Fei Chen

This study shows that induced microfold cells are essential for the function of pulmonary tertiary lymphoid organs, which support mucosal immunity against influenza.

This study shows ovarian aging can shift in both directions depending on the systemic environment through inter-organ communication and molecular changes.

The paper identifies pre-hematopoietic stem cells and their niche using spatial transcriptomics in the AGM region, revealing spatial signaling patterns and cellular interactions that support HSC development.

This paper designs an orthogonal self-labeling protein, LUCI-tag, using deep learning, which enables rapid and payload-agnostic labeling of proteins in live cells.

AlphaGenome Atlas predicts regulatory effects of non-coding variants across the human genome, improving their prioritization and interpretation.

This study uses spatial transcriptomics and lineage tracing to show how tumor subclones drive microenvironmental changes that promote metastasis in a mouse model.

TissueFormer is a foundation model that predicts spatial gene expression from histology images at single-cell resolution and scales to diagnostic tasks.

This study uses spatial transcriptomics to show that aging disrupts spatial and temporal coordination of folliculogenesis in mouse ovaries, leading to tissue disorganization and reproductive decline.

This study shows that reduced Satb2 gene dosage in cortical projection neurons leads to chromatin and circuit defects, causing cognitive and sensory impairments in a mouse model of SATB2-associated syndrome.

The paper shows that type I interferon primes alveolar epithelial cells for regeneration by enhancing their response to reparative signals from tissue-resident macrophages after viral infection.

Vermeer generates synthetic microscopy images of protein localization using protein sequences and cell morphology, outperforming previous methods in quality and flexibility.

The paper identifies technical variation caused by probe set barcoding in single-cell RNA sequencing and shows how Flex v2 reduces this issue.

The paper identifies Kat8 and the NSL complex as essential for lung epithelial repair and maps transcription factor dependencies in alveolar repair trajectories using SAGE.

This paper introduces UTMM, a method to simultaneously measure transcriptomes and mechanical properties in intact embryos, revealing coupling between RNA expression and intracellular compliance during early development.

This study identifies IL13 as a survival factor for Hodgkin lymphoma cells by analyzing the tumor microenvironment with spatial and single-cell resolution.

LARIS identifies cell type-specific and spatially restricted ligand-receptor interactions in spatial transcriptomics data with high accuracy and scalability.

The paper introduces SPICE, a framework that uses splicing assays and generative design to create cell-specific gene regulation elements for research and therapy.

The paper identifies crater-shaped structures in melanoma that enhance immune response to checkpoint blockade therapy in humans and zebrafish.

The paper induces menstruation in mice to study endometrial shedding regulation, revealing a new paradigm for spatially regulated fibroblast differentiation.

Glimmer improves spatial representation learning by adaptively learning graphs that balance molecular similarity and spatial proximity across scales, outperforming existing methods in clustering and spatial conservation.

This study uses spatial transcriptomics and TCR sequencing in mice to analyze thymus changes across lifespan, revealing structural and transcriptional alterations linked to immune decline.

PHOTON captures subcellular RNA localization using imaging and sequencing, revealing m6A's role in stress granule mRNA partitioning.

This paper introduces PUPS, a method that predicts protein subcellular localization in single cells using protein sequences and cellular images, showing generalization to unseen proteins and cell lines.

This paper introduces a probabilistic model for analyzing multisample spatial transcriptomics data, identifying spatial metagenes and interactions across tissues.

SlideCNA detects spatial copy number alterations from Slide-seq data to identify sub-clones in metastatic breast cancer.

PASTA enhances spatial biology detection sensitivity while maintaining compatibility with multiple modalities and multiplexing strategies.

This study introduces STAG-seq, a method combining transcriptomics and genotyping to functionally analyze genetic variants in immune cells, revealing their impact on gene expression and disease mechanisms.

TissueMosaic performs cross-sample differential analysis of spatial transcriptomics data using self-supervised representation learning to improve detection of genes associated with tissue structure changes.

The paper develops a tool for continuous, long-range, targeted diversification of endogenous mammalian genomes and uses it to explore the function of genetic variants in both coding and non-coding regions.

The paper introduces ExIGS, a method linking nuclear abnormalities to chromatin repression hotspots in progeria fibroblasts.