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An improved ontological representation of dendritic cells as a paradigm for all cell types
<span title="">2009</span>
<i title="Springer Nature">
<a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a>
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ontologies, including the Cell Ontology (CL), designed to provide a standardized representation of cell types for data annotation. ...
Results: To enhance the CL's utility for computational analyses, we developed a method for the ontological representation of cells and applied this method to develop a dendritic cell ontology (DC-CL). ...
We would like to thank Melissa Haendel and Ceri Van Syke for helpful discussion of how to improve the Cell Ontology. ...
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Hematopoietic Cell Types: Prototype for a Revised Cell Ontology
<span title="2009-08-19">2009</span>
<i title="Springer Science and Business Media LLC">
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The Cell Ontology (CL) aims for the representation of in vivo and in vitro cell types from all of biology. ...
The methods and improvement to the CL in this area represent a paradigm for improvement of the whole of the ontology over time. ...
Acknowledgements We thank NIAID for the support of the workshop and follow-up teleconferences. ...
<span class="external-identifiers">
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Hematopoietic Cell Types: Prototype for a Revised Cell Ontology
<span title="2009-08-04">2009</span>
<i title="Springer Nature America, Inc">
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The Cell Ontology covers cell types from all of biology. ...
A list of in vitro methods for preparing cell cultures, although the Cell Ontology may be used to describe the resulting cells if they correspond to an in vivo cell type. ...
Acknowledgments Acknowledgments Participants in NIAID Cell Ontology Workshop Martin Zand ...
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Hematopoietic Cell Types: Prototype for a Revised Cell Ontology
<span title="2009-08-18">2009</span>
<i title="Springer Nature America, Inc">
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The Cell Ontology covers cell types from all of biology. ...
A list of in vitro methods for preparing cell cultures, although the Cell Ontology may be used to describe the resulting cells if they correspond to an in vivo cell type. ...
Acknowledgments Acknowledgments Participants in NIAID Cell Ontology Workshop Martin Zand ...
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Hematopoietic Cell Types: Prototype for a Revised Cell Ontology
<span title="2009-08-18">2009</span>
<i title="Springer Nature">
<a target="_blank" rel="noopener" href="https://fatcat.wiki/container/gfizkffjyzhple2sfhgk46dk2e" style="color: black;">Nature Precedings</a>
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The Cell Ontology covers cell types from all of biology. ...
A list of in vitro methods for preparing cell cultures, although the Cell Ontology may be used to describe the resulting cells if they correspond to an in vivo cell type. ...
Acknowledgments Acknowledgments Participants in NIAID Cell Ontology Workshop Martin Zand ...
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Hematopoietic cell types: Prototype for a revised cell ontology
<span title="">2011</span>
<i title="Elsevier BV">
<a target="_blank" rel="noopener" href="https://fatcat.wiki/container/p4kk6lusgrhyxecgig72iasi5q" style="color: black;">Journal of Biomedical Informatics</a>
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The Cell Ontology (CL) aims for the representation of in vivo and in vitro cell types from all of biology. ...
The methods and improvements to the CL in this area represent a paradigm for improvement of the entire ontology over time. ...
Acknowledgements We thank NIAID for the support of the workshop and follow-up teleconferences. ...
<span class="external-identifiers">
<a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.jbi.2010.01.006">doi:10.1016/j.jbi.2010.01.006</a>
<a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/20123131">pmid:20123131</a>
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Big data and single cell transcriptomics: implications for ontological representation
[article]
<span title="2018-01-31">2018</span>
<i title="Cold Spring Harbor Laboratory">
bioRxiv
</i>
<span class="release-stage" >pre-print</span>
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these discoveries are having on the representation of cell types in the reference Cell Ontology (CL). ...
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 unprecedented rate. ...
paradigm for all cell types. ...
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Knowledge sharing and collaboration in translational research, and the DC-THERA Directory
<span title="2011-10-03">2011</span>
<i title="Oxford University Press (OUP)">
<a target="_blank" rel="noopener" href="https://fatcat.wiki/container/op7ztx4fhvairowgqifu7dnvsi" style="color: black;">Briefings in Bioinformatics</a>
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This dimension of 'big data' research calls for the development of computational tools to manage such a vast amount of data, as well as tools that can improve communication and access to information from ...
fundamental research in dendritic cell immunobiology. ...
They wish to thank Olivier Lefevre for the work on the DC-BASE integration and Luca Beltrame for his work in the integration of Pathway Analysis functionalities. ...
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A general framework for the combined morphometric, transcriptomic, and physiological analysis of cells using metric geometry
[article]
<span title="2022-05-20">2022</span>
<i title="Cold Spring Harbor Laboratory">
bioRxiv
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<span class="release-stage" >pre-print</span>
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Morphology is an essential phenotype in the characterization of cells and their states, as it is closely related to cell function. ...
