AIMC Topic: DNA

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A generative model for constructing nucleic acid sequences binding to a protein.

BMC genomics Dec 27, 2019
BACKGROUND: Interactions between protein and nucleic acid molecules are essential to a variety of cellular processes. A large amount of interaction data generated by high-throughput technologies have triggered the development of several computational...
Base Sequence Nucleic Acid Conformation Neural Networks, Computer Algorithms Aptamers, Nucleotide Proteins DNA Protein Binding Transcription Factors Humans
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iProDNA-CapsNet: identifying protein-DNA binding residues using capsule neural networks.

BMC bioinformatics Dec 27, 2019
BACKGROUND: Since protein-DNA interactions are highly essential to diverse biological events, accurately positioning the location of the DNA-binding residues is necessary. This biological issue, however, is currently a challenging task in the age of ...
Neural Networks, Computer Software Algorithms Humans Amino Acids DNA-Binding Proteins Amino Acid Sequence Position-Specific Scoring Matrices Reproducibility of Results ROC Curve DNA
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Super-Soft and Super-Elastic DNA Robot with Magnetically Driven Navigational Locomotion for Cell Delivery in Confined Space.

Angewandte Chemie (International ed. in English) Dec 23, 2019
Soft organisms such as earthworms can access confined, narrow spaces, inspiring scientists to fabricate soft robots for in vivo manipulation of cells or tissues and minimally invasive surgery. We report a super-soft and super-elastic magnetic DNA hyd...
Robotics DNA Animals Hydrogels Porosity Mice Microscopy, Fluorescence Drug Carriers Myocytes, Smooth Muscle Shear Strength Nucleic Acid Amplification Techniques Magnetics Doxorubicin Gene Transfer Techniques
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Representation learning of genomic sequence motifs with convolutional neural networks.

PLoS computational biology Dec 19, 2019
Although convolutional neural networks (CNNs) have been applied to a variety of computational genomics problems, there remains a large gap in our understanding of how they build representations of regulatory genomic sequences. Here we perform systema...
Transcription Factors Databases, Genetic DNA Amino Acid Motifs Deep Learning Genome, Human Humans Genomics Neural Networks, Computer Binding Sites Computational Biology Computer Simulation
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In vitro selection of DNA aptamers and their integration in a competitive voltammetric biosensor for azlocillin determination in waste water.

Analytica chimica acta Dec 16, 2019
The uncontrolled usage of veterinary antibiotics has led to their widespread pollution in waterways and milk products. Potential impact of antibiotic residues on the environment and human health such as increased antibiotic resistance of microorganis...
Electrochemical Techniques Biosensing Techniques Wastewater Base Sequence Limit of Detection Water Pollutants, Chemical Anti-Bacterial Agents Drinking Water Azlocillin DNA Aptamers, Nucleotide
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Ranking of non-coding pathogenic variants and putative essential regions of the human genome.

Nature communications Nov 20, 2019
A gene is considered essential if loss of function results in loss of viability, fitness or in disease. This concept is well established for coding genes; however, non-coding regions are thought less likely to be determinants of critical functions. H...
Genes, Reporter Chromatin Introns INDEL Mutation Enhancer Elements, Genetic DNA Gene Expression Mutation Genome, Human Humans Supervised Machine Learning Nucleic Acid Conformation Genetic Variation Computer Simulation
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Profiling of Exosomal Biomarkers for Accurate Cancer Identification: Combining DNA-PAINT with Machine- Learning-Based Classification.

Small (Weinheim an der Bergstrasse, Germany) Sep 3, 2019
Exosomes are endosome-derived vesicles enriched in body fluids such as urine, blood, and saliva. So far, they have been recognized as potential biomarkers for cancer diagnostics. However, the present single-variate analysis of exosomes has greatly li...
Humans Machine Learning Cell Line, Tumor Nanoparticles Nanotechnology DNA Biomarkers, Tumor Silicon Dioxide Exosomes Neoplasms
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Automated estimation of the number of contributors in autosomal short tandem repeat profiles using a machine learning approach.

Forensic science international. Genetics Aug 23, 2019
The number of contributors (NOC) to (complex) autosomal STR profiles cannot be determined with absolute certainty due to complicating factors such as allele sharing and allelic drop-out. The precision of NOC estimations can be improved by increasing ...
Gene Frequency Microsatellite Repeats DNA Fingerprinting Algorithms DNA Humans Alleles Machine Learning DNA Degradation, Necrotic
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Response to: 'On using machine learning algorithms to define clinically meaningful patient subgroups' by Knevel and Huizinga.

Annals of the rheumatic diseases Aug 17, 2019
Algorithms DNA Humans Machine Learning
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BindSpace decodes transcription factor binding signals by large-scale sequence embedding.

Nature methods Aug 12, 2019
The decoding of transcription factor (TF) binding signals in genomic DNA is a fundamental problem. Here we present a prediction model called BindSpace that learns to embed DNA sequences and TF labels into the same space. By training on binding data f...
Chromatin Immunoprecipitation Transcription Factors DNA Binding Sites Algorithms Protein Binding Computational Biology Humans Machine Learning
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