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Search · four archives
26 papers · ranked by Valyu relevance
Getnet Molla Desta, Alemayehu Godana Birhanu
In recent years, significant advancements in biochemistry, materials science, engineering, and computer-aided testing have driven the development of high-throughput tools for profiling genetic information. Single-cell RNA sequencing (scRNA-seq) technologies have established themselves as key tools for dissecting…
Dylan Molho, Jiayuan Ding, Zhaoheng Li, Hongzhi Wen + 11 more
'Yixin Wang' 'Julian Venegas' 'Wei Jin' 'Renming Liu' 'Runze Su' 'Patrick Danaher' 'Robert Yang' 'Yu L. Lei' 'Yuying Xie' 'Jiliang Tang'] Single-cell technologies are revolutionizing the entire field of biology. The large volumes of data generated by single-cell technologies are high-dimensional, sparse, heterogeneous…
Nafiseh Erfanian, A. Ali Heydari, Pablo Iañez, Afshin Derakhshani + 5 more
Traditional bulk sequencing methods are limited to measuring the average signal in a group of cells, potentially masking heterogeneity, and rare populations. The single-cell resolution, however, enhances our understanding of complex biological systems and diseases, such as cancer, the immune system, and chronic…
Andrew Liao, Zehao Zhang, Andras Sziraki, Abdulraouf Abdulraouf + 4 more
Large-scale single-cell atlas efforts have revealed many aging-or disease-associated cell types, yet these populations are often underrepresented in heterogeneous tissues, limiting detailed molecular and dynamic analyses. To address this, we developed EnrichSci—a highly scalable, microfluidics-free platform that…
P. Marafini, DG. Smith, AR. Lamstaes, RE. Contreras + 22 more
Existing tools for single cell genomics require complex physical frameworks for the indexing of cellular nucleic acids, including proprietary instrumentation, droplet emulsions, and laborious combinatorial indexing schemes. The complexity and cost of these tools significantly constrains the use of single cell…
Maria A. Dimitriu, Irina Lazar-Contes, Martin Roszkowski, Isabelle M. Mansuy
'Isabelle M. Mansuy'] Recent advances in methods for single-cell analyses and barcoding strategies have led to considerable progress in research. The development of multiplexed assays offers the possibility to conduct parallel analyses of multiple factors and processes for comprehensive characterization of cellular and…
Haoxuan Luo, Ansar Hussain, Musavir Abbas, Lun Yuan + 5 more
Droplet-based single-cell RNA sequencing (scRNA-seq) has redefined biological research by resolving cellular heterogeneity with an unprecedented precision. This review synthesizes the technological evolution of the 10× Genomics Chromium platform, its Gel Bead-in-Emulsion (GEM)s technology, and end-to-end workflows…
Anna E. Elz, Derrik Gratz, Annalyssa Long, David Sowerby + 2 more
The rapid development of updated and new commercially available single-cell transcriptomics platforms provides users with a range of experimental options. Cost, sensitivity, throughput, flexibility, and ease of use, all influence the selection of an optimal workflow. We performed a comprehensive comparison of…
Hongfei Li, Jiechen Wang, Qing Liu, Quan Zou + 1 more
Joint profiling technologies combining single-cell chromatin accessibility (CA) and transcriptome sequencing enable cellular heterogeneity analysis from both gene and cis-regulatory element perspectives, greatly advancing molecular biology at a cellular resolution. These techniques have been used to construct gene…
Jafar Isbarov, Elmir Mahammadov
analysis Authors: ['Jafar Isbarov' 'Elmir Mahammadov'] Single-cell analysis is an increasingly relevant approach in "omics" studies. In the last decade, it has been applied to various fields, including cancer biology, neuroscience, and, especially, developmental biology. This rise in popularity has been accompanied…
Mahnoor N. Gondal -, Syed Hamad Hassan Shah, Arul M. Chinnaiyan, Marcin Cieslik
Rapid advancements in high-throughput single-cell RNA-seq (scRNA-seq) technologies and experimental protocols have led to the generation of vast amounts of genomic data that populates several online databases and repositories. Here, we systematically examined large-scale scRNA-seq databases, categorizing them based on…
Shuang Ge, Shuqing Sun, Huan Xu, Qiang Cheng + 1 more
Advances and Challenges from a Data Science Perspective Authors: ['Shuang Ge' 'Shuqing Sun' 'Huan Xu' 'Qiang Cheng' 'Zhixiang Ren'] The development of single-cell and spatial transcriptomics has revolutionized our capacity to investigate cellular properties, functions, and interactions in both cellular and spatial…
Su-Hyeon Lee, Junha Park, Byungjin Hwang
Single-cell technologies have undergone a significant transformation, expanding from their initial focus on transcriptomics to encompass a diverse range of modalities. Recent advancements have markedly improved scalability and reduced costs, facilitating the processing of larger cell populations and broadening the…
