A5101636050- Single-cell and spatial transcriptomics
- Cell Image Analysis Techniques
- Immune cells in cancer
- Ion-surface interactions and analysis
- Aquatic Ecosystems and Phytoplankton Dynamics
- Advanced biosensing and bioanalysis techniques
- Extracellular vesicles in disease
- AI in cancer detection
- Molecular Biology Techniques and Applications
- Inflammatory Bowel Disease
- Gene expression and cancer classification
- Brain Tumor Detection and Classification
- DNA and Nucleic Acid Chemistry
- Freshwater macroinvertebrate diversity and ecology
- Cutaneous Melanoma Detection and Management
- Gold and Silver Nanoparticles Synthesis and Applications
- Gut microbiota and health
- Aquatic Invertebrate Ecology and Behavior
- Machine Learning in Bioinformatics
- RNA modifications and cancer
- Advanced Neural Network Applications
- Colorectal Cancer Screening and Detection
- Medical Image Segmentation Techniques
- CAR-T cell therapy research
- Neurogenetic and Muscular Disorders Research
Stanford University
2019-2024
Tianjin University
2023-2024
Broad Institute
2024
Xi'an University of Architecture and Technology
2023
Urbana University
2020
University of Illinois Urbana-Champaign
2017-2020
To define the cellular composition and architecture of cutaneous squamous cell carcinoma (cSCC), we combined single-cell RNA sequencing with spatial transcriptomics multiplexed ion beam imaging from a series human cSCCs matched normal skin. cSCC exhibited four tumor subpopulations, three recapitulating epidermal states, tumor-specific keratinocyte (TSK) population unique to cancer, which localized fibrovascular niche. Integration data mapped ligand-receptor networks specific types, revealing...
Highly multiplexed protein imaging is emerging as a potent technique for analyzing distribution within cells and tissues in their native context. However, existing cell annotation methods utilizing high-plex spatial proteomics data are resource intensive necessitate iterative expert input, thereby constraining scalability practicality extensive datasets. We introduce MAPS (Machine learning Analysis of Proteomics Spatial biology), machine approach facilitating rapid precise type...
Abstract Immune checkpoint inhibition (ICI) has fundamentally changed cancer treatment. However, only a minority of patients with metastatic triple negative breast (TNBC) benefit from ICI, and the determinants response remain largely unknown. To better understand factors influencing patient outcome, we assembled longitudinal cohort tissue multiple timepoints, including primary tumor, pre-treatment on-treatment tumor 117 treated ICI (nivolumab) in phase II TONIC trial. We used highly...
Glucose is a universal bioenergy source; however, its role in controlling protein interactions unappreciated, as are actions during differentiation-associated intracellular glucose elevation. Azido-glucose click chemistry identified binding to variety of RNA proteins (RBPs), including the DDX21 helicase, which was found be essential for epidermal differentiation. bound ATP-binding domain DDX21, altering conformation, inhibiting helicase activity, and dissociating dimers. elevation...
Abstract The ability to align individual cellular information from multiple experimental sources is fundamental for a systems-level understanding of biological processes. However, currently available tools are mainly designed single-cell transcriptomics matching and integration, generally rely on large number shared features across datasets cell matching. This approach underperforms when applied proteomic due the limited parameters simultaneously accessed lack markers these experiments....
Multiplex imaging technologies are now routinely capable of measuring more than 40 antibody-labeled parameters in single cells. However, lateral spillage signals densely packed tissues presents an obstacle to the assignment high-dimensional spatial features individual cells for accurate cell-type annotation. We devised a method correct cell surface markers between adjacent termed REinforcement Dynamic Spillover EliminAtion (REDSEA). The use REDSEA decreased contaminating from neighboring It...
We describe the preparation of cross-linked, polymeric organic nanoparticles (ONPs) with a single, covalently linked DNA strand. The structure and functionalities ONPs are controlled by synthesis their parent linear block copolymers that provide monovalency, fluorescence narrow size distribution. ONP can also guide deposition chloroaurate ions allowing gold (AuNPs) to be prepared using as templates. strand on AuNPs is shown preserve its functions.
The intricate and dynamic interactions between the host immune system its microbiome constituents undergo shifts in response to perturbations intestinal tissue environment. Our ability study these events on systems level is significantly limited by
Brain tumor segmentation is a key step in brain cancer diagnosis. Segmentation of sub-regions, including necrotic, enhancing, and edematous regions, can provide more detailed guidance for clinical Weakly supervised methods have received much attention because they do not require time-consuming pixel-level annotations. However, existing weakly focus on the entire region while ignoring challenging task multi-label sub-regions. In this article, we propose approach to solve problem. To best our...
Highly multiplexed protein imaging is emerging as a potent technique for analyzing distribution within cells and tissues in their native context. However, existing cell annotation methods utilizing high-plex spatial proteomics data are resource intensive necessitate iterative expert input, thereby constraining scalability practicality extensive datasets. We introduce MAPS ( M achine learning A nalysis of P roteomics S patial biology), machine approach facilitating rapid precise type...
DNA–nanoparticle conjugates can be synthesized with independent control over size, valence and elemental composition using a template-based strategy.
The ability to align individual cellular information from multiple experimental sources, techniques and systems is fundamental for a true systems-level understanding of biological processes. While single-cell transcriptomic studies have transformed our appreciation the complexities contributions diverse cell types disease, they can be limited in their assess protein-level phenotypic beyond. Therefore, matching integrating datasets which utilize robust protein measurements across modalities...
Multiplexed ion beam imaging (MIBI) has been previously used to profile multiple parameters in two dimensions single cells within tissue slices. Here, a mathematical and technical framework for three-dimensional subcellular MIBI is presented. We term the approach tomography (IBT) wherein images are acquired iteratively across successive, scans later compiled into 3D format. For IBT, were imaged at 0.2-4 pA current 1,000 axial scans. Consecutive subsets of binned over 3 20 slices (above...
Cell population delineation and identification is an essential step in single-cell spatial-omics studies. Spatial-omics technologies can simultaneously measure information from three complementary domains related to this task: expression levels of a panel molecular biomarkers at resolution, relative positions cells, images tissue sections, but existing computational methods for performing task on datasets often relinquish one or more domains. The additional reliance the availability "atlas"...
The subcellular localization of a protein is important for its function and interaction with other molecules, mislocalization linked to numerous diseases. While atlas-scale efforts have been made profile across various cell lines, existing datasets only contain limited pairs proteins lines which do not cover all human proteins. We present method that uses both sequences cellular landmark images perform
The Segment Anything Model 2 (SAM2) has recently demonstrated exceptional performance in zero-shot prompt segmentation for natural images and videos. However, it faces significant challenges when applied to medical images. Since its release, many attempts have been made adapt SAM2's capabilities the imaging domain. These efforts typically involve using a substantial amount of labeled data fine-tune model's weights. In this paper, we explore SAM2 from different perspective via making full use...
A shift in reservoir stratification and mixing significantly affects the water column ecosystem, which turn leads to changes phytoplankton abundance community structure. To explore effects of on structure a diversion reservoir, 1-year survey was divided into period 2020, 2021, redundancy analysis (RDA), variance partitioning (VPA) Pearson correlation were used analyse key drivers affecting functional groups, using Xikeng Reservoir as case study. During study period, 8 phyla, 69 genera 9...