional Reproductive Output (ERO) in Apes and Humans

The paper uses genomic diversity data to estimate the variance ratio of reproductive output in males and females across apes and humans, finding evidence for exceptional reproductive output in some males.

Long-read sequencing of 945 Han individuals identifies novel structural variants associated with phenotypic diversity and disease susceptibility

The paper identifies novel structural variants in Han Chinese genomes using long-read sequencing and links them to phenotypic diversity and disease susceptibility.

AncestryPainter 2.0: Visualizing ancestry composition and admixture history graph

AncestryPainter 2.0 visualizes ancestry composition and admixture history using improved graphical and statistical modules.

Brain eQTLs of European, African American, and Asian ancestry improve interpretation of schizophrenia GWAS

This study identifies population-specific eQTLs in brain tissues from European, African American, and Asian ancestry individuals, revealing new schizophrenia risk genes and variants missed in European-only datasets.

On the contribution of genetic heterogeneity to complex traits

The paper identifies genetic heterogeneity in plants and humans using machine learning, finding allelic heterogeneity in maize eQTL and potential synthetic associations in human GWAS data.

Structural evolution of trypsinogen gene redundancy confers risk for pancreas diseases

The paper investigates the structural evolution of trypsinogen genes and links haplotype variations to pancreas disease risk.

Brain transcriptional regulatory architecture and schizophrenia etiology converge between East Asian and European ancestral populations

This study identifies eQTL and sQTL in East Asian brains, finds convergence in transcriptional regulatory architecture with European populations, and links these to schizophrenia risk genes and pathways.

AdmixSim: A Forward-Time Simulator for Various and Complex Scenarios of Population Admixture

AdmixSim generates synthetic admixture data under complex scenarios, enabling accurate simulation of population admixture dynamics and facilitating comparative studies.

Genome-wide Association study of facial morphology identifies novel genetic loci in Han Chinese

This study identifies five novel genetic loci associated with facial morphology traits in Han Chinese through a genome-wide association analysis of 3D facial data.

Novel genetic loci affecting facial shape variation in humans

This study identifies 24 genetic loci associated with facial shape variation in humans through GWAS and confirms 13 of them in a multi-ethnic cohort.

Comparative genetic architectures of schizophrenia in East Asian and European populations

This study identifies schizophrenia genetic associations in East Asian and European populations, finding similar genetic effects across ancestries but highlighting challenges in polygenic risk prediction across groups.

De novo assembly of a Tibetan genome and identification of novel structural variants associated with high altitude adaptation

The paper assembles a high-quality Tibetan genome and identifies structural variants linked to high altitude adaptation and archaic hominid ancestry.

Genome-wide Variants of Eurasian Facial Shape Differentiation and a prospective model of DNA based Face Prediction

The paper identifies six genome-wide significant loci associated with facial shape differences between Europeans and Han Chinese and develops a DNA-based 3D face prediction model.

Trio deep-sequencing does not reveal unexpected mutations in Cas9-edited monkeys

The paper uses whole genome trio sequencing to assess off-target effects of Cas9 editing in monkeys and finds no unexpected mutations.

Inference of Multiple-wave Admixtures by Length Distribution of Ancestral Tracks

The paper introduces MultiWaver, a method to infer multiple-wave admixture histories from ancestral tracks, validated on real datasets.

Modeling Continuous Admixture

The paper develops a method to infer admixture history using weighted LD, improving accuracy in complex admixture scenarios with isolation after continuous gene flow.

Inference of multiple-wave population admixture by modeling decay of linkage disequilibrium with multiple exponential functions

This paper introduces MALDmef, a method for inferring multiple-wave admixture by modeling LD decay with multiple exponential functions, showing improved accuracy over existing methods in simulated and real data.

Length Distribution of Ancestral Tracks under a General Admixture Model and Its Applications in Population History Inference

This paper derives the length distribution of ancestral tracks under a general admixture model and applies it to infer population histories with high accuracy.

Investigating the Evolutionary Importance of Denisovan Introgressions in Papua New Guineans and Australians

This study identifies Denisovan introgressions in Papua New Guineans and Australians, finds they are under positive selection and related to important evolutionary functions, and proposes a method for detecting archaic hominin introgressions.