Chengxiang Qiu

The paper introduces OPTIMuS PRIME-Del, a CRISPR-based method for multiplexed, precise deletion of cis-regulatory elements, validated through molecular tagging and scRNA-seq analysis.

The paper identifies chromatin-opening transcription factors in mouse embryonic stem cells using CRISPRa screens, revealing autonomous, opportunistic, and hierarchical mechanisms.

A prime-editing recorder in one mouse embryo yields a dated, zygote-rooted lineage tree of 1.28M cells at E13.5, enabling clonal dominance, sibling-fate and cell-type coupling analyses.

The paper develops STEAM, an evolution-augmented deep learning model, to predict mammalian enhancer landscapes across species using comparative genomics and single-cell data.

This study profiles 5.3 million cells from 55 rhesus macaques across their lifespan to map age-related changes in brain cell types and identify molecular signatures linked to aging and Alzheimer's disease.

The paper describes a method to generate human embryo-like structures by pre-patterning stem cells and mixing them, resulting in models with extended anterior-posterior organization and neural features.

The paper develops monoclonal gastruloids from single mouse embryonic stem cells and uses DNA Typewriter to reveal heritable lineage biases in early development.

The paper develops monoclonal embryoids with genetic barcoding to overcome clonal complexity bottlenecks in mosaic organoid screens, enabling more accurate quantification of genetic perturbation effects.

This study combines bulk RNA-Seq datasets to create a transcriptomic landscape of meningiomas, identifies subtypes with distinct biology and prognosis, and provides an interactive tool for outcome prediction.

This paper introduces Sunbear, a framework for integrating multi-condition and multi-modal single-cell profiles across time to infer temporal profiles and predict dynamic relationships in mouse embryonic development.

12.4 million single-nucleus transcriptomes from 83 staged mouse embryos (E8 to P0) yield 190 cell types, a zygote-to-pup cell-type tree, and rapid postnatal transcriptional shifts.

This study induces human gastruloids with embryo-like structures using retinoic acid and shows they match E9.5 mouse embryos in developmental stage through single-cell RNA-seq and computational staging.

The paper uses single-cell RNA sequencing to systematically phenotype mouse genetic models, identifying molecular and cellular changes across multiple mutants and wildtypes.

The paper maps genetic variants to cell types in the kidney to identify disease mechanisms and drug targets.

This paper reconstructs cellular trajectories of mammalian embryogenesis using scRNA-seq data and identifies key transcription factors at branch points.

This study identifies 16 genome-wide significant loci associated with diabetic kidney disease, including a protective variant in the COL4A3 gene.