Qin Zhu

CONCORD is a self-supervised framework that integrates single-cell datasets across batches, technologies, and species, producing high-resolution cell atlases with improved biological resolution and reduced noise.

HybriSeq enables sensitive single-cell RNA profiling by combining in situ hybridization, split-pool barcoding, and sequencing to detect transcripts without end bias.

This study identifies that APC loss in colorectal cancer drives a β-CATENIN-independent fetal intestinal transcriptional program through YAP activation, leading to bistable stem cell states and enhanced tumorigenesis.

The paper introduces MULTI-ATAC, a method to reduce batch effects in scATAC-seq by pooling samples before transposition, enabling scalable and batch-free experiments.

deMULTIplex2 improves sample demultiplexing in scRNA-seq by accurately associating cell tags with sample tags, outperforming existing methods on large, noisy, and imbalanced datasets.

The paper identifies a pre-hematopoietic (pre-HE) stage in mouse embryos and shows RUNX1 regulates the transition to hemogenic endothelium, leading to distinct HSPC populations in intra-arterial clusters.

scATAC-pro is a software tool for processing, analyzing, and visualizing scCAS data, providing quality assessment and downstream analysis utilities.

The paper defines the transcriptomes and epigenomes of key developmental stages of HSC ontogeny in mice and constructs transcriptional regulatory networks using computational methods.

The paper uses single-cell RNA sequencing and lineage tracing in mouse kidneys to reveal sex differences, cell diversity, and lineage convergence in nephron development.

The paper maps lineage and transcriptome relationships in C. elegans embryogenesis using single-cell transcriptomics, revealing lineage-transcriptome correlation breakdown in late divisions.

PIVOT provides an R-based application with a graphical interface to simplify transcriptomics data analysis for non-programmers by integrating multiple tools and enabling interactive exploration.