Sai Ma

The paper maps gene expression, chromatin accessibility, and DNA methylation in developing human brain cells to understand regulatory interactions and their role in disease.

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.

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.

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.

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

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.

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.

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.

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

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

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.

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

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.

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.

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.

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.

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

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.

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.

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

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