AIMC Topic: Gene Expression Regulation

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Cross-species regulatory sequence activity prediction.

PLoS computational biology Jul 20, 2020
Machine learning algorithms trained to predict the regulatory activity of nucleic acid sequences have revealed principles of gene regulation and guided genetic variation analysis. While the human genome has been extensively annotated and studied, mod...
Genomics Genetic Variation Computational Biology Gene Expression Regulation Epigenomics Humans Genome, Human Sequence Analysis, DNA Models, Genetic Neural Networks, Computer Species Specificity Models, Statistical Databases, Genetic Quantitative Trait Loci Machine Learning Mutation Software Hepatocytes Algorithms Animals Mice
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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...
Humans Neural Networks, Computer Software Protein Isoforms Exons Alternative Splicing Computational Biology Sequence Analysis, RNA High-Throughput Nucleotide Sequencing Gene Expression Regulation
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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...
Humans Machine Learning Epigenesis, Genetic Transcription Factors Databases, Genetic Regenerative Medicine Human Umbilical Vein Endothelial Cells Histone Code Gene Expression Regulation Algorithms Cells Chromatin Immunoprecipitation Sequencing Phenotype Pluripotent Stem Cells RNA-Seq Gene Regulatory Networks
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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...
Predictive Value of Tests Datasets as Topic Gene Expression Regulation Computational Biology Databases, Genetic MicroRNAs RNA, Long Noncoding Deep Learning Gene Regulatory Networks Genetic Predisposition to Disease Genetic Association Studies
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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 ...
Rapamycin-Insensitive Companion of mTOR Protein Regulatory-Associated Protein of mTOR T-Box Domain Proteins T-bet Transcription Factor Gene Expression Regulation Killer Cells, Natural Forkhead Box Protein O1 Mechanistic Target of Rapamycin Complex 2 Mice, Inbred C57BL Mice, Knockout Machine Learning Proto-Oncogene Proteins c-akt Bone Marrow Cells Phenotype Transcriptome Animals Single-Cell Analysis Gene Expression Profiling RNA-Seq Genotype Cluster Analysis
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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...
Bone Marrow Humans RNA-Seq Retina Algorithms Mice Gene Expression Regulation Animals Macaca Monocytes Leukocytes, Mononuclear Islets of Langerhans Cluster Analysis Deep Learning Single-Cell Analysis
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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 ...
Datasets as Topic Gene Expression Regulation Computational Biology Databases, Genetic RNA, Long Noncoding Data Mining Humans Neoplasms Deep Learning Genetic Predisposition to Disease Genetic Association Studies
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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. ...
MicroRNAs Humans Gene Expression Regulation Algorithms Computer Simulation Animals Sequence Analysis, RNA Models, Genetic Neural Networks, Computer
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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 Dialysis Solutions Peritoneum Epithelium Humans Glycosaminoglycans Cells, Cultured Gene Expression Regulation Oxidative Stress 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...
Brain Animals RNA-Seq Mice RNA, Messenger Gene Expression Regulation Humans Trinucleotide Repeats Machine Learning Proteomics Huntington Disease Disease Models, Animal Huntingtin Protein MicroRNAs Gene Knock-In Techniques Neurons
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