AIMC Topic: Cell Lineage

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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 CpG Islands DNA Demethylation Cell Lineage Enhancer Elements, Genetic Animals Chromatin Mice 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.
Fibroblasts B-Lymphocytes Extracellular Matrix Cell Lineage Transcriptome Gene Regulatory Networks Immunotherapy Gene Expression Regulation, Neoplastic Humans Prognosis Female Angiopoietin-Like Protein 4 Breast Neoplasms Tumor Microenvironment Gene Expression Profiling
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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 Animals Cell Tracking 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...
Cell Lineage Enhancer Elements, Genetic Chromatin Consensus Sequence Promoter Regions, Genetic Single-Cell Analysis Organ Specificity Gene Regulatory Networks Drosophila melanogaster Eukaryotic Cells Mice Molecular Sequence Annotation Databases, Genetic Humans Unsupervised Machine Learning Software Internet Animals Genetic Heterogeneity Gene Expression Regulation
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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 ...
Humans Neural Networks, Computer Transcription Factors Cell Communication Genome, Human Histones Binding Sites Machine Learning Software Protein Binding Epigenesis, Genetic Eukaryotic Cells Cell Lineage Atlases as Topic Chromatin Chromatin Immunoprecipitation
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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...
Induced Pluripotent Stem Cells Morphogenesis Bone Morphogenetic Protein 4 Smad Proteins Cell Lineage Cell Tracking Humans Neural Networks, Computer Cells, Cultured Image Processing, Computer-Assisted Cell Movement Cell Differentiation Cell Count
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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...
Holography Principal Component Analysis Humans Cell Lineage Flow Cytometry Neural Networks, Computer Eosinophils Spectrum Analysis, Raman Cell Separation 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....
RNA, Small Cytoplasmic Supervised Machine Learning Humans High-Throughput Nucleotide Sequencing Software Datasets as Topic Transcriptome Sequence Analysis, RNA Cell Lineage Single-Cell Analysis Animals Gene Expression Regulation, Neoplastic Gene Expression Profiling Mice Cluster Analysis Pancreatic Neoplasms
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Quantitative Modelling of the Waddington Epigenetic Landscape.

Methods in molecular biology (Clifton, N.J.) Jan 1, 2019
C.H. Waddington introduced the epigenetic landscape as a metaphor to represent cellular decision-making during development. Like a population of balls rolling down a rough hillside, developing cells follow specific trajectories (valleys) and eventual...
Neural Networks, Computer Phenotype Gene Regulatory Networks Epigenomics Models, Genetic Stem Cells Cell Differentiation Cell Lineage Humans
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Deep learning of the splicing (epi)genetic code reveals a novel candidate mechanism linking histone modifications to ESC fate decision.

Nucleic acids research Dec 1, 2017
Alternative splicing (AS) is a genetically and epigenetically regulated pre-mRNA processing to increase transcriptome and proteome diversity. Comprehensively decoding these regulatory mechanisms holds promise in getting deeper insights into a variety...
Alternative Splicing Embryonic Stem Cells Histone Code Sequence Analysis, RNA High-Throughput Nucleotide Sequencing Epigenesis, Genetic Tumor Suppressor Proteins Cell Line Ubiquitin-Protein Ligases Cell Differentiation Cell Lineage Humans Neural Networks, Computer Machine Learning
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