Hanying Yan
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View article: Smart spatial omics (S2-omics) optimizes region-of-interest selection to capture molecular heterogeneity in diverse tissues v2
Smart spatial omics (S2-omics) optimizes region-of-interest selection to capture molecular heterogeneity in diverse tissues v2 Open
A protocol describing the application of S2-omics on a colorectal cancer tissue section, designing 10x VisiumHD experiment. S2-omics is an end-to-end workflow that automatically selects regions of interest for spatial omics experiments usi…
View article: Designing smart spatial omics experiments with S2-omics v2
Designing smart spatial omics experiments with S2-omics v2 Open
A protocol describing the application of S2-omics on a colorectal cancer tissue section, designing 10x VisiumHD experiment. S2-omics is an end-to-end workflow that automatically selects regions of interest for spatial omics experiments usi…
View article: Designing smart spatial omics experiments with S2-omics v1
Designing smart spatial omics experiments with S2-omics v1 Open
A protocol describing the application of S2-omics on a colorectal cancer tissue section, designing 10x VisiumHD experiment. S2-omics is an end-to-end workflow that automatically selects regions of interest for spatial omics experiments usi…
View article: Designing smart spatial omics experiments with S2Omics
Designing smart spatial omics experiments with S2Omics Open
Spatial omics technologies have transformed biomedical research by enabling high-resolution molecular profiling while preserving the native tissue architecture. These advances provide unprecedented insights into tissue structure and functi…
View article: Scaling up spatial transcriptomics for large-sized tissues: uncovering cellular-level tissue architecture beyond conventional platforms with iSCALE
Scaling up spatial transcriptomics for large-sized tissues: uncovering cellular-level tissue architecture beyond conventional platforms with iSCALE Open
Recent advances in spatial transcriptomics (ST) technologies have transformed our ability to profile gene expression while preserving crucial spatial context within tissues. However, existing ST platforms are constrained by high costs, lon…
View article: Segmentation Matters: Recognizing the Cell Segmentation Challenge in Spatial Transcriptomics
Segmentation Matters: Recognizing the Cell Segmentation Challenge in Spatial Transcriptomics Open
Probe-based in situ hybridization spatial transcriptomics has emerged as a state-of-the-art for neuroscience research. Accurate segmentation of neurons and non-neuronal cells, a critical step for downstream analysis, remains a big challeng…
View article: Comprehensive Multimodal Profiling of Atherosclerosis Reveals Bhlhe40 as a Potential Regulator of Vascular Smooth Muscle Cell Phenotypic Modulation
Comprehensive Multimodal Profiling of Atherosclerosis Reveals Bhlhe40 as a Potential Regulator of Vascular Smooth Muscle Cell Phenotypic Modulation Open
Background Vascular smooth muscle cells (VSMCs) play a central role in atherosclerosis by undergoing phenotypic modulation from a quiescent, contractile state to a range of synthetic phenotypes, including fibroblast-like, macrophage-like, …
View article: Author Correction: Resolving tissue complexity by multimodal spatial omics modeling with MISO
Author Correction: Resolving tissue complexity by multimodal spatial omics modeling with MISO Open
View article: Scaling up spatial transcriptomics for large-sized tissues: uncovering cellular-level tissue architecture beyond conventional platforms with iSCALE
Scaling up spatial transcriptomics for large-sized tissues: uncovering cellular-level tissue architecture beyond conventional platforms with iSCALE Open
Recent advances in spatial transcriptomics (ST) technologies have transformed our ability to profile gene expression while retaining the crucial spatial context within tissues. However, existing ST platforms suffer from high costs, long tu…
View article: Segmentation Matters: Cell Segmentation Challenge in Spatial Transcriptomics
Segmentation Matters: Cell Segmentation Challenge in Spatial Transcriptomics Open
View article: Leveraging deep single-soma RNA sequencing to explore the neural basis of human somatosensation
Leveraging deep single-soma RNA sequencing to explore the neural basis of human somatosensation Open
View article: Monocyte Single-Cell Multimodal Profiling in Cardiovascular Disease Risk States
Monocyte Single-Cell Multimodal Profiling in Cardiovascular Disease Risk States Open
BACKGROUND: Monocytes are a critical innate immune system cell type that serves homeostatic and immunoregulatory functions. They have been identified historically by the cell surface expression of CD14 and CD16. However, recent single-cell…
View article: Single-cell multi-omic and spatial profiling of human kidneys implicates the fibrotic microenvironment in kidney disease progression
Single-cell multi-omic and spatial profiling of human kidneys implicates the fibrotic microenvironment in kidney disease progression Open
View article: ADAMTS7 Promotes Smooth Muscle Cell Foam Cell Expansion in Atherosclerosis
ADAMTS7 Promotes Smooth Muscle Cell Foam Cell Expansion in Atherosclerosis Open
Human genetic studies have repeatedly associated SNPs near the gene ADAMTS7 with atherosclerotic cardiovascular disease. Subsequent investigations in mice demonstrated that ADAMTS7 is proatherogenic, induced in response to vascular injury,…
View article: Single-cell multimodal profiling of monocytes reveals diverse phenotypes and alterations linked to cardiovascular disease risks
Single-cell multimodal profiling of monocytes reveals diverse phenotypes and alterations linked to cardiovascular disease risks Open
Monocytes are a critical innate immune system cell type that serves homeostatic and immunoregulatory functions. The Cell surface expression of CD14 and CD16 has historically identified them, however, recent single-cell studies have uncover…
