AIMC Topic: Transcription Factors

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DeepReg: a deep learning hybrid model for predicting transcription factors in eukaryotic and prokaryotic genomes.

Scientific reports Apr 21, 2024
Deep learning models (DLMs) have gained importance in predicting, detecting, translating, and classifying a diversity of inputs. In bioinformatics, DLMs have been used to predict protein structures, transcription factor-binding sites, and promoters. ...
Deep Learning Computational Biology Genome Transcription Factors Prokaryotic Cells Eukaryotic Cells Neural Networks, Computer Binding Sites Eukaryota
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Binding Mechanism of Inhibitors to BRD4 and BRD9 Decoded by Multiple Independent Molecular Dynamics Simulations and Deep Learning.

Molecules (Basel, Switzerland) Apr 19, 2024
Bromodomain 4 and 9 (BRD4 and BRD9) have been regarded as important targets of drug designs in regard to the treatment of multiple diseases. In our current study, molecular dynamics (MD) simulations, deep learning (DL) and binding free energy calcula...
Humans Molecular Docking Simulation Deep Learning Bromodomain Containing Proteins Transcription Factors Protein Binding Triazoles Molecular Dynamics Simulation Nuclear Proteins Cell Cycle Proteins Binding Sites Thermodynamics Azepines
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ASPTF: A computational tool to predict abiotic stress-responsive transcription factors in plants by employing machine learning algorithms.

Biochimica et biophysica acta. General subjects Mar 14, 2024
BACKGROUND: Abiotic stresses pose serious threat to the growth and yield of crop plants. Several studies suggest that in plants, transcription factors (TFs) are important regulators of gene expression, especially when it comes to coping with abiotic ...
Transcription Factors Plants Plant Proteins Algorithms Computational Biology Stress, Physiological Gene Expression Regulation, Plant Machine Learning
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DARDN: A Deep-Learning Approach for CTCF Binding Sequence Classification and Oncogenic Regulatory Feature Discovery.

Genes Jan 23, 2024
Characterization of gene regulatory mechanisms in cancer is a key task in cancer genomics. CCCTC-binding factor (CTCF), a DNA binding protein, exhibits specific binding patterns in the genome of cancer cells and has a non-canonical function to facili...
Transcription Factors DNA CCCTC-Binding Factor Precursor T-Cell Lymphoblastic Leukemia-Lymphoma Humans Deep Learning
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Hold out the genome: a roadmap to solving the cis-regulatory code.

Nature Dec 13, 2023
Gene expression is regulated by transcription factors that work together to read cis-regulatory DNA sequences. The 'cis-regulatory code' - how cells interpret DNA sequences to determine when, where and how much genes should be expressed - has proven ...
Models, Genetic Transcription Factors Regulatory Sequences, Nucleic Acid DNA Machine Learning Genomics
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Cell-type-directed design of synthetic enhancers.

Nature Dec 12, 2023
Transcriptional enhancers act as docking stations for combinations of transcription factors and thereby regulate spatiotemporal activation of their target genes. It has been a long-standing goal in the field to decode the regulatory logic of an enhan...
Neuroglia Enhancer Elements, Genetic Humans Synthetic Biology Gene Expression Regulation Cells Deep Learning Repressor Proteins Drosophila melanogaster Brain Transcription Factors Animals Animals, Genetically Modified
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FUN-PROSE: A deep learning approach to predict condition-specific gene expression in fungi.

PLoS computational biology Nov 16, 2023
mRNA levels of all genes in a genome is a critical piece of information defining the overall state of the cell in a given environmental condition. Being able to reconstruct such condition-specific expression in fungal genomes is particularly importan...
Gene Expression Saccharomyces cerevisiae Deep Learning Computational Biology Transcription Factors
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Improving Enhancer Identification with a Multi-Classifier Stacked Ensemble Model.

Journal of molecular biology Oct 16, 2023
Enhancers are DNA regions that are responsible for controlling the expression of genes. Enhancers are usually found upstream or downstream of a gene, or even inside a gene's intron region, but are normally located at a distant location from the genes...
Computational Biology Transcription Factors Sequence Analysis, DNA Machine Learning DNA Enhancer Elements, Genetic
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KDeep: a new memory-efficient data extraction method for accurately predicting DNA/RNA transcription factor binding sites.

Journal of translational medicine Oct 16, 2023
This paper addresses the crucial task of identifying DNA/RNA binding sites, which has implications in drug/vaccine design, protein engineering, and cancer research. Existing methods utilize complex neural network structures, diverse input types, and ...
Binding Sites Neural Networks, Computer Transcription Factors Protein Binding DNA
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DeepCAC: a deep learning approach on DNA transcription factors classification based on multi-head self-attention and concatenate convolutional neural network.

BMC bioinformatics Sep 18, 2023
Understanding gene expression processes necessitates the accurate classification and identification of transcription factors, which is supported by high-throughput sequencing technologies. However, these techniques suffer from inherent limitations su...
DNA Computational Biology Neural Networks, Computer Transcription Factors Deep Learning
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