Xin Li

Distinct duration and diet dependent lipid profiles and renal complicationsin GCK-MODY

This study shows that GCK-MODY has diet- and duration-dependent effects on lipid profiles and kidney disease in mice, revealing long-term complications previously unrecognized.

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.

Pan-tissue Transcriptome Analysis Reveals Sex-dimorphic Human Aging

This study analyzes transcriptomes across 35 human tissues to show sex-dimorphic aging patterns and their links to Alzheimer's disease and hormone levels.

Cell-Graph Compass: Modeling Single Cells with Graph Structure Foundation Model

Cell-Graph Compass (CGC) is a foundation model that uses graph structures to represent single cells, capturing multiple biological perspectives and achieving state-of-the-art results in downstream tasks.

GeneCompass: Deciphering Universal Gene Regulatory Mechanisms with Knowledge-Informed Cross-Species Foundation Model

GeneCompass is a cross-species foundation model pre-trained on single-cell transcriptomes from human and mouse, integrating biological knowledge to improve gene regulatory mechanism understanding and downstream tasks.

CellPolaris: Decoding Cell Fate through Generalization Transfer Learning of Gene Regulatory Networks

CellPolaris uses transfer learning to generate cell-type-specific gene regulatory networks from transcriptomic data, achieving state-of-the-art results in predicting regulatory factors and simulating cell fate transitions.

Integration of rare large-effect expression variants improves polygenic risk prediction

This study integrates rare large-effect expression variants into polygenic risk scores, showing improved prediction of complex traits by including these variants in risk assessment.

Systematic assessment of regulatory effects of human disease variants in pluripotent cells

The paper maps regulatory effects of human disease variants in pluripotent cells, identifying cis- and trans-QTL across 18,556 genes and linking them to GWAS traits.

A vast resource of allelic expression data spanning human tissues

The paper presents a large ASE resource from GTEx v8 with 431 million SNP-level and 153 million haplotype-level measurements, and extends phASER to estimate cis regulatory variant effect sizes.

Cell type specific genetic regulation of gene expression across human tissues

The paper uses bulk RNA-seq data to estimate cell type abundances and identifies cell type interaction QTLs that provide finer resolution of tissue specificity than bulk cis-eQTLs.

Determinants of telomere length across human tissues

The paper examines telomere length variation across 6,391 tissue samples from 952 individuals, showing tissue-specific differences, positive correlations between tissues, and associations with age and ancestry.

Diverse transcriptomic signatures across human tissues identify functional rare genetic variation

Integrating expression, allelic expression and splicing across tissues identifies rare variants with relevance to traits.

A Quantitative Proteome Map of the Human Body

The paper quantifies protein levels across 32 human tissues and compares them to transcriptome data, revealing insights into post-transcriptional regulation and disease mechanisms.

Ocular disease mechanisms elucidated by genetics of human fetal retinal pigment epithelium gene expression

This study identifies fRPE-specific genes and variants associated with AMD and myopia, revealing novel e/sQTL and mechanisms linking a common variant to both diseases.

Genetic dysregulation of gene expression and splicing during a ten-year period of human aging

The paper analyzes gene expression and splicing changes in human aging using longitudinal RNA sequencing data from the PIVUS study, finding stability in most genetic regulation but dynamic changes in a subset of genes.

Identification of rare-disease genes in diverse undiagnosed cases using whole blood transcriptome sequencing and large control cohorts

This study evaluates the use of whole blood transcriptome sequencing for diagnosing rare diseases, finding an 8.5% diagnostic rate across 56 undiagnosed cases.

Exploring the phenotypic consequences of tissue specific gene expression variation inferred from GWAS summary statistics

The paper develops S-PrediXcan to compute gene expression associations from GWAS summary data and applies it to 44 GTEx tissues and 100+ phenotypes, finding tissue-specific effects and colocalized associations.

The impact of structural variation on human gene expression

This study identifies structural variants (SVs) as significant contributors to gene expression, finding they are more frequent causal variants than previously estimated and have larger effect sizes.

The impact of rare variation on gene expression across tissues

The paper identifies rare variants contributing to extreme gene expression changes across tissues and introduces RIVER, a Bayesian method to prioritize functional variants.

Impact of the X chromosome and sex on regulatory variation

This study examines how the X chromosome and sex influence gene regulation and disease by analyzing gene expression and regulatory variation in whole blood from 922 individuals.