AIMC Topic: DNA

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Using Artificial Neural Networks to Model Errors in Biochemical Manipulation of DNA Molecules.

IEEE/ACM transactions on computational biology and bioinformatics Oct 10, 2022
In recent years, the non-biological applications of DNA molecules have made considerable progress; most of these applications were performed in vitro, involving biochemical operations such as synthesis, amplification and sequencing. Because errors ma...
Sequence Analysis, DNA DNA Neural Networks, Computer
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Artificial intelligence-augmented histopathologic review using image analysis to optimize DNA yield from formalin-fixed paraffin-embedded slides.

Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc Oct 5, 2022
To achieve minimum DNA input requirements for next-generation sequencing (NGS), pathologists visually estimate macrodissection and slide count decisions. Unfortunately, misestimation may cause tissue waste and increased laboratory costs. We developed...
Formaldehyde Paraffin Embedding Humans Artificial Intelligence Neoplasms DNA
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DPProm: A Two-Layer Predictor for Identifying Promoters and Their Types on Phage Genome Using Deep Learning.

IEEE journal of biomedical and health informatics Oct 4, 2022
With the number of phage genomes increasing, it is urgent to develop new bioinformatics methods for phage genome annotation. Promoter, a DNA region, is important for gene transcriptional regulation. In the era of post-genomics, the availability of da...
Humans Deep Learning Promoter Regions, Genetic Bacteriophages Genomics DNA
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Context dependent prediction in DNA sequence using neural networks.

PeerJ Sep 20, 2022
One way to better understand the structure in DNA is by learning to predict the sequence. Here, we trained a model to predict the missing base at any given position, given its left and right flanking contexts. Our best-performing model was a neural n...
Nucleosomes Mice Base Sequence Neural Networks, Computer Humans DNA Genome, Human Animals
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A machine learning technique for identifying DNA enhancer regions utilizing CIS-regulatory element patterns.

Scientific reports Sep 7, 2022
Enhancers regulate gene expression, by playing a crucial role in the synthesis of RNAs and proteins. They do not directly encode proteins or RNA molecules. In order to control gene expression, it is important to predict enhancers and their potency. G...
Computational Biology DNA Machine Learning Software Enhancer Elements, Genetic
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Improving the prediction of DNA-protein binding by integrating multi-scale dense convolutional network with fault-tolerant coding.

Analytical biochemistry Aug 29, 2022
Accurate prediction of DNA-protein binding (DPB) is of great biological significance for studying the regulatory mechanism of gene expression. In recent years, with the rapid development of deep learning techniques, advanced deep neural networks have...
DNA-Binding Proteins Protein Binding DNA Neural Networks, Computer Software
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Taxonomic classification of DNA sequences beyond sequence similarity using deep neural networks.

Proceedings of the National Academy of Sciences of the United States of America Aug 26, 2022
Taxonomic classification, that is, the assignment to biological clades with shared ancestry, is a common task in genetics, mainly based on a genome similarity search of large genome databases. The classification quality depends heavily on the databas...
Base Sequence Genome DNA DNA Barcoding, Taxonomic Software Algorithms Deep Learning Genomics
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iDRBP-ECHF: Identifying DNA- and RNA-binding proteins based on extensible cubic hybrid framework.

Computers in biology and medicine Aug 13, 2022
Proteins interact with nucleic acids to regulate the life activities of organisms. Therefore, how to accurately and efficiently identify nucleic acid-binding proteins (NABPs) is particularly significant. Some sequence-based computational methods have...
DNA-Binding Proteins Binding Sites RNA-Binding Proteins DNA Machine Learning Algorithms Computational Biology
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ZayyuNet - A Unified Deep Learning Model for the Identification of Epigenetic Modifications Using Raw Genomic Sequences.

IEEE/ACM transactions on computational biology and bioinformatics Aug 8, 2022
Epigenetic modifications have a vital role in gene expression and are linked to cellular processes such as differentiation, development, and tumorigenesis. Thus, the availability of reliable and accurate methods for identifying and defining these cha...
Deep Learning Genomics RNA Epigenesis, Genetic Humans DNA
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IDRBP-PPCT: Identifying Nucleic Acid-Binding Proteins Based on Position-Specific Score Matrix and Position-Specific Frequency Matrix Cross Transformation.

IEEE/ACM transactions on computational biology and bioinformatics Aug 8, 2022
DNA-binding proteins (DBPs) and RNA-binding proteins (RBPs) are two important nucleic acid-binding proteins (NABPs), which play important roles in biological processes such as replication, translation and transcription of genetic material. Some prote...
DNA Algorithms Support Vector Machine DNA-Binding Proteins Amino Acid Sequence Databases, Protein Computational Biology Position-Specific Scoring Matrices RNA-Binding Proteins
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