AIMC Topic: Cell Lineage

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Transcriptomes of lineage-specific Drosophila neuroblasts profiled by genetic targeting and robotic sorting.

Development (Cambridge, England) Dec 23, 2015
A brain consists of numerous distinct neurons arising from a limited number of progenitors, called neuroblasts in Drosophila. Each neuroblast produces a specific neuronal lineage. To unravel the transcriptional networks that underlie the development ...
Animals Transcriptome Single-Cell Analysis Robotics Neurons Animals, Genetically Modified Sequence Analysis, RNA Transcription Factors Gene Targeting Drosophila Proteins Drosophila melanogaster Cell Lineage Gene Expression Regulation, Developmental
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Unsupervised lineage-based characterization of primate precursors reveals high proliferative and morphological diversity in the OSVZ.

The Journal of comparative neurology Jul 7, 2015
Generation of the primate cortex is characterized by the diversity of cortical precursors and the complexity of their lineage relationships. Recent studies have reported miscellaneous precursor types based on observer classification of cell biology f...
Stem Cell Niche Genetic Vectors Pattern Recognition, Automated Brain Tissue Culture Techniques Immunohistochemistry Cluster Analysis Stem Cells Macaca fascicularis Green Fluorescent Proteins Unsupervised Machine Learning Hydrozoa Markov Chains Cell Lineage Video Recording Animals Image Processing, Computer-Assisted Microscopy, Confocal
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Temporally discordant chromatin accessibility and DNA demethylation define short- and long-term enhancer regulation during cell fate specification.

Cell reports May 27, 2025
Chromatin and DNA modifications mediate the transcriptional activity of lineage-specifying enhancers, but recent work challenges the dogma that joint chromatin accessibility and DNA demethylation are prerequisites for transcription. To understand thi...
Neural Stem Cells DNA Demethylation CpG Islands Animals Cell Lineage Mice Enhancer Elements, Genetic Chromatin DNA Methylation Cell Differentiation
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Transcriptome-wide analysis reveals potential roles of CFD and ANGPTL4 in fibroblasts regulating B cell lineage for extracellular matrix-driven clustering and novel avenues for immunotherapy in breast cancer.

Molecular medicine (Cambridge, Mass.) May 8, 2025
BACKGROUND: The remodeling of the extracellular matrix (ECM) plays a pivotal role in tumor progression and drug resistance. However, the compositional patterns of ECM in breast cancer and their underlying biological functions remain elusive.
B-Lymphocytes Extracellular Matrix Cell Lineage Angiopoietin-Like Protein 4 Humans Gene Regulatory Networks Prognosis Tumor Microenvironment Female Immunotherapy Gene Expression Profiling Breast Neoplasms Gene Expression Regulation, Neoplastic Transcriptome Fibroblasts
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Deep learning-based enhancement of fluorescence labeling for accurate cell lineage tracing during embryogenesis.

Bioinformatics (Oxford, England) Nov 1, 2024
MOTIVATION: Automated cell lineage tracing throughout embryogenesis plays a key role in the study of regulatory control of cell fate differentiation, morphogenesis and organogenesis in the development of animals, including nematode Caenorhabditis ele...
Embryonic Development Signal-To-Noise Ratio Cell Lineage Caenorhabditis elegans Cell Tracking Animals Deep Learning Image Processing, Computer-Assisted
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scEnhancer: a single-cell enhancer resource with annotation across hundreds of tissue/cell types in three species.

Nucleic acids research Jan 7, 2022
Previous studies on enhancers and their target genes were largely based on bulk samples that represent 'average' regulatory activities from a large population of millions of cells, masking the heterogeneity and important effects from the sub-populati...
Molecular Sequence Annotation Cell Lineage Enhancer Elements, Genetic Chromatin Consensus Sequence Gene Expression Regulation Promoter Regions, Genetic Organ Specificity Drosophila melanogaster Software Animals Single-Cell Analysis Gene Regulatory Networks Eukaryotic Cells Unsupervised Machine Learning Internet Genetic Heterogeneity Humans Mice Databases, Genetic
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Epitome: predicting epigenetic events in novel cell types with multi-cell deep ensemble learning.

Nucleic acids research Nov 8, 2021
The accumulation of large epigenomics data consortiums provides us with the opportunity to extrapolate existing knowledge to new cell types and conditions. We propose Epitome, a deep neural network that learns similarities of chromatin accessibility ...
Protein Binding Epigenesis, Genetic Transcription Factors Cell Communication Genome, Human Humans Neural Networks, Computer Machine Learning Software Chromatin Chromatin Immunoprecipitation Histones Eukaryotic Cells Binding Sites Cell Lineage Atlases as Topic
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Deep neural net tracking of human pluripotent stem cells reveals intrinsic behaviors directing morphogenesis.

Stem cell reports May 11, 2021
Lineage tracing is a powerful tool in developmental biology to interrogate the evolution of tissue formation, but the dense, three-dimensional nature of tissue limits the assembly of individual cell trajectories into complete reconstructions of devel...
Smad Proteins Cell Lineage Cell Tracking Induced Pluripotent Stem Cells Morphogenesis Cell Movement Cell Differentiation Cell Count Bone Morphogenetic Protein 4 Neural Networks, Computer Cells, Cultured Image Processing, Computer-Assisted Humans
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Label-free optical hemogram of granulocytes enhanced by artificial neural networks.

Optics express May 13, 2019
An outstanding challenge for immunology is the classification of immune cells in a label-free fashion with high speed. For this purpose, optical techniques such as Raman spectroscopy or digital holographic microscopy have been used successfully to id...
Principal Component Analysis Flow Cytometry Eosinophils Cell Separation Holography Humans Cell Lineage Neural Networks, Computer Spectrum Analysis, Raman Neutrophils
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SuperCT: a supervised-learning framework for enhanced characterization of single-cell transcriptomic profiles.

Nucleic acids research May 7, 2019
Characterization of individual cell types is fundamental to the study of multicellular samples. Single-cell RNAseq techniques, which allow high-throughput expression profiling of individual cells, have significantly advanced our ability of this task....
Supervised Machine Learning High-Throughput Nucleotide Sequencing Datasets as Topic Cell Lineage RNA, Small Cytoplasmic Sequence Analysis, RNA Gene Expression Regulation, Neoplastic Cluster Analysis Pancreatic Neoplasms Gene Expression Profiling Transcriptome Single-Cell Analysis Mice Humans Software Animals
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