AIMC Topic: DNA
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Restarting and recentering genetic algorithm variations for DNA fragment assembly: The necessity of a multi-strategy approach.
Bio Systems
Aug 10, 2016
DNA Fragment assembly - an NP-Hard problem - is one of the major steps in of DNA sequencing. Multiple strategies have been used for this problem, including greedy graph-based algorithms, deBruijn graphs, and the overlap-layout-consensus approach. Thi...
gDNA-Prot: Predict DNA-binding proteins by employing support vector machine and a novel numerical characterization of protein sequence.
Journal of theoretical biology
Jul 1, 2016
DNA-binding proteins are the functional proteins in cells, which play an important role in various essential biological activities. An effective and fast computational method gDNA-Prot is proposed to predict DNA-binding proteins in this paper, which ...
DanQ: a hybrid convolutional and recurrent deep neural network for quantifying the function of DNA sequences.
Nucleic acids research
Apr 15, 2016
Modeling the properties and functions of DNA sequences is an important, but challenging task in the broad field of genomics. This task is particularly difficult for non-coding DNA, the vast majority of which is still poorly understood in terms of fun...
Classifying Force Spectroscopy of DNA Pulling Measurements Using Supervised and Unsupervised Machine Learning Methods.
Journal of chemical information and modeling
Apr 4, 2016
Dynamic force spectroscopy (DFS) measurements on biomolecules typically require classifying thousands of repeated force spectra prior to data analysis. Here, we study classification of atomic force microscope-based DFS measurements using machine-lear...
Recombination spot identification Based on gapped k-mers.
Scientific reports
Mar 31, 2016
Recombination is crucial for biological evolution, which provides many new combinations of genetic diversity. Accurate identification of recombination spots is useful for DNA function study. To improve the prediction accuracy, researchers have propos...
LS-GKM: a new gkm-SVM for large-scale datasets.
Bioinformatics (Oxford, England)
Mar 15, 2016
UNLABELLED: gkm-SVM is a sequence-based method for predicting and detecting the regulatory vocabulary encoded in functional DNA elements, and is a commonly used tool for studying gene regulatory mechanisms. Here we introduce new software, LS-GKM, whi...
Predicting transcription factor site occupancy using DNA sequence intrinsic and cell-type specific chromatin features.
BMC bioinformatics
Jan 11, 2016
BACKGROUND: Understanding the mechanisms by which transcription factors (TF) are recruited to their physiological target sites is crucial for understanding gene regulation. DNA sequence intrinsic features such as predicted binding affinity are often ...
On fuzzy semantic similarity measure for DNA coding.
Computers in biology and medicine
Dec 31, 2015
A coding measure scheme numerically translates the DNA sequence to a time domain signal for protein coding regions identification. A number of coding measure schemes based on numerology, geometry, fixed mapping, statistical characteristics and chemic...
Preparation of Concentrated Chitosan/DNA Nanoparticle Formulations by Lyophilization for Gene Delivery at Clinically Relevant Dosages.
Journal of pharmaceutical sciences
Dec 23, 2015
Chitosan/DNA polyplexes have been optimized for efficient and safe in vitro and in vivo gene delivery. Clinical application of this technology requires the development of formulations with higher concentrations to reach therapeutic dosages. Polyplexe...
Isolation and analysis of cell-free fetal DNA from maternal peripheral blood in Chinese women.
Genetics and molecular research : GMR
Dec 22, 2015
Non-invasive prenatal diagnosis is used to detect the genetic material of the fetus by isolating the cell-free fetal DNA (cffDNA) from maternal peripheral blood. In order to establish an isolation method for cffDNA from maternal peripheral blood in C...
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