Xiaoyin Chen

The paper introduces Seq-o-Matic, an open-source automated in situ sequencer that reduces hands-on time and improves sequencing consistency across tissue sections.

The paper maps gene expression and axonal projections of neurons in the mouse primary visual cortex to reveal how retinotopy and cell-type-specific collateralization organize visual-stream output.

The paper uses single-cell projection mapping in mice and marmosets to show that thalamocortical projections are spatially segregated in marmosets but follow a conserved gradient in both species.

The paper identifies topographic organization in locus coeruleus norepinephrine neurons, linking their morphology, gene expression, and activity to specific brain regions and learning-related behaviors.

The paper introduces xIV-LDDMM, a toolkit for cross-scale and cross-modality mapping of 3D imaging and spatial-omics data using image-varifold measures.

The paper introduces axonal BARseq, a high-throughput method for mapping single-neuron projections in the brain, and demonstrates its application in mapping over 8,000 mouse auditory cortex neurons from a single brain.

The paper identifies coordinated gene expression between spatially adjacent cells across multiple brain datasets, revealing biological processes and potential therapeutic targets.

This study uses barcoded rabies virus with single-cell and in situ sequencing to map synaptic connectivity in the mouse brain, distinguishing cortical cell types by their connectivity patterns.

The paper uses BARseq to analyze transcriptomic signatures in mouse cortex, showing that cell type composition defines area identity and is shaped by peripheral inputs.

The paper uses high-throughput sequencing to analyze neuronal projections in the mouse olfactory system and finds structured connectivity along the anterior-posterior axis.

The paper introduces ExBarSeq, a method for high-resolution multiplexing of barcodes and synaptic proteins in neurons, demonstrating its application in mouse brain tissue.

The paper provides a detailed cellular-resolution map of the mouse primary motor cortex, defining cell types and their connectivity.

BarDensr demixes spatial transcriptomics data by modeling the imaging process and using convex optimization, achieving state-of-the-art signal recovery in dense or low-resolution data.

The paper introduces BARseq2 to map neuronal projections and gene expression in mice, finding shared cadherin signatures across cortical areas.

The paper introduces BARseq, a method for high-throughput mapping of neuronal projections in the mouse auditory cortex, revealing novel projection types in specific cell subtypes.

This paper introduces BaristaSeq, an optimized in situ barcode sequencing method that improves amplification efficiency and accuracy for lineage tracing and neuronal projection mapping.