AIMC Topic: Transcription, Genetic

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Exogenous Chemicals Impact Virus Receptor Gene Transcription: Insights from Deep Learning.

Environmental science & technology May 15, 2023
Despite the fact that coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has been disrupting human life and health worldwide since the outbreak in late 2019, the impact of exogenous substance ...
Angiotensin-Converting Enzyme 2 Peptidyl-Dipeptidase A Transcription, Genetic Receptors, Virus Humans COVID-19 SARS-CoV-2 Deep Learning
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Accurate Prediction of Transcriptional Activity of Single Missense Variants in HIV Tat with Deep Learning.

International journal of molecular sciences Mar 24, 2023
Tat is an essential gene for increasing the transcription of all HIV genes, and affects HIV replication, HIV exit from latency, and AIDS progression. The Tat gene frequently mutates in vivo and produces variants with diverse activities, contributing ...
Transcription, Genetic Mutation, Missense tat Gene Products, Human Immunodeficiency Virus Transcriptional Activation Humans Deep Learning Acquired Immunodeficiency Syndrome
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Deep learning connects DNA traces to transcription to reveal predictive features beyond enhancer-promoter contact.

Nature communications Jun 8, 2021
Chromatin architecture plays an important role in gene regulation. Recent advances in super-resolution microscopy have made it possible to measure chromatin 3D structure and transcription in thousands of single cells. However, leveraging these comple...
Neural Networks, Computer Promoter Regions, Genetic Drosophila melanogaster Transcription, Genetic Enhancer Elements, Genetic Genome, Insect Chromatin Gene Silencing Deep Learning DNA Multigene Family Gene Expression Regulation Algorithms Computer Simulation Animals
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Neural network aided approximation and parameter inference of non-Markovian models of gene expression.

Nature communications May 11, 2021
Non-Markovian models of stochastic biochemical kinetics often incorporate explicit time delays to effectively model large numbers of intermediate biochemical processes. Analysis and simulation of these models, as well as the inference of their parame...
Neural Networks, Computer Computer Simulation Transcription, Genetic Stochastic Processes Feedback, Physiological Models, Genetic Kinetics Gene Expression Regulation
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A deep learning framework combined with word embedding to identify DNA replication origins.

Scientific reports Jan 12, 2021
The DNA replication influences the inheritance of genetic information in the DNA life cycle. As the distribution of replication origins (ORIs) is the major determinant to precisely regulate the replication process, the correct identification of ORIs ...
Replication Origin Kluyveromyces Schizosaccharomyces Saccharomycetales DNA Replication Neural Networks, Computer Algorithms Deep Learning Databases, Genetic Saccharomyces cerevisiae Transcription, Genetic
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Identification of the human DPR core promoter element using machine learning.

Nature Sep 9, 2020
The RNA polymerase II (Pol II) core promoter is the strategic site of convergence of the signals that lead to the initiation of DNA transcription, but the downstream core promoter in humans has been difficult to understand. Here we analyse the human ...
TATA Box Transcription, Genetic Cells RNA Polymerase II Consensus Sequence Base Sequence Promoter Regions, Genetic Mutagenesis Humans Computer Simulation Models, Genetic Support Vector Machine High-Throughput Nucleotide Sequencing HeLa Cells Datasets as Topic Gene Expression Regulation
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Deep Learning Modeling of Androgen Receptor Responses to Prostate Cancer Therapies.

International journal of molecular sciences Aug 14, 2020
Gain-of-function mutations in human androgen receptor (AR) are among the major causes of drug resistance in prostate cancer (PCa). Identifying mutations that cause resistant phenotype is of critical importance for guiding treatment protocols, as well...
Humans Neural Networks, Computer Male Deep Learning Mutation Cell Line, Tumor Receptors, Androgen ROC Curve Transcription, Genetic Prostatic Neoplasms Androgen Receptor Antagonists
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Machine Learning and Network Analyses Reveal Disease Subtypes of Pancreatic Cancer and their Molecular Characteristics.

Scientific reports Jan 27, 2020
Given that the biological processes governing the oncogenesis of pancreatic cancers could present useful therapeutic targets, there is a pressing need to molecularly distinguish between different clinically relevant pancreatic cancer subtypes. To add...
Pancreatic Neoplasms Exome Sequencing Transcription, Genetic RNA, Messenger Humans Proteome Machine Learning DNA Methylation Biomarkers, Tumor MicroRNAs Transcriptome Cell Line, Tumor RNA-Seq
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An improved catalogue of putative synaptic genes defined exclusively by temporal transcription profiles through an ensemble machine learning approach.

BMC genomics Dec 23, 2019
BACKGROUND: Assembly and function of neuronal synapses require the coordinated expression of a yet undetermined set of genes. Previously, we had trained an ensemble machine learning model to assign a probability of having synaptic function to every p...
Machine Learning Animals Gene Expression Profiling Gene Ontology Synapses Drosophila melanogaster Transcription, Genetic
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Whole-genome deep-learning analysis identifies contribution of noncoding mutations to autism risk.

Nature genetics May 27, 2019
We address the challenge of detecting the contribution of noncoding mutations to disease with a deep-learning-based framework that predicts the specific regulatory effects and the deleterious impact of genetic variants. Applying this framework to 1,7...
RNA Processing, Post-Transcriptional Genetic Association Studies Transcription, Genetic Autism Spectrum Disorder Computational Biology Mutation RNA, Untranslated Deep Learning Gene Expression Genes, Reporter Alleles Genomics Humans Gene Expression Regulation Genetic Predisposition to Disease Algorithms Genome, Human Phenotype
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