AIMC Topic: Organ Specificity

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Putative synaptic genes defined from a Drosophila whole body developmental transcriptome by a machine learning approach.

BMC genomics Sep 15, 2015
BACKGROUND: Assembly and function of neuronal synapses require the coordinated expression of a yet undetermined set of genes. Although roughly a thousand genes are expected to be important for this function in Drosophila melanogaster, just a few hund...
Models, Biological Gene Expression Profiling Synapses Drosophila Datasets as Topic Humans Gene Expression Regulation, Developmental Organ Specificity Transcriptome Machine Learning Computational Biology Algorithms Rats Animals
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A deep learning model trained on expressed transcripts across different tissue types reveals cell-type codon-optimization preferences.

Nucleic acids research Mar 20, 2025
Species-specific differences in protein translation can affect the design of protein-based drugs. Consequently, efficient expression of recombinant proteins often requires codon optimization. Publicly available optimization tools do not always result...
Humans Neural Networks, Computer Brain Hepatocytes Organ Specificity Codon Protein Biosynthesis Codon Usage Animals Deep Learning Recombinant Proteins Liver
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Interpretable predictive models of genome-wide aryl hydrocarbon receptor-DNA binding reveal tissue-specific binding determinants.

Toxicological sciences : an official journal of the Society of Toxicology Nov 28, 2023
The aryl hydrocarbon receptor (AhR) is an inducible transcription factor whose ligands include the potent environmental contaminant 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). Ligand-activated AhR binds to DNA at dioxin response elements (DREs) conta...
Genome, Human Organ Specificity Humans Machine Learning Receptors, Aryl Hydrocarbon Basic Helix-Loop-Helix Transcription Factors
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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...
Humans Software Animals Promoter Regions, Genetic Organ Specificity Unsupervised Machine Learning Drosophila melanogaster Internet Molecular Sequence Annotation Chromatin Genetic Heterogeneity Consensus Sequence Gene Expression Regulation Eukaryotic Cells Cell Lineage Single-Cell Analysis Enhancer Elements, Genetic Gene Regulatory Networks Mice Databases, Genetic
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DISMIR: Deep learning-based noninvasive cancer detection by integrating DNA sequence and methylation information of individual cell-free DNA reads.

Briefings in bioinformatics Nov 5, 2021
Detecting cancer signals in cell-free DNA (cfDNA) high-throughput sequencing data is emerging as a novel noninvasive cancer detection method. Due to the high cost of sequencing, it is crucial to make robust and precise predictions with low-depth cfDN...
Computational Biology Sequence Analysis, DNA DNA Methylation Cell-Free Nucleic Acids Early Detection of Cancer Humans Neoplasms Deep Learning Organ Specificity Nucleotide Motifs Neoplasm Staging High-Throughput Nucleotide Sequencing Liquid Biopsy DNA, Neoplasm
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Ultrasound-on-chip platform for medical imaging, analysis, and collective intelligence.

Proceedings of the National Academy of Sciences of the United States of America Jul 6, 2021
Over the past half-century, ultrasound imaging has become a key technology for assessing an ever-widening range of medical conditions at all stages of life. Despite ultrasound's proven value, expensive systems that require domain expertise in image a...
Micro-Electrical-Mechanical Systems Imaging, Three-Dimensional Acoustics Organ Specificity Artificial Intelligence Ultrasonography
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Predicting regulatory variants using a dense epigenomic mapped CNN model elucidated the molecular basis of trait-tissue associations.

Nucleic acids research Jan 11, 2021
Assessing the causal tissues of human complex diseases is important for the prioritization of trait-associated genetic variants. Yet, the biological underpinnings of trait-associated variants are extremely difficult to infer due to statistical noise ...
Deep Learning Genome-Wide Association Study Polymorphism, Single Nucleotide Humans Linkage Disequilibrium Genetic Diseases, Inborn Chromatin Immunoprecipitation Histone Code Epigenome Epigenomics Organ Specificity Datasets as Topic Models, Genetic Molecular Sequence Annotation Transcription Factors Binding Sites Causality
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SilencerDB: a comprehensive database of silencers.

Nucleic acids research Jan 8, 2021
Gene regulatory elements, including promoters, enhancers, silencers, etc., control transcriptional programs in a spatiotemporal manner. Though these elements are known to be able to induce either positive or negative transcriptional control, the comm...
Transcription, Genetic Sus scrofa Databases, Nucleic Acid Silencer Elements, Transcriptional Buffaloes Organ Specificity Drosophila melanogaster Molecular Sequence Annotation Chickens Rats Cell Line Internet Animals User-Computer Interface Mice Humans Machine Learning
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Uncovering tissue-specific binding features from differential deep learning.

Nucleic acids research Mar 18, 2020
Transcription factors (TFs) can bind DNA in a cooperative manner, enabling a mutual increase in occupancy. Through this type of interaction, alternative binding sites can be preferentially bound in different tissues to regulate tissue-specific expres...
Homeodomain Proteins Gene Expression Regulation, Developmental Chromatin Immunoprecipitation Branchial Region Myeloid Ecotropic Viral Integration Site 1 Protein Embryo, Mammalian Organ Specificity Protein Isoforms Binding Sites Models, Genetic Animals Deep Learning Protein Binding Mice Computational Biology Poisson Distribution RNA High-Throughput Nucleotide Sequencing
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ME-Class2 reveals context dependent regulatory roles for 5-hydroxymethylcytosine.

Nucleic acids research Mar 18, 2019
Since the discovery of 5-hydroxymethylcytosine (5hmC) as a prominent DNA modification found in mammalian genomes, an emergent question has been what role this mark plays in gene regulation. 5hmC is hypothesized to function as an intermediate in the d...
Sulfites Datasets as Topic Methylation Promoter Regions, Genetic Animals Mice Sequence Analysis, RNA Organ Specificity Databases, Genetic Humans Genome Machine Learning Genes Brain 5-Methylcytosine
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