Shiping Liu

This study uses spatial transcriptomics and snRNA-seq to identify 25 forebrain regions and characterize dynamic changes in the human fetal cortex and striatum during late first and early second trimesters.

Contrasting a pretrained genomic language model's attention between case and control haplotypes ranked HBB first on chromosome 11 and recovered more known β-thalassemia variants than GWAS, without per-variant tests.

This study reconstructs the evolutionary assembly of a conserved cortical axis across vertebrates using spatial transcriptomics and single-nucleus RNA-seq, revealing conserved molecular programs and convergent evolution in brain circuitry.

OneGenome-Rice (OGR) is a genomic foundation model for rice pre-trained on 422 genomes, outperforming existing models in 11 tasks and enabling downstream applications like trait analysis and gene expression prediction.

Genos-m is a foundation model for human-associated microbial genomes that outperforms existing models in gene-fitness prediction and community structure analysis.

The paper maps cis-regulatory elements in the macaque cortex using snATAC-seq and links them to disease-related genes and risk SNPs.

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.

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.

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.

This study uses single-cell spatial transcriptomics to identify molecular and cellular changes in hippocampal sclerosis associated with MTLE, revealing vulnerable subregions and novel pathological features.

The paper creates a high-resolution spatial transcriptomic atlas of the mouse brain using snRNA-seq and Stereo-seq, identifying new cell clusters, region-specific genes, and transcription factor regulons.

Spateo provides a framework for spatiotemporal modeling of single-cell spatial transcriptomics data to study cell-cell interactions and organ development in 3D space.

This study maps gene expression and developmental trajectories in zebrafish embryos using Stereo-seq and scRNA-seq, identifying spatial gene modules and signaling interactions.

CDCP is a platform for sharing and analyzing single-cell datasets, offering visualization and analysis tools for researchers.

The paper introduces DESJ-detection, a tool for analyzing differential splicing in single-cell RNA sequencing data, and identifies splicing differences in liver tumor-infiltrating T cells.

The paper uses single-cell RNA-seq to study liver and gallbladder development from the embryonic endoderm, identifying key transcription factors and gene expression changes during differentiation.

The paper integrates single-cell ATAC and transcriptomic data with spatial transcriptomics to map regulatory features and disease vulnerabilities in macaque cortex.

The DNBelab C4 portable, negative-pressure microfluidic device performs high-throughput single-cell transcriptome profiling, resolving species-specific cells and tissue heterogeneity in murine lung and cerebral cortex comparably to existing platforms.

The paper presents a single-cell transcriptomic analysis of nucleated cells in umbilical cord blood, identifying cell types, subpopulations, and transcriptional programs that may impact transplant outcomes.

The paper reports the chromosome-level genome of the white-spotted bamboo shark and shows chromosome rearrangements contribute to phenotypic diversity in cartilaginous fishes.

The paper introduces scCAT-seq, a method to simultaneously assay chromatin accessibility and transcriptome in single cells, and demonstrates its application in human pre-implantation embryos to reveal regulatory heterogeneity.

This study compares the sensitivity and accuracy of the BGISEQ-500 and Illumina HiSeq platforms for single-cell RNA sequencing using a standardized resource of 468 unique single-cells and 1,297 matched single cDNA samples.