Transcription factors (TFs) are proteins essential for regulating genetic transcriptions by binding to transcription factor binding sites (TFBSs) in DNA sequences. Accurate predictions of TFBSs can contribute to the design and construction of metabol...
Frontiers in bioscience (Landmark edition)
Feb 21, 2024
BACKGROUND: Cerebral Cavernous Malformations (CCMs) are brain vascular abnormalities associated with an increased risk of hemorrhagic strokes. Familial CCMs result from autosomal dominant inheritance involving three genes: (), (), and (). CCM1 and...
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2024
Deep learning has emerged as a powerful tool for solving complex problems, including reconstruction of gene regulatory networks within the realm of biology. These networks consist of transcription factors and their associations with genes they regula...
Precise targeting of transcription factor binding sites (TFBSs) is essential to comprehending transcriptional regulatory processes and investigating cellular function. Although several deep learning algorithms have been created to predict TFBSs, the ...
Interactions between DNA and transcription factors (TFs) play an essential role in understanding transcriptional regulation mechanisms and gene expression. Due to the large accumulation of training data and low expense, deep learning methods have sho...
Cancer is a disease of gene dysregulation, where cells acquire somatic and epigenetic alterations that drive aberrant cellular signaling. These alterations adversely impact transcriptional programs and cause profound changes in gene expression. Inter...
We present a physics-based machine learning approach to predict in vitro transcription factor binding affinities from structural and mechanical DNA properties directly derived from atomistic molecular dynamics simulations. The method is able to predi...
MOTIVATION: Histone modifications are epigenetic markers that impact gene expression by altering the chromatin structure or recruiting histone modifiers. Their accurate identification is key to unraveling the mechanisms by which they regulate gene ex...
In the evolutionary history of plants, variation in cis-regulatory elements (CREs) resulting in diversification of gene expression has played a central role in driving the evolution of lineage-specific traits. However, it is difficult to predict expr...
PURPOSE: Prior studies have demonstrated the significance of specific cis-regulatory variants in retinal disease; however, determining the functional impact of regulatory variants remains a major challenge. In this study, we utilized a machine learni...