Fangming Xie

Spatial Single-Cell Mapping of Transcriptional Differences Across Genetic Backgrounds in Mouse Brains

The paper introduces ATLAS, a method to map transcriptional differences across genetic backgrounds in mouse brains, revealing significant cell type distribution changes between sexes and genetic models.

CIPHER: An end-to-end framework for designing optimized aggregated spatial transcriptomics experiments

CIPHER optimizes aggregate spatial transcriptomics experiments by jointly designing gene signatures and cell embeddings, improving decoding accuracy and experimental reliability.

Establishing a continuum of cell types in the visual cortex

The paper shows that the L2/3 continuum in the mouse visual cortex develops through two phases: a genetically programmed initial phase and a visually experience-driven second phase.

Spatial profiling of the interplay between cell type- and vision-dependent transcriptomic programs in the visual cortex

The paper uses spatial transcriptomics and computational methods to show that vision affects both cell state and cell type composition in the visual cortex during critical periods.

Gradients of Recognition Molecules Wire Visuomotor Transformation

The paper identifies molecular gradients in Drosophila neurons that regulate synaptic connectivity for visuomotor transformation.

Robust enhancer-gene regulation identified by single-cell transcriptomes and epigenomes

The paper identifies gene-CRE pairs in mouse brain cells by integrating single-cell transcriptomes and epigenomes, controlling for gene co-expression.

The BRAIN Initiative Cell Census Data Ecosystem: A User's Guide

The paper provides a guide to the BRAIN Initiative Cell Census Network (BICCN) data ecosystem, its tools, and resources for analyzing brain cell types across species.

Epigenomic and chromosomal architectural reconfiguration in developing human frontal cortex and hippocampus

The paper investigates epigenomic and 3D chromatin conformation changes in human frontal cortex and hippocampus development using sn-m3C-seq, finding distinct chromatin conformations in neurons and glial cells and linking risk variants to regulatory regions.

Single nucleus multi-omics links human cortical cell regulatory genome diversity to disease risk variants

The paper develops a multi-omic single-nucleus sequencing method and framework to analyze regulatory genome diversity in human cortical cells and link it to disease risk variants.

Evolution of cellular diversity in primary motor cortex of human, marmoset monkey, and mouse

The paper compares cellular diversity in the primary motor cortex across human, marmoset, and mouse using single-nucleus transcriptomics and epigenomics, finding conserved cell types and species-specific adaptations.

A multimodal cell census and atlas of the mammalian primary motor cortex

The paper generates a multimodal cell census and atlas of the mammalian primary motor cortex, revealing a unified molecular genetic landscape and cross-species taxonomy of cell types.

An integrated transcriptomic and epigenomic atlas of mouse primary motor cortex cell types

The paper creates a comprehensive atlas of mouse primary motor cortex cell types using integrated transcriptomic and epigenomic data from over 600,000 samples.

SnapATAC: A Comprehensive Analysis Package for Single Cell ATAC-seq

SnapATAC is a software package for analyzing scATAC-seq data, revealing regulatory elements and transcriptional regulators in mouse brain cells.