AIMC Topic: DNA
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Physicochemical property based computational scheme for classifying DNA sequence elements of Saccharomyces cerevisiae.
Computational biology and chemistry
Dec 26, 2018
GenerationE of huge "omics" data necessitates the development and application of computational methods to annotate the data in terms of biological features. In the context of DNA sequence, it is important to unravel the hidden physicochemical signatu...
Unlocking the hidden talent of DNA: Unexpected catalytic activity for colorimetric assay of alkaline phosphatase.
Analytica chimica acta
Dec 21, 2018
Carboxylic acids have been efficiently used to activate HO to form even more potent oxidant-peroxy acids through enzyme-catalyzed processes. By employing acetic acid as the activator, herein we report for the first time that cofactor-free DNA display...
An SVM-based method for assessment of transcription factor-DNA complex models.
BMC bioinformatics
Dec 21, 2018
BACKGROUND: Atomic details of protein-DNA complexes can provide insightful information for better understanding of the function and binding specificity of DNA binding proteins. In addition to experimental methods for solving protein-DNA complex struc...
Setting Up a Surface-Enhanced Raman Scattering Database for Artificial-Intelligence-Based Label-Free Discrimination of Tumor Suppressor Genes.
Analytical chemistry
Dec 4, 2018
The quality of input data in deep learning is tightly associated with the ultimate performance of the machine learner. Taking advantage of the unique merits of surface-enhanced Raman scattering (SERS) methodology in the collection and construction of...
Porcine single nucleotide polymorphisms and their functional effect: an update.
BMC research notes
Dec 4, 2018
OBJECTIVE: To aid in the development of a comprehensive list of functional variants in the swine genome, single nucleotide polymorphisms (SNP) were identified from whole genome sequence of 240 pigs. Interim data from 72 animals in this study was publ...
Deep learning identifies genome-wide DNA binding sites of long noncoding RNAs.
RNA biology
Nov 28, 2018
Long noncoding RNAs (lncRNAs) can exert their function by interacting with the DNA via triplex structure formation. Even though this has been validated with a handful of experiments, a genome-wide analysis of lncRNA-DNA binding is needed. In this pap...
Sensitive detection of uracil-DNA glycosylase (UDG) activity based on terminal deoxynucleotidyl transferase-assisted formation of fluorescent copper nanoclusters (CuNCs).
Talanta
Nov 24, 2018
As an important base excision repair (BER) enzyme, uracil-DNA glycosylase (UDG) can repair the uracil-induced DNA lesion and maintain the genomic integrity. Herein, we have proposed a sensitive UDG assay based on the terminal deoxynucleotidyl transfe...
Deepbinner: Demultiplexing barcoded Oxford Nanopore reads with deep convolutional neural networks.
PLoS computational biology
Nov 20, 2018
Multiplexing, the simultaneous sequencing of multiple barcoded DNA samples on a single flow cell, has made Oxford Nanopore sequencing cost-effective for small genomes. However, it depends on the ability to sort the resulting sequencing reads by barco...
A novel helper qPCR system for platinum detection via Pt-DNA coordination.
Analytica chimica acta
Nov 8, 2018
A novel real-time polymerase chain reaction (qPCR) platform for the simple and robust detection of platinum is described for the first time. Compared with conventional qPCR, a helper template, which is related to the active template for performing qP...
Weakly-Supervised Convolutional Neural Network Architecture for Predicting Protein-DNA Binding.
IEEE/ACM transactions on computational biology and bioinformatics
Aug 7, 2018
Although convolutional neural networks (CNN) have outperformed conventional methods in predicting the sequence specificities of protein-DNA binding in recent years, they do not take full advantage of the intrinsic weakly-supervised information of DNA...
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