Here we report a computational framework, named CAJAL, for the morphometric and multi-modal analysis of single-cell data. ...
Zhaolan Zhou for his constructive comments on the manuscript, Matthew Jozwik for assisting with the conversion of files for the DVB analysis, and Jiazhen Rong and Alice Wang for collaboration on related ...
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The Genopolis Microarray Database
<span title="">2007</span>
<i title="Springer Nature">
<a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a>
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The Genopolis database has been implemented as a dedicated system for the scientific community studying dendritic and macrophage cells functions and host-parasite interactions. ...
Gene expression databases are key resources for microarray data management and analysis and the importance of a proper annotation of their content is well understood. ...
IT consultant, Helen Parkinson and Tim Rayner for their support in the development of the export to ArrayExpress and Sekmed srl for its contributions to this project. ...
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Ascorbic acid supports ex vivo generation of plasmacytoid dendritic cells from circulating hematopoietic stem cells
<span title="2021-09-02">2021</span>
<i title="eLife Sciences Publications, Ltd">
<a target="_blank" rel="noopener" href="https://fatcat.wiki/container/en4qj5ijrbf5djxx7p5zzpjyoq" style="color: black;">eLife</a>
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Plasmacytoid dendritic cells (pDCs) constitute a rare type of immune cell with multifaceted functions, but their potential use as a cell-based immunotherapy is challenged by the scarce cell numbers that ...
Ascorbic acid induces transcriptional signatures associated with pDC-specific innate immune pathways suggesting an undescribed role of ascorbic acid for pDC functionality. ...
Introduction Plasmacytoid dendritic cells (pDCs) represent a rare and unique type of immune cell that plays a central role particularly in the detection and control of viral infections. ...
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Discovering novel cell types across heterogeneous single-cell experiments
[article]
<span title="2020-02-26">2020</span>
<i title="Cold Spring Harbor Laboratory">
bioRxiv
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We present MARS, a meta-learning algorithm for annotating known and novel cell types that reconciles the heterogeneity by transferring latent cell representations across multiple datasets. ...
Remarkably, MARS estimates meaningful cell-type-specific signatures of aging and visualizes them as trajectories reflecting temporal relationships of cells in a tissue. ...
Here we introduce MARS, an approach for annotating known/seen as well as novel/unseen cell types in heterogeneous and time-varying single-cell datasets. ...
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Interactive Rough-Granular Computing in Wisdom Technology
[chapter]
<span title="">2013</span>
<i title="Springer International Publishing">
<a target="_blank" rel="noopener" href="https://fatcat.wiki/container/2w3awgokqne6te4nvlofavy5a4" style="color: black;">Lecture Notes in Computer Science</a>
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INTERACTIONS
A human dendritic cell (blue pseudo-
color) in close interaction with a
lymphocyte (yellow pseudo-color). ...
of hunk configurations + G links + representations of G elementary actions type defined by acceptance postcondition s G links between hunks and their configurations) a reasoning process for reaching decisions ...
As a methodology, computing with words provides a foundation for a computational theory of perceptions -a theory which may have an important bearing on how humans make -and machines might makeperception ...
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A Multimodal and Integrated Approach to Interrogate Human Kidney Biopsies with Rigor and Reproducibility: The Kidney Precision Medicine Project
[article]
<span title="2019-11-06">2019</span>
<i title="Cold Spring Harbor Laboratory">
bioRxiv
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and which can serve as a model for similar personalized medicine projects. ...
We describe a pipeline for generating a reliable and authentic single cell/region 3D molecular atlas of human adult kidney with emphasis on quality assurance, quality control, validation and harmonization ...
An ontological representation of the cell markers has been initiated to seamlessly link gene, cell type and spatial tissue location at an integrative semantic level (31) . ...
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Chronic Chemogenetic Stimulation of the Nucleus Accumbens Produces Lasting Reductions in Binge Drinking and Ameliorates Alcohol-Related Morphological and Transcriptional Changes
<span title="2020-02-18">2020</span>
<i title="MDPI AG">
<a target="_blank" rel="noopener" href="https://fatcat.wiki/container/5hwrtdnkjvclroyxzt4ty5ijb4" style="color: black;">Brain Sciences</a>
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Binge drinking is a dangerous pattern of behavior. ...
Lastly, we found that LMK235, an HDAC4/5 inhibitor, reduced binge-like drinking. Thus, we were able to target specific molecular pathways using pharmacology to mimic the behavioral effects of DREADDs. ...
Conflicts of Interest: The authors declare no conflicts of interests. Brain Sci. 2020, 10, 109 ...
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