AIMC Topic: DNA

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iDHS-Deep: an integrated tool for predicting DNase I hypersensitive sites by deep neural network.

Briefings in bioinformatics Sep 2, 2021
DNase I hypersensitive site (DHS) refers to the hypersensitive region of chromatin for the DNase I enzyme. It is an important part of the noncoding region and contains a variety of regulatory elements, such as promoter, enhancer, and transcription fa...
Protein Binding Transcription Factors DNA Humans Software Deep Learning Transcription, Genetic Enhancer Elements, Genetic Arabidopsis Genetic Loci Chromatin Datasets as Topic Deoxyribonuclease I Promoter Regions, Genetic Internet Oryza
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A transformer architecture based on BERT and 2D convolutional neural network to identify DNA enhancers from sequence information.

Briefings in bioinformatics Sep 2, 2021
Recently, language representation models have drawn a lot of attention in the natural language processing field due to their remarkable results. Among them, bidirectional encoder representations from transformers (BERT) has proven to be a simple, yet...
Computational Biology Humans Natural Language Processing DNA Computer Simulation Transcription, Genetic Sensitivity and Specificity Multilingualism Deep Learning Enhancer Elements, Genetic Models, Biological Data Accuracy Semantics
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Bound2Learn: a machine learning approach for classification of DNA-bound proteins from single-molecule tracking experiments.

Nucleic acids research Aug 20, 2021
DNA-bound proteins are essential elements for the maintenance, regulation, and use of the genome. The time they spend bound to DNA provides useful information on their stability within protein complexes and insight into the understanding of biologica...
Saccharomyces cerevisiae Single Molecule Imaging Time-Lapse Imaging DNA Kinetics DNA-Binding Proteins Machine Learning Algorithms Computer Simulation Protein Binding Computational Biology Escherichia coli
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Optical microlever assisted DNA stretching.

Optics express Aug 2, 2021
Optical microrobotics is an emerging field that has the potential to improve upon current optical tweezer studies through avenues such as limiting the exposure of biological molecules of interest to laser radiation and overcoming the current limitati...
Nucleic Acid Conformation Optics and Photonics Optical Tweezers DNA Proof of Concept Study Robotics
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dSPRINT: predicting DNA, RNA, ion, peptide and small molecule interaction sites within protein domains.

Nucleic acids research Jul 21, 2021
Domains are instrumental in facilitating protein interactions with DNA, RNA, small molecules, ions and peptides. Identifying ligand-binding domains within sequences is a critical step in protein function annotation, and the ligand-binding properties ...
DNA Protein Domains RNA Ions Ligands Binding Sites Humans Machine Learning Peptides
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A survey on deep learning in DNA/RNA motif mining.

Briefings in bioinformatics Jul 20, 2021
DNA/RNA motif mining is the foundation of gene function research. The DNA/RNA motif mining plays an extremely important role in identifying the DNA- or RNA-protein binding site, which helps to understand the mechanism of gene regulation and managemen...
Sequence Analysis, RNA Sequence Analysis, DNA Neural Networks, Computer RNA DNA Nucleotide Motifs
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keras_dna: a wrapper for fast implementation of deep learning models in genomics.

Bioinformatics (Oxford, England) Jul 12, 2021
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...
DNA Software Deep Learning Genome Genomics
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Enabling autonomous scanning probe microscopy imaging of single molecules with deep learning.

Nanoscale May 27, 2021
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...
Microscopy, Atomic Force Microscopy, Scanning Probe DNA Deep Learning Nanotechnology
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GraphBind: protein structural context embedded rules learned by hierarchical graph neural networks for recognizing nucleic-acid-binding residues.

Nucleic acids research May 21, 2021
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...
Protein Conformation Binding Sites Neural Networks, Computer DNA Software DNA-Binding Proteins Protein Binding RNA RNA-Binding Proteins
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Interpretation of deep learning in genomics and epigenomics.

Briefings in bioinformatics May 20, 2021
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...
Epigenesis, Genetic RNA Neural Networks, Computer DNA Protein Binding Chromatin Deep Learning Gene Expression Genomics Computational Biology
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