Kai Tan

LDB1-dependent enhancer connectivity defines T-cell leukemia identities and masks metabolic vulnerabilities

The paper identifies LDB1-dependent enhancer connectivity as critical for T-cell leukemia subtypes and reveals a metabolic vulnerability exploitable by statins.

N-Orbit: towards a universal model and metric for comparing tissue microenvironments

The paper introduces N-Orbit, a mathematical model for comparing tissue microenvironments by encoding cell type composition and spatial relationships, showing improved performance over existing metrics in neighborhood discrimination and clinical prediction.

Specific HLA Class I and II alleles are associated with a higher risk for tumor formation in Neurofibromatosis type 1

The paper identifies specific HLA class I and II alleles associated with increased risk of certain tumor types in NF1 patients using RNA-seq and DNA sequencing data.

A longitudinal single-cell and spatial multiomic atlas of pediatric high-grade glioma

This study creates a longitudinal multiomic atlas of pediatric high-grade glioma, revealing distinct tumor cell states and therapeutic targets not seen in adult glioblastoma.

SPTBN2 promotes an immunosuppressive tumor microenvironment and cross-resistance to anti-cancer therapies

This study identifies SPTBN2 as a regulator of immunosuppressive tumor microenvironment and cross-resistance to therapies, showing its role in suppressing CAR T-cell efficacy.

Harnessing the CD2 axis to broaden and enhance the efficacy of CAR T cell therapies

This paper develops anti-CD2 CAR T-cells that overcome fratricide and improve efficacy by incorporating a PD-1:CD2 switch receptor to restore CD2 signaling.

Query-driven generative AI synthesizes multi-modal spatial omics from histology

TissueCraftAI generates multi-modal spatial omics data from histology images using natural language prompts, outperforming existing methods in image generation and molecular data prediction.

An epigenetic basis for sustained inflammatory epithelial progenitor cell states in Crohn's disease

The paper identifies an inflammatory secretory progenitor cell state in Crohn's disease patients and shows its epigenetic regulation in stem cells.

Spatial and Single Cell Mapping of Castleman Disease Reveals Key Stromal Cell Types and Cytokine Pathways

This study maps the spatial and single-cell landscape of Castleman Disease, identifying key stromal cell types and cytokine pathways involved in disease pathology.

CelloType: A Unified Model for Segmentation and Classification of Tissue Images

CelloType is a multi-task learning model for cell segmentation and classification in tissue images, improving accuracy over existing methods.

Mapping the Cellular Biogeography of Human Bone Marrow Niches Using Single-Cell Transcriptomics and Proteomic Imaging

This study maps human bone marrow niches using single-cell transcriptomics and proteomic imaging, identifying distinct cellular environments and their roles in hematopoiesis and AML.

RUNX1 is required in granulocyte-monocyte progenitors to attenuate inflammatory cytokine production by neutrophils

This study shows that RUNX1 in granulocyte-monocyte progenitors limits neutrophil inflammatory cytokine production by restricting retrotransposon chromatin accessibility and type I interferon signaling.

Learning predictive models of tissue cellular neighborhoods from cell phenotypes with graph pooling

CytoCommunity identifies tissue cellular neighborhoods from spatial data using graph neural networks, revealing condition-specific patterns in cancer tissues.

Control of Ribosomal RNA Synthesis by Hematopoietic Transcription Factors

The paper identifies cell-type-specific transcription factors that bind rDNA and regulate rRNA transcription, showing CEBPA's role in promoting Pol I occupancy and rRNA synthesis in myeloid progenitors.

SINBAD: a flexible tool for single cell DNA methylation data

SINBAD is a tool for processing and analyzing single-cell DNA methylation data, offering preprocessing, quality assessment, and analysis modules.

CytoTalk: De novo construction of signal transduction networks using single-cell RNA-Seq data

CytoTalk constructs cell type-specific signal transduction networks from single-cell RNA-Seq data and validates them using spatial transcriptomics and perturbation experiments.

GLUER: integrative analysis of single-cell omics and imaging data by deep neural network

GLUER improves integration of single-cell multi-omics and imaging data, enhancing accuracy in matching cells across modalities and improving downstream analyses.

Predictive modeling of single-cell DNA methylome data enhances integration with transcriptome data

The paper introduces MAPLE, a framework that predicts gene activity from single-cell DNA methylation data, improving integration with transcriptome data for clustering and cell type identification.

RUNX1 haploinsufficiency causes a marked deficiency of megakaryocyte-biased hematopoietic progenitor cells: Mechanistic studies and drug correction

This study shows that RUNX1 haploinsufficiency reduces megakaryocyte-biased hematopoietic progenitor cells and identifies drug targets to correct this defect.

Developmental trajectory of pre-hematopoietic stem cell formation fromendothelium

The paper identifies a pre-hematopoietic (pre-HE) stage in mouse embryos and shows RUNX1 regulates the transition to hemogenic endothelium, leading to distinct HSPC populations in intra-arterial clusters.

scATAC-pro: a comprehensive workbench for single-cell chromatin accessibility sequencing data

scATAC-pro is a software tool for processing, analyzing, and visualizing scCAS data, providing quality assessment and downstream analysis utilities.

Spatial genome re-organization between fetal and adult hematopoietic stem cells

The paper examines 3D genome organization, epigenome, and transcriptome changes in fetal and adult mouse HSCs, finding stage-specific chromatin interactions and transcription factor roles.

Transcriptional regulatory network controlling the ontogeny of hematopoietic stem cells

The paper defines the transcriptomes and epigenomes of key developmental stages of HSC ontogeny in mice and constructs transcriptional regulatory networks using computational methods.

A lineage-resolved molecular atlas of C. elegans embryogenesis at single cell resolution

The paper maps lineage and transcriptome relationships in C. elegans embryogenesis using single-cell transcriptomics, revealing lineage-transcriptome correlation breakdown in late divisions.

Integrating brain methylome with GWAS for psychiatric risk gene discovery

The paper integrates brain DNA methylation data with GWAS to identify psychiatric risk genes, finding heritable CpG sites and methylation-trait associations linked to schizophrenia and bipolar disorder.