23 papers · ranked by Valyu relevance
Mohammad Shifat‐E‐Rabbi, Xuwang Yin, Cailey E. Fitzgerald, Gustavo K. Rohde
'Gustavo K. Rohde'] Cell image classification methods are currently being used in numerous applications in cell biology and medicine. Applications include understanding the effects of genes and drugs in screening experiments, understanding the role and subcellular localization of different proteins, as well as…
Matthew N. Bernstein, Zhongjie Ma, Michael Gleicher, Colin N. Dewey
Cell type annotation is a fundamental task in the analysis of single-cell RNA-sequencing data. In this work, we present CellO, a machine learning-based tool for annotating human RNA-seq data with the Cell Ontology. CellO enables accurate and standardized cell type classification by considering the rich hierarchical…
Yulia Panina, Peter Karagiannis, Andreas Kurtz, Glyn N. Stacey + 1 more
In modern biology, the correct identification of cell types is required for the developmental study of tissues and organs and the production of functional cells for cell therapies and disease modeling. For decades, cell types have been defined on the basis of morphological and physiological markers and, more recently…
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…
Sheng Wang, Angela Oliveira Pisco, Jim Karkanias, Russ B. Altman
Single cell technologies have rapidly generated an unprecedented amount of data that enables us to understand biological systems at single-cell resolution. However, analyzing datasets generated by independent labs remains challenging due to a lack of consistent terminology to describe cell types. Here, we present…
Konstantinos Zormpas‐Petridis, Henrik Failmezger, Ioannis Roxanis, Matthew Blackledge + 2 more
'Matthew Blackledge' 'Yann Jamin' 'Yinyin Yuan'] The spectacular response observed in clinical trials of immunotherapy in patients with previously uncurable Melanoma, a highly aggressive form of skin cancer, calls for a better understanding of the cancer-immune interface. Computational pathology provides a unique…
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…
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…
Inna Tabansky, Joel N. H. Stern, Donald W. Pfaff
Here, we propose a new approach to defining nerve “cell types” in reaction to recent advances in single cell analysis. Among cells previously thought to be equivalent, considerable differences in global gene expression and biased tendencies among differing developmental fates have been demonstrated within multiple…
Darlington Ahiale Akogo, Vincent Appiah, Xavier‐Lewis Palmer
Computer Vision for Analyzing and Classifying cells and tissues often require rigorous lab procedures and so automated Computer Vision solutions have been sought. Most work in such field usually requires Feature Extractions before the analysis of such features via Machine Learning and Machine Vision algorithms. We…
Tan, Shawn Zheng Kai, Puig-Barbe, Aleix + 66 more
Shawn Zheng Kai Tan 1,2,\ , Aleix Puig-Barbe 2,\ , Damien Goutte-Gattat 3,4 , Caroline Eastwood 5 , Brian Aevermann 6 , Alida Avola 5 , James P Balhoff 7 , Ismail Ugur Bayindir 5 , Jasmine Belfiore 5 , Anita Reane Caron 2 , David S Fischer 8 , Nancy George 9 , Benjamin M Gyori 10 , Melissa A Haendel 11 , Charles Tapley…
Jeff J. Doyle
The concept of “cell type,” though fundamental to cell biology, is controversial. Cells have historically been classified into types based on morphology, physiology, or location. More recently, single cell transcriptomic studies have revealed fine-scale differences among cells with similar gross phenotypes.…
Anna Maria Masci, Cecilia N Arighi, Alexander D Diehl, Anne E Lieberman + 4 more
'Anne E Lieberman' 'Chris Mungall' 'Richard H Scheuermann' 'Barry Smith' 'Lindsay G Cowell'] Background Recent increases in the volume and diversity of life science data and information and an increasing emphasis on data sharing and interoperability have resulted in the creation of a large number of biological…
Shann-Ching Chen, Robert F Murphy
Background Knowledge of the subcellular location of a protein is critical to understanding how that protein works in a cell. This location is frequently determined by the interpretation of fluorescence microscope images. In recent years, automated systems have been developed for consistent and objective interpretation…
Tiago Lubiana, Paola Roncaglia, Chris Mungall, Ellen M. Quardokus + 3 more
'Joshua D. Fortriede' 'David Osumi-Sutherland' 'Alexander D. Diehl'] - 1 School of Pharmaceutical Sciences, University of São Paulo, São Paulo, SP, Brazil - 2 Ronin Institute for Independent Scholarship - 3 European Bioinformatics Institute, European Molecular Biology Laboratory (EMBL-EBI), Wellcome Genome Campus…
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…
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…
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…
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Acoustic measurements of batteries are known to be correlated to their state-of-charge, creating opportunities for state estimation that do not rely on electrical signals. State estimators are typically parametric models fitted from data, often from the broad toolbox of machine learning. Such models can be easily…
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Altered differentiation of blood cell precursors and their clonal expansion occurs in various types of leukaemia. One treatment strategy is to induce differentiation into the mature form, which is capable of undergoing apoptosis. It has been found that low doses of doxorubicin (DOX) induce phenotypic and morphological…
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This paper addresses the challenges in cell line development (CLD), the lengthy and ambiguous clone screening in upstream biopharmaceutical production. Typically, only a small subset of the later stages of CLD data is used for manually selecting lead clones. Addressing this issue, we introduce a multivariate data…
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Ensuring the trustworthiness of machine learning (ML) models in high-stake applications is crucial. One such application is predicting anti-cancer drug sensitivity, where ML models are built with the final goal of integrating them into treatment recommendation systems for personalized medicine. Here, we propose a…
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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…