Tong Li

Function-driven geometry directs human pilosebaceous unit development

The paper builds a spatiotemporal map of human pilosebaceous unit development using single-cell multiomics and machine learning, showing how epithelial-mesenchymal interactions drive organogenesis and how sebaceous gland programs are disrupted in tumors.

Multi-scale modeling of human tissues from spatial transcriptomics with TERRA

TERRA is a foundation model for spatial transcriptomics that predicts tissue behavior under perturbation and identifies multi-scale biological insights across tissues.

Spatial atlas of the ovary identifies molecular events in primordial follicle activation in humans

This study creates a comprehensive spatial atlas of the human ovarian cortex, revealing molecular mechanisms of primordial follicle activation and follicle niche organization.

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.

Multiplexed high-content imaging uncovers morphological diversity of lymphocyte activation and dysfunction

The paper introduces TGlow, a high-content imaging platform for single-cell phenotyping of human lymphocytes, revealing distinct morphological states and drug responses.

A spatial transcriptomic atlas of autism-associated genes identifies convergence in the developing human thalamus

The paper presents a spatial transcriptomic atlas of autism-associated genes in the developing human brain, identifying convergence in the thalamus and germinal zones.

Mapping and reprogramming human tissue microenvironments with MintFlow

MintFlow is a generative AI algorithm that predicts how tissue perturbations reprogram cell states in disease, revealing novel cell populations and therapeutic targets in three human conditions.

Spatiotemporal map of the developing human reproductive tract at single-cell resolution

This study creates a single-cell spatial atlas of the developing human reproductive tract, identifying genes and mechanisms involved in sexual dimorphism and organ development.

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.

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.

OME-Zarr: a cloud-optimized bioimaging file format with international community support

This paper describes OME-Zarr, a cloud-optimized bioimaging file format developed through community collaboration to improve scalability and data access.

Human skeletal muscle ageing atlas

This study creates a single-cell and single-nucleus transcriptomic atlas of human skeletal muscle ageing, revealing mechanisms in muscle stem cells, myofibers, and the microenvironment.

Cell2location maps fine-grained cell types in spatial transcriptomics

cell2location uses a Bayesian model to integrate single-cell and spatial transcriptomics, mapping cell types in situ across mouse brain regions and human lymph node immune compartments.

Mapping the temporal and spatial dynamics of the human endometrium in vivo and in vitro

This study maps the temporal and spatial dynamics of the human endometrium using single-cell and spatial reference maps, identifying key signaling pathways regulating cell fate in vivo and in vitro.

PoSTcode: Probabilistic image-based spatial transcriptomics decoder

PoSTcode improves transcript decoding from spatial transcriptomic images by reducing mislabeling and doublet signals.

Transcriptome-wide spatial RNA profiling maps the cellular architecture of the developing human neocortex

This paper introduces a new spatial transcriptomic technology, WTA, and applies it to map the cellular architecture of the developing human neocortex, showing spatial enrichment of autism-related genes.

MiR-505-3p is a Repressor of the Puberty Onset in Female Mice

This study identifies miR-505-3p as a repressor of puberty onset in female mice, showing delayed puberty and reduced fertility with its overexpression and earlier puberty with its knockout.