AIMC Topic: Cells

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Identification of the human DPR core promoter element using machine learning.

Nature Sep 9, 2020
The RNA polymerase II (Pol II) core promoter is the strategic site of convergence of the signals that lead to the initiation of DNA transcription, but the downstream core promoter in humans has been difficult to understand. Here we analyse the human ...
Gene Expression Regulation Base Sequence Promoter Regions, Genetic HeLa Cells Datasets as Topic RNA Polymerase II Consensus Sequence TATA Box Mutagenesis Transcription, Genetic Cells Humans Computer Simulation Models, Genetic Support Vector Machine High-Throughput Nucleotide Sequencing
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Machine learning uncovers cell identity regulator by histone code.

Nature communications Jun 1, 2020
Conversion between cell types, e.g., by induced expression of master transcription factors, holds great promise for cellular therapy. Our ability to manipulate cell identity is constrained by incomplete information on cell identity genes (CIGs) and t...
Machine Learning Algorithms Phenotype Humans Transcription Factors Databases, Genetic Human Umbilical Vein Endothelial Cells RNA-Seq Gene Regulatory Networks Epigenesis, Genetic Chromatin Immunoprecipitation Sequencing Cells Pluripotent Stem Cells Histone Code Regenerative Medicine Gene Expression Regulation
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Automated Classification of Apoptosis in Phase Contrast Microscopy Using Capsule Network.

IEEE transactions on medical imaging May 22, 2019
Automatic and accurate classification of apoptosis, or programmed cell death, will facilitate cell biology research. The state-of-the-art approaches in apoptosis classification use deep convolutional neural networks (CNNs). However, these networks ar...
Microscopy, Phase-Contrast Neural Networks, Computer Cell Line, Tumor Image Processing, Computer-Assisted Apoptosis Cytological Techniques Cells Humans
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Cell Identity Codes: Understanding Cell Identity from Gene Expression Profiles using Deep Neural Networks.

Scientific reports Feb 20, 2019
Understanding cell identity is an important task in many biomedical areas. Expression patterns of specific marker genes have been used to characterize some limited cell types, but exclusive markers are not available for many cell types. A second appr...
Cells Cell Compartmentation Deep Learning Organ Specificity Humans Neural Networks, Computer Algorithms Gene Expression Profiling
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Large-Scale Multi-Class Image-Based Cell Classification With Deep Learning.

IEEE journal of biomedical and health informatics Oct 31, 2018
Recent advances in ultra-high-throughput microscopy have enabled a new generation of cell classification methodologies using image-based cell phenotypes alone. In contrast to current single-cell analysis techniques that rely solely on slow and costly...
Humans Microscopy Cells Deep Learning Image Processing, Computer-Assisted Cytological Techniques Algorithms Databases, Factual
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Cell ontology in an age of data-driven cell classification.

BMC bioinformatics Dec 21, 2017
BACKGROUND: Data-driven cell classification is becoming common and is now being implemented on a massive scale by projects such as the Human Cell Atlas. The scale of these efforts poses a challenge. How can the results be made searchable and accessib...
Mice Computational Biology Models, Statistical Humans Biological Ontologies Cells Databases, Factual Animals
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Cell type discovery and representation in the era of high-content single cell phenotyping.

BMC bioinformatics Dec 21, 2017
BACKGROUND: A fundamental characteristic of multicellular organisms is the specialization of functional cell types through the process of differentiation. These specialized cell types not only characterize the normal functioning of different organs a...
Biological Ontologies Humans Single-Cell Analysis Cells Computational Biology Biomarkers Sequence Analysis, RNA
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The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability.

Journal of biomedical semantics Jul 4, 2016
BACKGROUND: The Cell Ontology (CL) is an OBO Foundry candidate ontology covering the domain of canonical, natural biological cell types. Since its inception in 2005, the CL has undergone multiple rounds of revision and expansion, most notably in its ...
Natural Language Processing Biological Ontologies Cells Nervous System
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The cellular microscopy phenotype ontology.

Journal of biomedical semantics May 18, 2016
BACKGROUND: Phenotypic data derived from high content screening is currently annotated using free-text, thus preventing the integration of independent datasets, including those generated in different biological domains, such as cell lines, mouse and ...
Phenotype Cells Single-Cell Analysis Microscopy Biological Ontologies
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Exploring Host-Microbiome Interactions using an in Silico Model of Biomimetic Robots and Engineered Living Cells.

Scientific reports Jul 16, 2015
The microbiome's underlying dynamics play an important role in regulating the behavior and health of its host. In order to explore the details of these interactions, we created an in silico model of a living microbiome, engineered with synthetic biol...
Cells Genetic Engineering Biomimetics Host-Pathogen Interactions Computer Simulation Robotics Models, Biological Microbiota
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