25 papers · ranked by Valyu relevance
Ting Zhang, Antony R. Warden, Yiyang Li, Xianting Ding
Recently emerged mass cytometry (cytometry by time-of-flight [CyTOF]) technology permits the identification and quantification of inherently diverse cellular systems, and the simultaneous measurement of functional attributes at the single-cell resolution. By virtue of its multiplex ability with limited need for…
Ramy Gadalla, Babak Noamani, Bethany L. MacLeod, Russell J. Dickson + 13 more
'Mengdi Guo' 'Wenxi Xu' 'Sabelo Lukhele' 'Heidi J. Elsaesser' 'Albiruni R. Abdul Razak' 'Naoto Hirano' 'Tracy L. McGaha' 'Ben Wang' 'Marcus Butler' 'Cynthia J. Guidos' 'Pam S. Ohashi' 'Lillian L. Siu' 'David G. Brooks'] Flow cytometry is a widely applied approach for exploratory immune profiling and biomarker discovery…
Yuqiu Yang, Kaiwen Wang, Zeyu Lu, Tao Wang + 1 more
Cytometry by time-of-flight (CyTOF) is a proteomic analysis technique capable of providing information on millions of cells. Along with technological development, researchers have devised many data analysis tools to offer deeper insights into the CyTOF data at the single-cell level. However, objective evaluations of…
Weiyang Tao, Anirban Sinha, Khadir Raddassi, Aridaman Pandit
High-dimensional cell phenotyping is a powerful tool to study molecular and cellular changes in health and diseases. CyTOF enables high-dimensional cell phenotyping using tens of surface and intra-cellular markers. To utilize the full potential of CyTOF, we need advanced clustering and machine learning methodologies to…
Yuqiu Yang, Kaiwen Wang, Zeyu Lu, Tao Wang + 1 more
Recently, many analysis tools have been devised to offer insights into data generated via cytometry by time-of-flight (CyTOF). However, objective evaluations of these methods remain absent as most evaluations are conducted against real data where the ground truth is generally unknown. In this paper, we develop…
Kaiwen Wang, Yuqiu Yang, Fangjiang Wu, Bing Song + 2 more
While experimental and informatic techniques around single cell sequencing (scRNA-seq) are advanced, research around mass cytometry (CyTOF) data analysis has severely lagged behind. However, CyTOF profiles the proteomics makeup of single cells and is much more relevant for investigation of disease phenotypes than…
Dimitrios N. Sidiropoulos, Genevieve L. Stein-O’Brien, Ludmila Danilova, Nicole E. Gross + 8 more
'Ludmila Danilova' 'Nicole E. Gross' 'Soren Charmsaz' 'Stephanie Xavier' 'James Leatherman' 'Hao Wang' 'Mark Yarchoan' 'Elizabeth M. Jaffee' 'Elana J. Fertig' 'Won Jin Ho'] Mass cytometry, or cytometry by TOF (CyTOF), provides a robust means of determining protein-level measurements of more than 40 markers…
Kaiwen Wang, Yuqiu Yang, Fangjiang Wu, Bing Song + 2 more
'Tao Wang'] While experimental and informatic techniques around single cell sequencing (scRNA-seq) are advanced, research around mass cytometry (CyTOF) data analysis has severely lagged behind. CyTOF data are notably different from scRNA-seq data in many aspects. This calls for the evaluation and development of…
Julia Casado, Oskari Lehtonen, Ville Rantanen, Katja Kaipio + 7 more
Single-cell proteomics technologies, such as mass cytometry, have enabled characterization of cell-to-cell variation and cell populations at a single cell resolution. These large amounts of data, however, require dedicated, interactive tools for translating the data into knowledge. We present a comprehensive…
Isaac Robinson, Emma Pierce‐Hoffman
t-SNE and hierarchical clustering are popular methods of exploratory data analysis, particularly in biology. Building on recent advances in speeding up t-SNE and obtaining finer-grained structure, we combine the two to create tree-SNE, a hierarchical clustering and visualization algorithm based on stacked…
Arthur Lui, Ju‐Hee Lee, Peter F. Thall, May Daher + 2 more
'Rafet Barar'] A Bayesian feature allocation model (FAM) is presented for identifying cell subpopulations based on multiple samples of cell surface or intracellular marker expression level data obtained by cytometry by time of flight (CyTOF). Cell subpopulations are characterized by differences in expression patterns…
Joshua Scurll
Clustering and visualizing high-dimensional (HD) data are important tasks in a variety of fields. For example, in bioinformatics, they are crucial for analyses of single-cell data such as mass cytometry (CyTOF) data. Some of the most effective algorithms for clustering HD data are based on representing the data by…
Ruolan Deng, Yi-Lan Li, Ji-Long Liu
