AIMC Topic: DNA

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Predicting DNA Methylation States with Hybrid Information Based Deep-Learning Model.

IEEE/ACM transactions on computational biology and bioinformatics Apr 3, 2019
DNA methylation plays an important role in the regulation of some biological processes. Up to now, with the development of machine learning models, there are several sequence-based deep learning models designed to predict DNA methylation states, whic...
Humans Deep Learning Cell Line, Tumor DNA High-Throughput Nucleotide Sequencing Histone Code Computational Biology Sequence Analysis, DNA DNA Methylation
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Machine Learning Prediction of DNA Charge Transport.

The journal of physical chemistry. B Mar 13, 2019
First-principles calculations of charge transfer in DNA molecules are computationally expensive given that conducting charge carriers interact with intra- and intermolecular atomic motion. Screening sequences, for example, to identify excellent elect...
DNA Electron Transport Electric Conductivity Machine Learning
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Evolutionarily informed deep learning methods for predicting relative transcript abundance from DNA sequence.

Proceedings of the National Academy of Sciences of the United States of America Mar 6, 2019
Deep learning methodologies have revolutionized prediction in many fields and show potential to do the same in molecular biology and genetics. However, applying these methods in their current forms ignores evolutionary dependencies within biological ...
Base Sequence Deep Learning Transcription, Genetic Models, Theoretical Sequence Analysis, DNA Evolution, Molecular DNA Gene Expression Regulation
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iEnhancer-5Step: Identifying enhancers using hidden information of DNA sequences via Chou's 5-step rule and word embedding.

Analytical biochemistry Feb 26, 2019
An enhancer is a short (50-1500bp) region of DNA that plays an important role in gene expression and the production of RNA and proteins. Genetic variation in enhancers has been linked to many human diseases, such as cancer, disorder or inflammatory b...
Enhancer Elements, Genetic Sequence Analysis, DNA DNA Humans Computational Biology Support Vector Machine
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Standardizing Automated DNA Assembly: Best Practices, Metrics, and Protocols Using Robots.

SLAS technology Feb 15, 2019
The advancement of synthetic biology requires the ability to create new DNA sequences to produce unique behaviors in biological systems. Automation is increasingly employed to carry out well-established assembly methods of DNA fragments in a multiple...
Synthetic Biology Practice Guidelines as Topic Cloning, Molecular Automation, Laboratory Robotics DNA Genetic Engineering
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Automation of the standard DNA differential extraction on the Hamilton AutoLys STAR system: A proof-of-concept study.

Forensic science international. Genetics Feb 13, 2019
For several decades, a common approach for processing sexual assault evidence has been to use the "standard" differential extraction to separate the evidence into a non-sperm-cell fraction and a sperm-cell fraction for further analysis. In this stand...
Microsatellite Repeats DNA Fingerprinting Sex Offenses Polymerase Chain Reaction Specimen Handling Male Robotics DNA Semen Automation Humans Female
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Prediction of TF-Binding Site by Inclusion of Higher Order Position Dependencies.

IEEE/ACM transactions on computational biology and bioinformatics Jan 10, 2019
Most proposed methods for TF-binding site (TFBS) predictions only use low order dependencies for predictions due to the lack of efficient methods to extract higher order dependencies. In this work, we first propose a novel method to extract higher or...
Humans Proteins Transcription Factors Neural Networks, Computer Mice DNA Animals Databases, Genetic Computational Biology Binding Sites Protein Binding Models, Statistical
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Convolutional neural network based on SMILES representation of compounds for detecting chemical motif.

BMC bioinformatics Dec 31, 2018
BACKGROUND: Previous studies have suggested deep learning to be a highly effective approach for screening lead compounds for new drugs. Several deep learning models have been developed by addressing the use of various kinds of fingerprints and graph ...
Proteins DNA Humans Models, Chemical Pharmaceutical Preparations Deep Learning Neural Networks, Computer Binding Sites Protein Binding Software
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PDRLGB: precise DNA-binding residue prediction using a light gradient boosting machine.

BMC bioinformatics Dec 31, 2018
BACKGROUND: Identifying specific residues for protein-DNA interactions are of considerable importance to better recognize the binding mechanism of protein-DNA complexes. Despite the fact that many computational DNA-binding residue prediction approach...
Binding Sites DNA DNA-Binding Proteins Protein Conformation Computational Biology Support Vector Machine Machine Learning Humans Algorithms Protein Binding
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Prediction of DNA-Binding Residues in Local Segments of Protein Sequences with Fuzzy Cognitive Maps.

IEEE/ACM transactions on computational biology and bioinformatics Dec 28, 2018
While protein-DNA interactions are crucial for a wide range of cellular functions, only a small fraction of these interactions was annotated to date. One solution to close this annotation gap is to employ computational methods that accurately predict...
Computational Biology DNA Machine Learning Fuzzy Logic DNA-Binding Proteins Algorithms Databases, Protein
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