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…
Stefan Semrau
Since the discovery of cells by Robert Hooke and Antoni van Leeuwenhoek in the 17th century, thousands of different cell types have been identified, most recently by sequencing-based single-cell profiling techniques. Yet, for many organisms we still do not know, how many different cell types they are precisely composed…
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…
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…
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…
Yuriy A. Karetin, Juan Riesgo-Escovar
A comprehensive statistical analysis using a wide range of linear and non-linear morphological parameters enabled identification of the main stages in the in vitro dynamics of cell behavior of immune cells of the marine invertebrate Asterias amurensis (Echinodermata, Asteroidea). Three stages may be distinguished in…
Yuanxiao Gao, Román Zapién-Campos, Yuriy Pichugin, Arne Traulsen
The specialization of cells is a hallmark of complex multicellularity. Cell differentiation enables the emergence of specialized cell types that carry out separate functions previously executed by a multifunctional ancestor cell. One view is that initial cell differentiation occurred randomly, especially for…
Wei Zhang, Xianglin Zhang, Qiao Liu, Lei Wei + 4 more
In recent years, computational methods for quantifying cell type proportions from transcription data have gained significant attention, particularly those reference-based methods which have demonstrated high accuracy. However, there is currently a lack of comprehensive evaluation and guidance for available…
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…
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…
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…
Claude Lambert
It is good to see that the Journal of Clinical Medicine has recently published several good papers, highlighting the special input of cell analysis using flow cytometry. These papers use flow cytometry in a very wide field, from very small cell-derived particles to huge cells, such as myocytes, and different detection…
Matthew Smart, Anton Zilman
Multicellular organisms comprise a diverse collection of stable tissues built from different cell types. It remains unclear how large numbers of interacting cells can precisely coordinate their gene expression during tissue self-organization. We develop a generalized model of multicellular gene expression that includes…
Elena Emili, Alberto Pérez-Posada, Virginia Vanni, David Salamanca-Díaz + 3 more
'David Salamanca-Díaz' 'Dianalí Ródriguez-Fernández' '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…
Caroline Högel-Starck, Veera A. Timonen, Gantugs Atarsaikhan, Isabel Mogollon + 17 more
Recent molecular profiling and phenotyping methods combined with machine learning based analyses enable genotype-phenotype discovery at an unprecedented scale. The challenge now lies in unraveling the biological mechanisms underpinning these associations. High content imaging is a cost-effective approach for…
Yeganeh Madadi, Aboozar Monavarfeshani, Hao Chen, W. Daniel Stamer + 2 more
'Robert W. Williams' 'Siamak Yousefi'] Abstract—Single-cell RNA sequencing (scRNA-seq) provides a high throughput, quantitative and unbiased framework for scientists in many research fields to identify and characterize cell types within heterogeneous cell populations from various tissues. However, scRNA-seq based…
Davey Plugers, Kunihiko Kaneko
feedback Authors: ['Davey Plugers' 'Kunihiko Kaneko'] In multi-cellular organisms, cells differentiate into multiple types as they divide. States of these cell types, as well as their numbers, are known to be robust to external perturbations; as conceptualized by Waddington's epigenetic landscape where cells embed…
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…
Kalki Kukreja, Nikit Patel, Sean G Megason, Allon M Klein
As tissues develop, cells divide and differentiate concurrently. Conflicting evidence shows that cell division is either dispensable or required for formation of cell types. To determine the role of cell division in differentiation, we arrested the cell cycle in zebrafish embryos using two independent approaches and…
Authors not listed
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…
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…
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…
Aslan Kamil Mahmut, Fourneaux Camille, Yilmaz Alperen, Stavros Stavrakis + 5 more
Cell lineage tracking is a long-standing and unresolved problem in biology. Microfluidic technologies have the potential to address this problem, by virtue of their ability to manipulate and process single-cells in a rapid, controllable and efficient manner. Indeed, when coupled with traditional imaging approaches…
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…