Sai Ma

Disrupted chromatin architecture blocks B lymphopoiesis in Down syndrome

The paper develops ChromE-seq to study 3D chromatin architecture in fetal hematopoiesis, finding that T21 disrupts B-lineage development by altering chromatin connectivity and regulatory circuits.

A CRISPR-Based Humanized Model Reveals Cooperative Role of STAG2 Loss in Familial GATA2-Deficient MDS Progression

This paper uses a CRISPR-based humanized model to show that STAG2 loss cooperates with GATA2 deficiency to drive MDS progression through increased HSC self-renewal and myeloid bias.

Human skin rejuvenation via mRNA

This paper presents a single-cell atlas of skin aging and identifies ATF3 as a regulator of aging, leading to an mRNA-based treatment that reduces cell senescence and enhances skin rejuvenation.

Uhrf1 loss disrupts Ctcf-associated chromatin organization during early mouse embryogenesis

This study shows that Uhrf1 loss causes DNA methylation loss and chromatin disruption in mouse embryos, leading to developmental failure and altered lineage specification.

OmicGlaze: Spatial Multi-Omic Mapping of Traumatic Brain Injury

OmicGlaze provides a spatial multi-omic framework to analyze TBI, identifying gene regulatory networks and region-specific biological changes.

Early microglial priming in Alzheimer's disease revealed by ME-seq

The paper introduces ME-seq, a technology that profiles DNA methylation, gene expression, and chromatin accessibility in single nuclei, revealing early microglial priming in Alzheimer's disease.

Liver Zonation Disruption Fuels Hepatocellular Carcinoma in Chronic Liver Disease

This study identifies zonation disruption, specifically aberrant β-catenin expansion, as a novel driver of hepatocellular carcinoma in chronic liver disease, revealing a distinct human HCC subtype with therapeutic implications.

Cell-type-resolved NRXN1 isoforms across human brain tissues and hiPSC cortical organoids

The paper develops an integrative sequencing strategy to catalog NRXN1 isoforms across human brain tissues and hiPSC organoids, revealing cell-type-specific splicing patterns and therapeutic potential of ASO targeting.

A single-cell spatial transcriptomic census of human skin anatomy

The paper constructs a spatial transcriptomic atlas of human skin, identifying 45 cell types across 15 sites and revealing neighborhood disruptions in disease.

Myeloid progenitor dysregulation fuels immunosuppressive macrophages in tumors

The paper identifies NRF2-driven myeloid progenitor dysregulation that sustains immunosuppressive macrophages in tumors, showing NRF2 inhibition reduces their survival and enhances antitumor immunity.

Targeting ZNRF3 and RNF43 to Restore Regeneration and Reverse Metabolic Dysfunction-Associated Steatotic Liver Disease

This study shows that deleting ZNRF3 and RNF43 in hepatocytes after MASH onset restores liver regeneration and reverses steatosis, inflammation, and fibrosis without causing tumorigenesis or hepatotoxicity.

Expanding GABAergic Neuronal Diversity in PSC-Derived Disease Models

This study develops a method to generate diverse GABAergic neurons from PSCs using TFs and signaling inhibition, showing distinct subtype compositions and disease relevance.

Droplet-based bisulfite sequencing for high-throughput profiling of single-cell DNA methylomes

This paper introduces Drop-BS, a droplet-based microfluidic method for single-cell bisulfite sequencing, enabling high-throughput DNA methylome profiling of up to 10,000 cells in 2 days.

Single-cell multi-scale footprinting reveals the modular organization of DNA regulatory elements

The paper introduces PRINT, a deep learning method to correct chromatin accessibility data and analyze DNA-protein interactions, revealing structural and functional changes in cis-regulatory elements during hematopoiesis and aging.

Spatial-ATAC-seq: spatially resolved chromatin accessibility profiling of tissues at genome scale and cellular level

This paper introduces spatial-ATAC-seq, a method for spatially resolved chromatin accessibility profiling at the cellular level, and demonstrates its application in mouse embryos and human tonsil tissue.

Functional Inference of Gene Regulation using Single-Cell Multi-Omics

This paper develops FigR, a framework to integrate scATAC-seq and scRNA-seq data to infer gene regulatory networks and identify TF regulators in immune responses.

Cell-type-specific epigenomic variations associated with BRCA1 mutation in pre-cancer human breast tissues

The paper identifies cell-type-specific epigenomic differences in pre-cancerous breast tissues of BRCA1 mutation carriers compared to non-carriers.

Deep learning and alignment of spatially-resolved whole transcriptomes of single cells in the mouse brain with Tangram

The paper introduces Tangram, a method that aligns single-nucleus RNA-seq data with spatial data to create an anatomically integrated spatial map of the mouse brain.

Chromatin potential identified by shared single cell profiling of RNA and chromatin

The paper introduces SHARE-seq, a method to profile RNA and chromatin in single cells, and identifies DORCs that predict lineage commitment by chromatin accessibility changes.

Temporally-Divergent Regulatory Mechanisms Govern Neuronal Development and Diversification in the Neocortex

This study identifies temporally divergent regulatory mechanisms in neuronal development and maturation across mouse and marmoset neocortex.

Inference and effects of barcode multiplets in droplet-based single-cell assays

The paper identifies and quantifies barcode multiplets in 10x Chromium scATAC-seq data, showing their potential to confound single-cell analyses.