Hyeongseon Jeon, Juan Xie, Yeseul Jeon, Kyeong Joo Jung + 3 more
'Arkobrato Gupta' 'Won Chang' 'Dongjun Chung'] Gene expression profiling technologies have been used in various applications such as cancer biology. The development of gene expression profiling has expanded the scope of target discovery in transcriptomic studies, and each technology produces data with distinct…
Li Yao, Sagar R. Shah, Abdullah Ozer, Junke Zhang + 7 more
Biological systems exhibit remarkable heterogeneity, characterized by intricate interplay among diverse cell types. Resolving the regulatory processes of specific cell types is crucial for delineating developmental mechanisms and disease etiologies. While single-cell sequencing methods such as scRNA-seq and scATAC-seq…
Alvin Sheng, Sandra E. Safo, Thierry Chekouo
Recent advances in spatial transcriptomics have enabled researchers to profile gene expression at the single-cell spatial resolution, often for multiple tissue samples in a single study. This high-dimensional molecular profile for each cell can be used to sort cells into cell types with distinct functions, or segment…
Haiyue Bi, Xiaocheng Weng
The meticulous examination of the genomic, transcriptomic, epigenomic, and proteomic landscapes, conducted at the precise resolution of single cells, has emerged as an indispensable instrument for comprehending the inherent mechanisms governing cellular heterogeneity. These methodologies have provided unprecedented…
Louis Saddic, Giselle Kaneda, Amanda Momenzadeh, Lior Zilberberg + 7 more
Single-cell omics technology is a powerful tool in biomedical research. However, single cell proteomics has lagged due to an inability to amplify peptides in a similar fashion to nucleotide strings. Single cell proteomics is important because proteins are the main functional unit in cells, and they often poorly…
Gregory T. Booth, Riza M. Daza, Sanjay R. Srivatsan, José L. McFaline-Figueroa + 4 more
Single-cell chromatin accessibility has emerged as a powerful means of understanding the epigenetic landscape of diverse tissues and cell types, but profiling cells from many independent specimens is challenging and costly. Here we describe a novel approach, sciPlex-ATAC-seq, which uses unmodified DNA oligos as…
Kayleigh Casmey, Maria Zimmermann, Yuxin Xie, Sierra A. Codeluppi-Arrowsmith + 2 more
Single-cell omics technology has advanced rapidly since its inception, offering increasing precision, resolution, and technical diversity to explore cell-specific molecular features in the human brain and neuropsychiatric disorders. While traditional bulk genomic analyses have provided valuable insights into the…
Juerg Straubhaar, Alexandria D’Souza, Zachary Niziolek, Bogdan Budnik
Single-cell analysis has clearly established itself in biology and biomedical fields as an invaluable tool that allows one to comprehensively understand the relationship between cells, including their types, states, transitions, trajectories, and spatial position. Scientific methods such as fluorescence labeling…
Slavov, Nikolai
Over the last decade, proteomic analysis of single cells by mass spectrometry transitioned from an uncertain possibility to a set of robust and rapidly advancing technologies supporting the accurate quantification of thousands of proteins. We review the major drivers of this progress, from establishing feasibility to…
Authors not listed
Single-cell mass spectrometry (SCMS) has emerged as a powerful tool for analyzing metabolites in individual cells, including live cells. However, cell metabolites have rapid turnover rate, whereas maintaining metabolites’ profiles of live cells during sample transport, storage, or extended measurements can be…
Authors not listed
Desorption Electrospray Ionization Mass Spectrometry Imaging (DESI-MSI) is a powerful technique for molecular analysis of surfaces; however, its application of single cell studies has not been previously published. In the current work, a commercial DESI setup (DESI XS) coupled to a mass spectrometer was used to analyze…
Authors not listed
The WRN helicase has recently emerged as a promising therapeutic target for microsatellite instability (MSI)-high cancers. Here, we report LXW-P1, a potent WRN degrader derived from marine bromotyrosine alkaloids. Its molecular target was identified using an AI-guided, pathway-informed perturbation transcriptomics…
Authors not listed
The Single-probe is a multifunctional device that can be coupled to mass spectrometry (MS) for molecular analysis of microscale samples, such as single cells, tissue slices, and multicellular spheroids, under ambient conditions. In Single-probe single cell MS (SCMS) studies, this technique leverages direct sampling and…