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Gene Expression Regulation

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A network-based computational framework to predict and differentiate functions for gene isoforms using exon-level expression data.

Methods (San Diego, Calif.) Jun 10, 2020
MOTIVATION: Alternative splicing makes significant contributions to functional diversity of transcripts and proteins. Many alternatively spliced gene isoforms have been shown to perform specific biological functions under different contexts. In addit...
Alternative Splicing Neural Networks, Computer Software Computational Biology Sequence Analysis, RNA High-Throughput Nucleotide Sequencing Gene Expression Regulation Protein Isoforms Exons Humans
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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...
Phenotype RNA-Seq Gene Regulatory Networks Epigenesis, Genetic Humans Machine Learning Algorithms Gene Expression Regulation Transcription Factors Cells Pluripotent Stem Cells Databases, Genetic Histone Code Human Umbilical Vein Endothelial Cells Chromatin Immunoprecipitation Sequencing Regenerative Medicine
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A novel graph attention adversarial network for predicting disease-related associations.

Methods (San Diego, Calif.) May 21, 2020
Identifying complex human diseases at molecular level is very helpful, especially in diseases diagnosis, therapy, prognosis and monitoring. Accumulating evidences demonstrated that RNAs are playing important roles in identifying various complex human...
Deep Learning Datasets as Topic Gene Expression Regulation Gene Regulatory Networks Databases, Genetic Genetic Predisposition to Disease MicroRNAs Genetic Association Studies RNA, Long Noncoding Computational Biology Predictive Value of Tests
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Single-cell transcriptome reveals the novel role of T-bet in suppressing the immature NK gene signature.

eLife May 14, 2020
The transcriptional activation and repression during NK cell ontology are poorly understood. Here, using single-cell RNA-sequencing, we reveal a novel role for T-bet in suppressing the immature gene signature during murine NK cell development. Based ...
Bone Marrow Cells Gene Expression Regulation Killer Cells, Natural Forkhead Box Protein O1 Cluster Analysis Mice, Inbred C57BL Mice, Knockout Proto-Oncogene Proteins c-akt T-bet Transcription Factor Mechanistic Target of Rapamycin Complex 2 Rapamycin-Insensitive Companion of mTOR Protein Regulatory-Associated Protein of mTOR T-Box Domain Proteins Machine Learning Phenotype Animals Gene Expression Profiling Transcriptome Single-Cell Analysis RNA-Seq Genotype
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Deep learning enables accurate clustering with batch effect removal in single-cell RNA-seq analysis.

Nature communications May 11, 2020
Single-cell RNA sequencing (scRNA-seq) can characterize cell types and states through unsupervised clustering, but the ever increasing number of cells and batch effect impose computational challenges. We present DESC, an unsupervised deep embedding a...
Retina Gene Expression Regulation Macaca Islets of Langerhans Mice Monocytes Cluster Analysis Bone Marrow Humans Algorithms Deep Learning Animals Single-Cell Analysis Leukocytes, Mononuclear RNA-Seq
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SDLDA: lncRNA-disease association prediction based on singular value decomposition and deep learning.

Methods (San Diego, Calif.) May 5, 2020
In recent years, accumulating studies have shown that long non-coding RNAs (lncRNAs) not only play an important role in the regulation of various biological processes but also are the foundation for understanding mechanisms of human diseases. Due to ...
Humans Neoplasms Deep Learning Genetic Predisposition to Disease Genetic Association Studies Data Mining Computational Biology Datasets as Topic Databases, Genetic Gene Expression Regulation RNA, Long Noncoding
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Prediction of miRNA targets by learning from interaction sequences.

PloS one May 5, 2020
MicroRNAs (miRNAs) are involved in a diverse variety of biological processes through regulating the expression of target genes in the post-transcriptional level. So, it is of great importance to discover the targets of miRNAs in biological research. ...
Models, Genetic MicroRNAs Gene Expression Regulation Humans Neural Networks, Computer Algorithms Computer Simulation Animals Sequence Analysis, RNA
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Sulodexide modulates the dialysate effect on the peritoneal mesothelium.

Journal of physiology and pharmacology : an official journal of the Polish Physiological Society Mar 20, 2020
Peritoneal membrane damage during chronic peritoneal dialysis is the main cause of that treatment failure. Preservation of the mesothelial cells (MC) is important for the survival of the peritoneum. Evaluation of dialysates effect on the function of ...
Peritoneal Dialysis, Continuous Ambulatory Humans Peritoneum Dialysis Solutions Epithelium Cells, Cultured Glycosaminoglycans Oxidative Stress Gene Expression Regulation Anticoagulants
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Combining feature selection and shape analysis uncovers precise rules for miRNA regulation in Huntington's disease mice.

BMC bioinformatics Feb 24, 2020
BACKGROUND: MicroRNA (miRNA) regulation is associated with several diseases, including neurodegenerative diseases. Several approaches can be used for modeling miRNA regulation. However, their precision may be limited for analyzing multidimensional da...
Huntington Disease Huntingtin Protein Machine Learning Gene Knock-In Techniques Brain MicroRNAs Animals Neurons RNA-Seq Mice Gene Expression Regulation Humans RNA, Messenger Trinucleotide Repeats Proteomics Disease Models, Animal
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Combined Use of Three Machine Learning Modeling Methods to Develop a Ten-Gene Signature for the Diagnosis of Ventilator-Associated Pneumonia.

Medical science monitor : international medical journal of experimental and clinical research Feb 7, 2020
BACKGROUND This study aimed to use three modeling methods, logistic regression analysis, random forest analysis, and fully-connected neural network analysis, to develop a diagnostic gene signature for the diagnosis of ventilator-associated pneumonia ...
Databases, Genetic Area Under Curve Gene Expression Regulation Genome, Human Molecular Sequence Annotation Gene Ontology Pneumonia, Ventilator-Associated Machine Learning Algorithms Gene Expression Profiling Protein Interaction Maps Humans
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