View article: Inferring super-resolution tissue architecture by integrating spatial transcriptomics with histology
Inferring super-resolution tissue architecture by integrating spatial transcriptomics with histology Open
View article: Single-cell multimodal profiling of atherosclerosis identifies CD200 as a cell surface lineage marker of vascular smooth muscle cells and their derived cells
Single-cell multimodal profiling of atherosclerosis identifies CD200 as a cell surface lineage marker of vascular smooth muscle cells and their derived cells Open
Vascular smooth muscle cells (VSMCs) play a central role in the development of atherosclerosis due in part to their capability to phenotypically transition into either a protective or harmful state. However, the ability to identify and tra…
View article: High-Dimensional Single-Cell Multimodal Landscape of Human Carotid Atherosclerosis
High-Dimensional Single-Cell Multimodal Landscape of Human Carotid Atherosclerosis Open
Background Atherosclerotic plaques are complex tissues composed of a heterogeneous mixture of cells. However, we have limited understanding of the comprehensive transcriptional and phenotypical landscape of the cells within these lesions. …
View article: Human Macrophage Long Intergenic Noncoding RNA, <i>SIMALR</i> , Suppresses Inflammatory Macrophage Apoptosis via NTN1 (Netrin-1)
Human Macrophage Long Intergenic Noncoding RNA, <i>SIMALR</i> , Suppresses Inflammatory Macrophage Apoptosis via NTN1 (Netrin-1) Open
Background: Long noncoding RNAs (lncRNAs) have emerged as novel regulators of macrophage biology and inflammatory cardiovascular diseases. However, studies focused on lncRNAs in human macrophage subtypes, particularly human lncRNAs that ar…
View article: Intravenous immunoglobulin prevents peripheral liver transduction of intrathecally delivered AAV vectors
Intravenous immunoglobulin prevents peripheral liver transduction of intrathecally delivered AAV vectors Open
View article: Treating Transthyretin Amyloidosis via Adeno-Associated Virus Vector Delivery of Meganucleases.
Treating Transthyretin Amyloidosis via Adeno-Associated Virus Vector Delivery of Meganucleases. Open
Transthyretin amyloidosis (ATTR) is a progressive and fatal disease caused by transthyretin (TTR) amyloid fibril accumulation in tissues, which disrupts organ function. As the TTR protein is primarily synthesized by the liver, liver transp…
View article: Spatially resolved human kidney multi-omics single cell atlas highlights the key role of the fibrotic microenvironment in kidney disease progression
Spatially resolved human kidney multi-omics single cell atlas highlights the key role of the fibrotic microenvironment in kidney disease progression Open
Kidneys possess one of the most intricate three-dimensional cellular structures in the body, yet the spatial and molecular principles of kidney health and disease remain inadequately understood. Here, we have generated high-quality dataset…
View article: Intravenous immunoglobulin prevents peripheral liver transduction of intrathecally delivered AAV vectors
Intravenous immunoglobulin prevents peripheral liver transduction of intrathecally delivered AAV vectors Open
View article: Intranasal gene therapy to prevent infection by SARS-CoV-2 variants
Intranasal gene therapy to prevent infection by SARS-CoV-2 variants Open
SARS-CoV-2 variants have emerged with enhanced pathogenicity and transmissibility, and escape from pre-existing immunity, suggesting first-generation vaccines and monoclonal antibodies may now be less effective. Here we present an approach…
View article: Intranasal gene therapy to prevent infection by SARS-CoV-2 variants
Intranasal gene therapy to prevent infection by SARS-CoV-2 variants Open
SARS-CoV-2 variants have emerged with enhanced pathogenicity and transmissibility, and escape from pre-existing immunity, suggesting first-generation vaccines and monoclonal antibodies may now be less effective. This manuscript demonstrate…
View article: Long-term stable reduction of low-density lipoprotein in nonhuman primates following in vivo genome editing of PCSK9
Long-term stable reduction of low-density lipoprotein in nonhuman primates following in vivo genome editing of PCSK9 Open
View article: Increasing the Specificity of AAV-Based Gene Editing through Self-Targeting and Short-Promoter Strategies
Increasing the Specificity of AAV-Based Gene Editing through Self-Targeting and Short-Promoter Strategies Open
View article: Adeno-Associated Virus-Induced Dorsal Root Ganglion Pathology
Adeno-Associated Virus-Induced Dorsal Root Ganglion Pathology Open
The administration of adeno-associated virus (AAV) vectors to nonhuman primates (NHP) via the blood or cerebrospinal fluid (CSF) can lead to dorsal root ganglion (DRG) pathology. The pathology is minimal to moderate in most cases; clinical…
View article: [Study of denoising of simultaneous electroencephalogram-functional magnetic resonance imaging signal based on real-time constrained independent components analysis].
[Study of denoising of simultaneous electroencephalogram-functional magnetic resonance imaging signal based on real-time constrained independent components analysis]. Open
Simultaneous recording of electroencephalogram (EEG)-functional magnetic resonance imaging (fMRI) plays an important role in scientific research and clinical field due to its high spatial and temporal resolution. However, the fusion result…
View article: Discussion of Potentially Sensitive Topics With Young People
Discussion of Potentially Sensitive Topics With Young People Open
OBJECTIVES: To identify modifiable factors that facilitate discussion of potentially sensitive topics between health care providers and young people at preventive service visits after Patient Protection and Affordable Care Act implementati…