Jun Z. Li

The paper maps how local sequence context influences germline mutation rates using 1000 Genomes Project data, showing non-monotonic decay and higher-order interactions.

The paper identifies genetic loci associated with anxiety-like and nociceptive traits in outbred Sprague-Dawley rats using genome-wide association analysis.

The paper defines a 3D chromatin compartment blueprint that programs histone-to-protamine exchange during spermiogenesis using ATAC-seq, CUT&Tag, and Hi-C.

The paper identifies enhancer architecture differences in skeletal muscle between high and low cardiorespiratory fitness rats, linking them to gene expression and metabolic traits.

This study examines the transcriptomic and proteomic changes in cultured ovarian follicles, identifying gene expression patterns and differentially expressed genes between group culture conditions.

This paper presents a single-cell RNA sequencing atlas of the human uterus, identifying 39 cell subtypes and proposing a consensus annotation system, while highlighting dynamic changes and potential progenitor cells across menstrual cycle phases.

This study examines how endurance exercise training affects rat subcutaneous white adipose tissue, revealing sex-specific molecular responses and differences in adiposity and metabolism.

The paper presents an improved rat reference genome, mRatBN7.2, which enhances genomic, transcriptomic, and proteomics data mapping and identifies millions of genetic variations across rat strains.

This study identifies genetic loci associated with exploratory locomotion and anxiety-like traits in a selectively bred rat model using a genome-wide association approach.

This study profiles multi-omic changes in multiple tissues of rats during endurance exercise training, identifying molecular adaptations and sex-specific responses across time.

The paper identifies gene expression patterns in the hippocampus of rats that predict internalizing and externalizing behaviors, linking them to genetic variation and biological processes.

The paper describes a method to generate reproducible single-rosette brain organoids from human pluripotent stem cells and uses them to study structural phenotypes in neurodevelopmental disorders.

This study uses scRNA-seq to identify cellular heterogeneity in human fallopian tubes, revealing distinct cell types and changes in disease states.

The paper identifies splice-disruptive POU1F1 variants, including synonymous ones, associated with hypopituitarism using high-throughput splicing assays.

This study identifies Tcf21+ mesenchymal progenitors in mouse testis that contribute to somatic cell development, homeostasis, and regeneration.

The paper shows that Sertoli-cell androgen signaling is not required for meiotic prophase initiation but is essential for meiotic division phase competence in spermatocytes.

The paper uses single-cell RNA sequencing to compare spermatogenesis in human, macaque, and mouse testes, identifying conserved and divergent molecular features across species.

The paper identifies regions of potential mis-assembly in the rat reference genome using whole-genome sequencing data from eight inbred strains.

The paper analyzes rare variants to uncover mutation rate heterogeneity in the human genome, identifying genomic features that influence mutation rates.

The paper develops a theoretical framework and simulations to evaluate the statistical power of detecting copy number alterations in mixed DNA sequencing samples, considering factors like sequencing depth, CNA length, and mixing ratio.

Helmsman generates mutation spectra matrices efficiently, enabling mutation signature analysis on large datasets with high speed and low memory usage.

The paper predicts cell type composition in human brain transcriptomic datasets and shows how age, death manner, dissection, and psychiatric diagnosis affect cell type ratios.

The paper shows linkage disequilibrium can identify relatives using nonoverlapping genetic markers, with 30-36% accuracy for parent-offspring and sib pairs.

The paper identifies novel thrombosis suppressor loci using a sensitized mutagenesis screen in Factor V Leiden mice, finding F8 and the Tfpi/F3 axis, as well as Actr2, play key roles in thrombosis regulation.

The paper compares transcriptomes and metabolomes of postmortem brain samples from schizophrenia, bipolar disorder, major depressive disorder, and controls to identify molecular differences and potential therapeutic targets.

The paper identifies genomic regions under differential selection between two rat lines with divergent aerobic running capacity using SNP arrays and genome sequencing.