CTP synthase (CTPS) forms cytoophidia in all three domains of life. Here we focus on the function of cytoophidia in cell proliferation using Schizosaccharomyces pombe as a model system. We find that converting His^359^ of CTPS into Ala^359^ leads to cytoophidium disassembly. By reducing the level of CTPS protein or…
Xiao-Jing Liu, Yi-Lan Li, Shu-Yu Pang, Ji-Long Liu + 1 more
Cytoophidia are filamentous structures composed of CTP synthase (CTPS) and were initially discovered in ovarian cells of Drosophila. As a highly conserved membraneless organelle present across all three domains of life, cytoophidia display dynamic behaviors that are crucial for cellular homeostasis and function.…
Ruolan Deng, Yi-Lan Li, Ji-Long Liu
The de novo synthesis of cytidine 5’-triphosphate (CTP) is catalyzed by the enzyme CTP synthase (CTPS), which is known to form cytoophidia across all three domains of life. In this study, we use the budding yeast Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe as model organisms to compare…
Rui-Yu Weng, Lei Zhang, Ji-Long Liu
CTP synthase (CTPS), the rate-limiting enzyme in de novo synthesis of CTP, assembles into filamentous structures termed cytoophidia. Here we study the impact of Hippo pathway on the posterior follicle cells (PFCs) in Drosophila egg chambers. We find that the inactivation of Hippo pathway correlates with a reduction in…
Suvechhya Lamichhane, Rupak Timalsina, Cody Schultz, Ilja Fescenko + 4 more
'Kapildeb Ambal' 'S. H. Liou' 'Rebecca Y. Lai' 'Abdelghani Laraoui'] ABSTRACT: Nitrogen-vacancy (NV) magnetometry offers an alternative tool to detect iron levels in neurons and cells with a favorable combination of magnetic sensitivity and spatial resolution. Here we employ NV-T1 relaxometry to detect Fe in cytochrome…
Paul C. Bressloff
In this paper we develop a directional search-and-capture model of cytoneme-based morphogenesis. We consider a single cytoneme nucleating from a source cell and searching for a set of N target cells Ωk ⊂ Rd, k = 1, . . . , N, with d ≥ 2. We assume that each time the cytoneme nucleates, it grows in a random direction so…
Authors not listed
In this study, we reveal a long-standing mechanistic conundrum of the functions of two very similar isozymes, CYP1A1 and CYP1A2, that possess nearly identical active-site architectures yet display a perplexing difference in their reactivity toward the flavonoid α- naphthoflavone (ANF). CYP1A1 efficiently catalyses…
Davide Cardella, Louis Yu Pan Luk, Yu-Hsuan Tsai
Despite continuous advances, anticancer therapy still faces several technical hurdles such as selectivity on cellular and subcellular targets of therapeutics. Toward addressing these limitations, we have combined the use of proapoptotic peptides, cyanine dyes and folate to target the mitochondria of tumor cells. Hence…
Authors not listed
Tubulins are among the most successful targets for cancer chemotherapy. However, the emergence of drug resistance stimulates the continuous search for novel chemotherapeutics. Here, we discover that coumarin-30, a widely available laser dye, binds to the colchicine site of tubulin and inhibits microtubule dynamics and…
Simone Scalise, Giorgio Gosti, G. Ruocco, Giovanna Peruzzi + 1 more
'Mattia Miotto'] > The ability of a cancer cell population to achieve heterogeneity in their phenotype distributions offers advantages in tumor invasiveness and drug resistance. Studying the mechanisms behind such observed heterogeneity in mammalian cells presents challenges due for instance to the prolonged…
Authors not listed
Fluorescent dye-loaded polymeric nanoparticles have been extensively developed for cellular imaging as they are bright and versatile tools with large choice of polymers, dyes and surface chemistry. Here, we report preparation of fluorescent polymeric nanomaterials with high aspect ratio – nanorods, and study their…
Authors not listed
Celastrol, a potent natural triterpene which acted as a neuroprotective agent and was isolated from Celastrus paniculatus Willd. roots. Neuroblastoma (SH-SY5Y) cells play very important role in the study and observation of the neuroprotective effect of the isolated compound Celastrol, neuroblastoma cells have been used…
Authors not listed
Activatable small-molecule probes (ASMPs) enable dynamic biomarker visualization, yet nonspecific sequestration in hydrophobic protein microdomains compromises imaging fidelity. To address this, herein, a size-defined tetrahedral DNA framework (TDF) directs the interior encapsulation of an ASMP to fabricate a DNA…