Long Cai

Spatial second-order features predict glioma malignant transformation

This study identifies second-order spatial features, such as ligand-receptor interactions, as predictive of glioma malignant transformation using integrated spatial DNA and RNA profiling.

Whole-organism spatial transcriptomics at single-cell resolution in C. elegans

This paper develops a single-molecule fluorescence in situ hybridization workflow for whole-organism spatial transcriptomics in C. elegans, enabling single-cell resolution and multiplex gene profiling.

Regenerative base editing enables deep lineage recording

This paper introduces a regenerative molecular recording system called hypercascade that enables deep lineage reconstruction by maintaining a constant mutation rate over time.

Synaptic MEMOIR: mapping individual synapses of neurons with protein barcodes

Synaptic MEMOIR maps individual synapses in neuronal projections using protein barcodes, enabling single-synapse resolution in large brain volumes without high-resolution imaging.

Spatial Proofreading Amplification of in situ Transcript and Protein Signals

The paper introduces an enzyme-free signal amplification method for spatial transcriptomics that achieves over 500-fold signal amplification and enables multiplex readout.

Untangling overlapping barcodes in image-based spatial genomics

The paper presents a method to decode overlapping barcodes in spatial genomics with low false discovery rate, enabling super-resolution microscopy through coded barcodes.

High-resolution spatial multi-omics reveals cell-type specific nuclear compartments

This study uses high-resolution spatial multi-omics to analyze subnuclear compartments in single cells, revealing cell-type specific chromatin structures and their genomic associations.

The forkhead transcription factor FKH-7/FOXP acts in chemosensory neurons to regulate developmental decision-making

This study identifies a role for FKH-7/FOXP in chemosensory neurons regulating developmental decision-making and links it to autism-associated gene variants.

A Spatiotemporal Atlas of Mouse Gastrulation and Early Organogenesis to Explore Axial Patterning and Project In Vitro Models onto In Vivo Space

This study creates a spatiotemporal atlas of mouse gastrulation and early organogenesis using spatial transcriptomics and scRNA-seq, revealing gene expression dynamics and mesodermal fate decisions.

Spatial Transcriptomics Reveals the Temporal Architecture of the Seminiferous Epithelial Cycle and Precise Sertoli-Germ Synchronization

The paper uses spatial transcriptomics to map the temporal dynamics of the seminiferous epithelial cycle in mouse testis, revealing synchronized transcriptional patterns between Sertoli and germ cells.

Reconstructing cell histories in space with image-readable base editor recording

This paper introduces baseMEMOIR, a method that reconstructs high-resolution cell lineage trees and spatial dynamics using base editing and imaging, achieving 792 bits of memory in embryonic stem cells.

Spatial transcriptomics defines injury-specific microenvironments in the adult mouse kidney and novel cellular interactions in regeneration and disease

The paper uses spatial transcriptomics to identify injury-specific microenvironments and molecular interactions in the mouse kidney during injury and regeneration.

Integrated spatial genomics in tissues reveals invariant and cell type dependent nuclear architecture

The paper uses integrated spatial genomics to study nuclear architecture in mouse brain cortex cells, revealing chromatin fixed points and cell-type specific organization of nuclear bodies.

Highly multiplexed spatially resolved gene expression profiling of mouse organogenesis

This paper uses spatial transcriptomics to study mouse organogenesis, revealing spatial gene expression patterns and cell fate decisions not captured by single-cell RNA sequencing.

Imaging cell lineage with a synthetic digital recording system

A new genetic editing system termed intMEMOIR reveals the lineage histories of individual cells directly within their native tissue context.

Giotto, a toolbox for integrative analysis and visualization of spatial expression data

Giotto is a toolbox for analyzing and visualizing spatial transcriptomic and proteomic data, offering integration with single-cell RNA-seq and supporting diverse datasets.

Global architecture of the nucleus in single cells by DNA seqFISH+ and multiplexed immunofluorescence

The paper maps chromatin states, DNA loci, and gene expression in single mouse embryonic stem cells using DNA seqFISH+ and immunofluorescence, revealing nuclear zones and subpopulations with distinct chromatin features.

Decomposing spatially dependent and cell type specific contributions to cellular heterogeneity

The paper integrates single-cell transcriptomic and spatial data to analyze cell-type and spatial domain contributions to heterogeneity in the mouse visual cortex.

Higher-order inter-chromosomal hubs shape 3-dimensional genome organization in the nucleus

The paper introduces SPRITE, a method for detecting higher-order DNA interactions, and shows that nuclear bodies act as inter-chromosomal hubs shaping 3D genome organization.

Dynamics and spatial genomics of the nascent transcriptome in single mESCs by intron seqFISH

This study uses seqFISH to image nascent transcription active sites in single mouse embryonic stem cells, revealing dynamic spatial distribution and variability in transcription activity.

Challenges And Emerging Directions In Single-Cell Analysis

This paper discusses challenges and future directions in single-cell analysis, highlighting advances in technologies and computational methods for studying cellular heterogeneity.

Multiplexed dynamic imaging of genomic loci in single cells by combined CRISPR imaging and DNA sequential FISH

The paper introduces a method to multiplex label and track genomic loci in single cells using CRISPR imaging combined with DNA seqFISH, demonstrating it on telomere dynamics in mouse embryonic stem cells.