Search Results - "Cang, Zixuan"

Inferring spatial and signaling relationships between cells from single cell transcriptomic data by Cang, Zixuan, Nie, Qing

“…Single-cell RNA sequencing (scRNA-seq) provides details for individual cells; however, crucial spatial information is often lost. We present SpaOTsc, a method…”
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TopologyNet: Topology based deep convolutional and multi-task neural networks for biomolecular property predictions by Cang, Zixuan, Wei, Guo-Wei

“…Although deep learning approaches have had tremendous success in image, video and audio processing, computer vision, and speech recognition, their applications…”
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Representability of algebraic topology for biomolecules in machine learning based scoring and virtual screening by Cang, Zixuan, Mu, Lin, Wei, Guo-Wei

“…This work introduces a number of algebraic topology approaches, including multi-component persistent homology, multi-level persistent homology, and…”
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A topology-based network tree for the prediction of protein–protein binding affinity changes following mutation by Wang, Menglun, Cang, Zixuan, Wei, Guo-Wei

“…The ability to predict protein–protein interactions is crucial to our understanding of a wide range of biological activities and functions in the human body,…”
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Identifying multicellular spatiotemporal organization of cells with SpaceFlow by Ren, Honglei, Walker, Benjamin L., Cang, Zixuan, Nie, Qing

“…One major challenge in analyzing spatial transcriptomic datasets is to simultaneously incorporate the cell transcriptome similarity and their spatial…”
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A review of mathematical representations of biomolecular data by Nguyen, Duc Duy, Cang, Zixuan, Wei, Guo-Wei

“…Recently, machine learning (ML) has established itself in various worldwide benchmarking competitions in computational biology, including Critical Assessment…”
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Defining Epidermal Basal Cell States during Skin Homeostasis and Wound Healing Using Single-Cell Transcriptomics by Haensel, Daniel, Jin, Suoqin, Sun, Peng, Cinco, Rachel, Dragan, Morgan, Nguyen, Quy, Cang, Zixuan, Gong, Yanwen, Vu, Remy, MacLean, Adam L., Kessenbrock, Kai, Gratton, Enrico, Nie, Qing, Dai, Xing

“…Our knowledge of transcriptional heterogeneities in epithelial stem and progenitor cell compartments is limited. Epidermal basal cells sustain cutaneous tissue…”
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DEEPsc: A Deep Learning-Based Map Connecting Single-Cell Transcriptomics and Spatial Imaging Data by Maseda, Floyd, Cang, Zixuan, Nie, Qing

“…Single-cell RNA sequencing (scRNA-seq) data provides unprecedented information on cell fate decisions; however, the spatial arrangement of cells is often lost…”
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Deciphering tissue structure and function using spatial transcriptomics by Walker, Benjamin L., Cang, Zixuan, Ren, Honglei, Bourgain-Chang, Eric, Nie, Qing

“…The rapid development of spatial transcriptomics (ST) techniques has allowed the measurement of transcriptional levels across many genes together with the…”
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Single-cell transcriptomic analysis of zebrafish cranial neural crest reveals spatiotemporal regulation of lineage decisions during development by Tatarakis, David, Cang, Zixuan, Wu, Xiaojun, Sharma, Praveer P., Karikomi, Matthew, MacLean, Adam L., Nie, Qing, Schilling, Thomas F.

“…Neural crest (NC) cells migrate throughout vertebrate embryos to give rise to a huge variety of cell types, but when and where lineages emerge and their…”
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A multiscale model via single-cell transcriptomics reveals robust patterning mechanisms during early mammalian embryo development by Cang, Zixuan, Wang, Yangyang, Wang, Qixuan, Cho, Ken W Y, Holmes, William, Nie, Qing

“…During early mammalian embryo development, a small number of cells make robust fate decisions at particular spatial locations in a tight time window to form…”
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A Study of Gene Expression, Structure, and Contractility of iPSC-Derived Cardiac Myocytes from a Family with Heart Disease due to LMNA Mutation by Mehrabi, Mehrsa, Morris, Tessa A., Cang, Zixuan, Nguyen, Cecilia H. H., Sha, Yutong, Asad, Mira N., Khachikyan, Nyree, Greene, Taylor L., Becker, Danielle M., Nie, Qing, Zaragoza, Michael V., Grosberg, Anna

“…Genetic mutations to the Lamin A/C gene ( LMNA ) can cause heart disease, but the mechanisms making cardiac tissues uniquely vulnerable to the mutations remain…”
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LMNA -Related Dilated Cardiomyopathy: Single-Cell Transcriptomics during Patient-Derived iPSC Differentiation Support Cell Type and Lineage-Specific Dysregulation of Gene Expression and Development for Cardiomyocytes and Epicardium-Derived Cells with Lamin A/C Haploinsufficiency by Zaragoza, Michael V, Bui, Thuy-Anh, Widyastuti, Halida P, Mehrabi, Mehrsa, Cang, Zixuan, Sha, Yutong, Grosberg, Anna, Nie, Qing

“…-related dilated cardiomyopathy (DCM) is an autosomal-dominant genetic condition with cardiomyocyte and conduction system dysfunction often resulting in heart…”
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A mathematical method and software for spatially mapping intercellular communication

“…Communication between cells is crucial for coordinated cellular functions in multicellular organisms. We present an optimal transport theory-based tool to…”
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Topological and geometric analysis of cell states in single-cell transcriptomic data by Huynh, Tram, Cang, Zixuan

“…Single-cell RNA sequencing (scRNA-seq) enables dissecting cellular heterogeneity in tissues, resulting in numerous biological discoveries. Various…”
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Analysis and prediction of protein folding energy changes upon mutation by element specific persistent homology by Cang, Zixuan, Wei, Guo-Wei

“…Site directed mutagenesis is widely used to understand the structure and function of biomolecules. Computational prediction of mutation impacts on protein…”
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Integration of element specific persistent homology and machine learning for protein‐ligand binding affinity prediction by Cang, Zixuan, Wei, Guo‐Wei

“…Protein‐ligand binding is a fundamental biological process that is paramount to many other biological processes, such as signal transduction, metabolic…”
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The landscape of cell–cell communication through single-cell transcriptomics by Almet, Axel A., Cang, Zixuan, Jin, Suoqin, Nie, Qing

“…Cell–cell communication is a fundamental process that shapes biological tissue. Historically, studies of cell–cell communication have been feasible for one or…”
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Screening cell–cell communication in spatial transcriptomics via collective optimal transport by Cang, Zixuan, Zhao, Yanxiang, Almet, Axel A., Stabell, Adam, Ramos, Raul, Plikus, Maksim V., Atwood, Scott X., Nie, Qing

“…Spatial transcriptomic technologies and spatially annotated single-cell RNA sequencing datasets provide unprecedented opportunities to dissect cell–cell…”
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Protein pocket detection via convex hull surface evolution and associated Reeb graph by Zhao, Rundong, Cang, Zixuan, Tong, Yiying, Wei, Guo-Wei

“…Abstract Motivation Protein pocket information is invaluable for drug target identification, agonist design, virtual screening and receptor-ligand binding…”
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