Peng He

An Integrated Atlas of the Human Kidney Spanning Health and Diseases

The paper integrates multiple single-cell and single-nucleus RNA-sequencing datasets to create a comprehensive Human Kidney Cell Atlas, identifying cell types, states, and disease-associated populations.

piRNA direct the chromatin reader to its genomic targets

The paper shows that Rhi recruitment to genomic targets in Drosophila is mediated by a combination of H3K9me3 binding and a piRNA-guided scaffold involving Panx and Kipf.

An integrated single cell and spatial omics atlas of human prenatal development

Human Developmental Cell Atlas integrates ~4.6 million cells/nuclei from 4-22 post-conception weeks into 454 refined cell types and maps 114 spatial niches across 6PCW whole-embryo sections.

A trans-piRNA network and transcriptional antagonism shape piRNA cluster function

The paper shows that cytoplasmic inheritance of piRNAs is critical for piRNA biogenesis and that trans-acting piRNAs connect piRNA clusters into a functional network.

An atlas of TF driven gene programs across human cells

The paper creates a regulon atlas mapping TF activity across human cell types and uses it to link disease signatures to cell types and TFs, improving disease risk locus analysis.

Balancing precision with plasticity: Redefining the roles of transcription factors in early cell fate specification

This study identifies two classes of regulatory elements in Drosophila embryos that govern early gene expression, revealing distinct roles for pioneer factors in initiating and maintaining transcriptional activity.

WebAtlas pipeline for integrated single cell and spatial transcriptomic data

WebAtlas integrates single cell and spatial transcriptomic data into a cloud-optimised format for interactive exploration.

A multiomic atlas of human early skeletal development

This study constructs a multiomic atlas of human early skeletal development using single-nuclei transcriptomics, epigenomics, and spatial transcriptomics to uncover regulatory mechanisms and cell states involved in bone and joint formation.

A human embryonic limb cell atlas resolved in space and time

This paper creates a human embryonic limb cell atlas using single-cell and spatial transcriptomics, identifying novel cell populations and developmental patterns.

Automatic cell type harmonization and integration across Human Cell Atlas datasets

CellHint harmonizes cell types across Human Cell Atlas datasets, revealing new cell states and providing a cross-tissue database with 3.7 million cells.

Maternally inherited siRNAs initiate piRNA cluster formation

The paper shows maternally inherited siRNAs trigger de novo formation of piRNA clusters in Drosophila, which then sustain themselves without ongoing siRNA input.

A human prenatal skin cell atlas reveals immune cell regulation of skin morphogenesis

This study creates a prenatal human skin cell atlas, revealing immune cells' role in skin development and showing their impact on vascular and hair follicle formation.

A human fetal lung cell atlas uncovers proximal-distal gradients of differentiation and key regulators of epithelial fates

The paper constructs a human fetal lung cell atlas from 5-22 post conception weeks, identifying new cell states and regulators of epithelial fates.

An organoid CRISPRi screen revealed that SOX9 primes human fetal lung tip progenitors to receive WNT and RTK signals

The paper uses a CRISPRi screen in human fetal lung organoids to identify SOX9 as a key regulator of progenitor self-renewal, showing it primes cells to receive WNT and RTK signals.

Acquisition of alveolar fate and differentiation competence by human fetal lung epithelial progenitor cells

This study identifies a human fetal lung progenitor cell population with alveolar fate potential and develops an organoid system to study alveolar development mechanisms.

The changing mouse embryo transcriptome at whole tissue and single-cell resolution

The paper quantifies the mouse embryo transcriptome from E10.5 to birth using whole-tissue and single-cell RNA-seq, identifying key gene expression patterns and cell types.

Odd-paired is a late-acting pioneer factor coordinating with Zelda to broadly regulate gene expression in early embryos

The paper shows that Odd-paired (Opa) acts as a late-acting pioneer factor that coordinates with Zelda to regulate gene expression in early Drosophila embryos.

Integrated analyses of single-cell atlases reveal age, gender, and smoking status associations with cell type-specific expression of mediators of SARS-CoV-2 viral entry and highlights inflammatory programs in putative target cells

Across 1,176,683 airway and lung cells from 22 datasets, ACE2 rises with age, in males and in smokers' multiciliated cells, and is lowest in young children.