Guangdun Peng

In vivo multimodal lineage tracing of mammalian development by DeepTrack barcoding

The paper introduces DeepTrack, a lineage tracing model that combines cellular barcoding with single-cell multi-omics to study cell fate transitions and molecular changes during mammalian development.

Single-cell lineage tracing of human neuromesoderm organoids reveals TBX6-mediated posterior mesoderm fate diversification

The paper uses single-cell lineage tracing and multiomics profiling to map human neuromesoderm differentiation, revealing TBX6's role in posterior mesoderm fate diversification.

Steller: a high-resolution platform for spatial clonal tracing of mammalian brain development

Steller improves clonal detection sensitivity in spatial transcriptomics and reveals region-specific spatial clonal architectures in the developing mouse forebrain.

Divergent stem cell mechanisms governing the primary body axis and appendage regeneration in the axolotl

This study identifies divergent stem cell mechanisms in axolotl tail and limb regeneration, showing that TGF-β signaling determines lineage fate of muscle stem cells.

Learning phenotype associated signature in spatial transcriptomics with PASSAGE

PASSAGE identifies phenotype-associated spatial signatures in spatial transcriptomics data using a deep learning framework.

Dual nuclease single-cell lineage tracing by Cas9 and Cas12a

DuTracer improves single-cell lineage tracing by using two CRISPR systems to record deeper and more accurate lineage histories with reduced barcode dropout.

Systematic comparison of sequencing-based spatial transcriptomic methods

This study compares six sequencing-based spatial transcriptomic methods using reference tissues, highlighting molecular diffusion as a key variable affecting resolution and identifying unique attributes of spatial transcriptomic data.

Three-dimensional molecular architecture of mouse organogenesis

This study creates a 3D spatial transcriptome atlas of mouse embryos at embryonic day 13.5, integrating with single-cell data to reveal molecular regulation of organ development.

Time, Space and Single-Cell Resolved Molecular Trajectory of Cell Populations and the Laterality of the Body Plan at Gastrulation

The paper constructs a single-cell spatio-temporal atlas of molecular trajectories during gastrulation in mouse embryos, revealing asymmetric BMP signaling and its role in left-right body plan asymmetry.

Spatiotemporal orchestration of multicellular transcriptional programs and communications in the early stage of spinal cord injury

The paper maps the spatiotemporal gene expression and cell-cell interactions in a mouse model of acute spinal cord injury, identifying key molecular features and cell types involved in early injury response and recovery.

Spatial and molecular anatomy of germ layers in the gastrulating primate embryo

The paper maps spatial and molecular changes in germ layers during primate gastrulation using spatial transcriptomics and 3D modeling.

Simultaneous profiling of spatial gene expression and chromatin accessibility for mouse brain development

This study introduces MISAR-seq to jointly profile spatial gene expression and chromatin accessibility in developing mouse brains, revealing spatiotemporal regulatory principles.

AutoGenome: An AutoML Tool for Genomic Research

AutoGenome is an automated deep learning framework for genomic profiling data that uses a residual fully-connected neural network and AutoML to train high-performance models.

Cardiac differentiation at single cell resolution reveals a requirement of hypertrophic signaling for HOPX transcription

The paper maps cardiac differentiation at single-cell resolution, identifies HOPX dysregulation, and shows hypertrophic signaling is required for HOPX transcription in hPSC-derived cardiomyocytes.