25 papers · ranked by Valyu relevance
Tanya T Karagiannis, Stefano Monti, Paola Sebastiani
Changes of cell type composition across samples can carry biological significance and provide insight into disease and other conditions. Single cell transcriptomics has made it possible to study cell type composition at a fine resolution. Most single cell studies investigate compositional changes between samples for…
David Osumi-Sutherland, Chuan Xu, Maria Keays, Adam P. Levine + 4 more
'Peter V. Kharchenko' 'Aviv Regev' 'Ed S. Lein' 'Sarah A. Teichmann'] Massive single-cell profiling efforts have accelerated our discovery of the cellular composition of the human body, while at the same time raising the need to formalise this new knowledge. Here, we review current cell ontology efforts to harmonise…
Brian D. Aevermann, Mark Novotny, Trygve Bakken, Jeremy A. Miller + 5 more
Cells are fundamental functional units of multicellular organisms, with different cell types playing distinct physiological roles in the body. The recent advent of single cell transcriptional profiling using RNA sequencing is producing “big data”, enabling the identification of novel human cell types at an…
Patrick S. Stumpf, Fumio Arai, Ben D. MacArthur
Modern single cell experiments have revealed unexpected heterogeneity in apparently functionally ‘pure’ cell populations. However, we are still lacking a conceptual framework to understand this heterogeneity. Here, we propose that cellular memories – the ability of individual cells to record their developmental past…
Orr Levy, Shubham Tripathi, Scott D. Pope, Yang Y. Liu + 1 more
'Ruslan Medzhitov'] The diversity of gene expression plays a critical role in cellular specialization, adaptation to environmental changes, and overall cell functionality. This diversity varies dramatically across different cell types and is orchestrated by intricate, dynamic, and cell type-specific gene regulatory…
Patrick Günther, Joachim L. Schultze
The myeloid cell system shows very high plasticity, which is crucial to quickly adapt to changes during an immune response. From the beginning, this high plasticity has made cell type classification within the myeloid cell system difficult. Not surprising, naming schemes have been frequently changed. Recent…
Bradly Alicea
Cell type (e.g. pluripotent cell, fibroblast) is the end result of many complex processes that unfold due to evolutionary, developmental, and transformational stimuli. A cell's phenotype and the discrete, a priori states that define various cell subtypes (e.g. skin fibroblast, embryonic stem cell) are ultimately part…
Atsushi Kamimura, Kunihiko Kaneko
All life, including cells and artificial protocells, must integrate diverse molecules into a single unit in order to reproduce. Despite expected pressure to evolve a simple system with the fastest replication speed, the mechanism by which the use of the great variety of components, and the coexistence of diverse…
Siddhartha G. Jena, Archit Verma, Barbara E. Engelhardt
Genomics methods have uncovered patterns in a range of biological systems, but obscure important aspects of cell behavior: the shape, relative locations of, movement of, and interactions between cells in space. Spatial technologies that collect genomic or epigenomic data while preserving spatial information have begun…
Mark Szczelkun, Anna M. Ranzoni, Paulina M. Strzelecka, Ana Cvejic
'Ana Cvejic'] The blood and immune system are characterised by utmost diversity in its cellular components. This heterogeneity can solely be resolved with the application of single-cell technologies that enable precise examination of cell-to-cell variation. Single-cell transcriptomics is continuously pushing forward…
Daniel Osorio, Xue Yu, Yan Zhong, Guanxun Li + 4 more
Because of recent technological developments, single-cell assays such as single-cell RNA sequencing (scRNA-seq) have become much more widely available and have achieved unprecedented resolution in revealing cell heterogeneity. The extent of intrinsic cell-to-cell variability in gene expression, or single cell…
Niko Komin, Alexander Skupin
Cellular heterogeneity is an immanent property of biological systems that covers very different aspects of life ranging from genetic diversity to cell-to-cell variability driven by stochastic molecular interactions, and noise induced cell differentiation. Here, we review recent developments in characterizing cellular…
Ángel-Carlos Román, Alba Diaz-Pizarro, Nuria Del Valle-Del Pino, Marcos Olivera-Gómez + 4 more
In multicellular organisms, various cells perform distinct physiological and structural roles. Traditionally, cell identity has been defined through morphological features and molecular markers, but these methods have limitations. Our study explores the potential of subcellular morphology to define cellular identity…
Anca F. Savulescu, Caron Jacobs, Yutaka Negishi, Laurianne Davignon + 1 more
'Musa M. Mhlanga'] Mammalian cells display a broad spectrum of phenotypes, morphologies, and functional niches within biological systems. Our understanding of mechanisms at the individual cellular level, and how cells function in concert to form tissues, organs and systems, has been greatly facilitated by centuries of…
Sahand Amini, Jeffrey J. Doyle, Marc Libault
In 1665 Robert Hooke, looking at cork through his microscope, discovered that plants are composed of elementary structures he named “cells”. Variation in the expression of a single genome in a complex eukaryotic organism guides the initiation, maturation, physiology, and biochemistry of cells with different shapes and…
Aviv Regev, Sarah A. Teichmann, Eric S. Lander, Ido Amit + 54 more
The recent advent of methods for high-throughput single-cell molecular profiling has catalyzed a growing sense in the scientific community that the time is ripe to complete the 150-year-old effort to identify all cell types in the human body, by undertaking a Human Cell Atlas Project as an international collaborative…
Ian A. Hatton, Eric D. Galbraith, Nono S. C. Merleau, Teemu P. Miettinen + 2 more
'Teemu P. Miettinen' 'Benjamin McDonald Smith' 'Jeffery A. Shander'] Title: Significance A consistent and comprehensive quantitative framework of the cells in the human body could benefit many areas of biology. We compile data to estimate cell mass, size range, and cell count for some 1,200 cell groups, from the…
Elena Emili, Alberto Pérez-Posada, Maria D. Christodoulou, Jordi Solana
Allometry explores the relationship between an organism’s body size and its various components, offering insights into ecology, physiology, metabolism, and disease. The cell is the basic unit of biological systems, and yet, the study of cell type allometry remains relatively unexplored. Single-cell RNA sequencing…
Ezgi Dursun, Max Endele, Andrea Musumeci, Henrik Failmezger + 4 more
'Shu-Hung Wang' 'Achim Tresch' 'Timm Schroeder' 'Anne B. Krug'] Functionally distinct plasmacytoid and conventional dendritic cells (pDC and cDC) shape innate and adaptive immunity. They are derived from common dendritic cell progenitors (CDPs) in the murine bone marrow, which give rise to CD11c+ MHCII− precursors with…
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…
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Vertex models have been established as powerful tools for the cell-based simulation of epithelial tissues as they allow a detailed description of their mechanical development with respect to the properties of individual cells. Thus, they suit the challenges of simulating intestinal organoids which arise from the…
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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…
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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…
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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…
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RNA droplets assembled from co-transcriptionally folded nanostructures have recently emerged as a promising platform for constructing protocells and minimal synthetic cell models. In these systems, a custom-designed DNA template encodes an RNA nanostar, which is produced by transcription and self-assembles into…