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Variable-Length Promoter Strength Prediction Based on Graph Convolution
Engineering promoters play a crucial role in cellular factory design by allowing specific engineering gene expression and regulating its expression...
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3D Enhancer–promoter networks provide predictive features for gene expression and coregulation in early embryonic lineages
Mammalian embryogenesis commences with two pivotal and binary cell fate decisions that give rise to three essential lineages: the trophectoderm, the...
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Evaluation of cucumber UBL5 promoter as a tool for transgene expression and genome editing in plants
Transgene expression and genome editing can help improve cucumber varieties to better respond to climate change. This study aimed to evaluate the...
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The human EF1a promoter does not provide expression of the transgene in mice
In this work, we set out to create mice susceptible to the SARS-CoV-2 coronavirus. To ensure the ubiquitous expression of the human ACE2 gene we used...
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PredPromoter-MF(2L): A Novel Approach of Promoter Prediction Based on Multi-source Feature Fusion and Deep Forest
AbstractPromoters short DNA sequences play vital roles in initiating gene transcription. However, it remains a challenge to identify promoters using...
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PAUSE: principled feature attribution for unsupervised gene expression analysis
As interest in using unsupervised deep learning models to analyze gene expression data has grown, an increasing number of methods have been developed...
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Cellular reprogramming is driven by widespread rewiring of promoter-enhancer interactions
BackgroundLong-range interactions between promoters and cis -regulatory elements, such as enhancers, play critical roles in gene regulation. However,...
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The Role of CTCF-Mediated Chromatin Loo** in Enhancer-Promoter Communication
In vertebrates, gene transcription is performed by generic eukaryotic molecular machinery under influence of sequence-specific DNA-binding...
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An efficient CRISPR–Cas12a promoter editing system for crop improvement
Promoter editing represents an innovative approach to introduce quantitative trait variation (QTV) in crops. However, an efficient promoter editing...
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CDKN2A promoter methylation enhances self-renewal of glioblastoma stem cells and confers resistance to carmustine
BackgroundGlioblastoma, a highly aggressive form of brain cancer, poses significant challenges due to its resistance to therapy and high recurrence...
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msBERT-Promoter: a multi-scale ensemble predictor based on BERT pre-trained model for the two-stage prediction of DNA promoters and their strengths
BackgroundA promoter is a specific sequence in DNA that has transcriptional regulatory functions, playing a role in initiating gene expression....
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Integrative genomic analyses of promoter G-quadruplexes reveal their selective constraint and association with gene activation
G-quadruplexes (G4s) regulate DNA replication and gene transcription, and are enriched in promoters without fully appreciated functional relevance....
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HDAC1/2/3 are major histone desuccinylases critical for promoter desuccinylation
Lysine succinylation is one of the major post-translational modifications occurring on histones and is believed to have significant roles in...
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i5mC-DCGA: an improved hybrid network framework based on the CBAM attention mechanism for identifying promoter 5mC sites
Background5-Methylcytosine (5mC) plays a very important role in gene stability, transcription, and development. Therefore, accurate identification of...
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Synthetic sub-genomic transcript promoter from Horseradish Latent Virus (HRLV)
Main conclusionWe characterized an efficient chimeric sub-genomic transcript promoter from Horseradish Latent Virus, FHS4, active in both dicot and...
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EPI-Trans: an effective transformer-based deep learning model for enhancer promoter interaction prediction
BackgroundRecognition of enhancer–promoter Interactions (EPIs) is crucial for human development. EPIs in the genome play a key role in regulating...
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CENPA knockdown restrains cell progression and tumor growth in breast cancer by reducing PLA2R1 promoter methylation and modulating PLA2R1/HHEX axis
BackgroundBreast cancer is a lethal malignancy affecting females worldwide. It has been reported that upregulated centromere protein A (CENPA)...
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Su(var)3-9 mediates age-dependent increase in H3K9 methylation on TDP-43 promoter triggering neurodegeneration
Aging progressively modifies the physiological balance of the organism increasing susceptibility to both genetic and sporadic neurodegenerative...
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PriPath: identifying dysregulated pathways from differential gene expression via grou**, scoring, and modeling with an embedded feature selection approach
BackgroundCell homeostasis relies on the concerted actions of genes, and dysregulated genes can lead to diseases. In living organisms, genes or their...
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Identification of the inducible activity in the promoter of the soybean BBI-DII gene exposed to abiotic stress or abscisic acid
The expression of the soybean Bowman–Birk proteinase isoinhibitor DII ( BBI-DII ) gene and the inducible activity of its promoter were studied under...
