SUMMARY: Prediction of genomic annotations from DNA sequences using deep learning is today becoming a flourishing field with many applications. Nevertheless, there are still difficulties in handling data in order to conveniently build and train model...
Scanning probe microscopies allow investigating surfaces at the nanoscale, in real space and with unparalleled signal-to-noise ratio. However, these microscopies are not used as much as it would be expected considering their potential. The main limit...
Knowledge of the interactions between proteins and nucleic acids is the basis of understanding various biological activities and designing new drugs. How to accurately identify the nucleic-acid-binding residues remains a challenging task. In this pap...
Machine learning methods have been widely applied to big data analysis in genomics and epigenomics research. Although accuracy and efficiency are common goals in many modeling tasks, model interpretability is especially important to these studies tow...
Quantifying DNA properties is a challenging task in the broad field of human genomics. Since the vast majority of non-coding DNA is still poorly understood in terms of function, this task is particularly important to have enormous benefit for biology...
DNA N4-methylcytosine (4mC) is an important epigenetic modification that plays a vital role in regulating DNA replication and expression. However, it is challenging to detect 4mC sites through experimental methods, which are time-consuming and costly...
Modifications of protein, RNA and DNA play an important role in many biological processes and are related to some diseases. Therefore, accurate identification and comprehensive understanding of protein, RNA and DNA modification sites can promote rese...
DNA molecules can electrophoretically be driven through a nanoscale opening in a material, giving rise to rich and measurable ionic current blockades. In this work, we train machine learning models on experimental ionic blockade data from DNA nucleot...
Sheng wu yi xue gong cheng xue za zhi = Journal of biomedical engineering = Shengwu yixue gongchengxue zazhi
Jun 25, 2020
In this article, based on z-curve theory and position weight matrix (PWM), a model for nucleosome sequences was constructed. Nucleosome sequence dataset was transformed into three-dimensional coordinates, PWM of the nucleosome sequences was calculate...
MOTIVATION: DNA N4-methylcytosine (4mC) is a crucial epigenetic modification. However, the knowledge about its biological functions is limited. Effective and accurate identification of 4mC sites will be helpful to reveal its biological functions and ...
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