AIMC Topic: DNA

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Reconstructing cell cycle and disease progression using deep learning.

Nature communications Sep 6, 2017
We show that deep convolutional neural networks combined with nonlinear dimension reduction enable reconstructing biological processes based on raw image data. We demonstrate this by reconstructing the cell cycle of Jurkat cells and disease progressi...
Diabetic Retinopathy Neural Networks, Computer Machine Learning Computer Simulation Humans Jurkat Cells Cell Cycle Mitosis Cell Division Reproducibility of Results Disease Progression DNA Flow Cytometry
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Next-Generation Global Biomonitoring: Large-scale, Automated Reconstruction of Ecological Networks.

Trends in ecology & evolution Mar 27, 2017
We foresee a new global-scale, ecological approach to biomonitoring emerging within the next decade that can detect ecosystem change accurately, cheaply, and generically. Next-generation sequencing of DNA sampled from the Earth's environments would p...
High-Throughput Nucleotide Sequencing Ecology Machine Learning Ecosystem Environmental Monitoring Sequence Analysis, DNA DNA Biodiversity
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DNA methylation-based forensic age prediction using artificial neural networks and next generation sequencing.

Forensic science international. Genetics Feb 28, 2017
The ability to estimate the age of the donor from recovered biological material at a crime scene can be of substantial value in forensic investigations. Aging can be complex and is associated with various molecular modifications in cells that accumul...
Aged Adult Aging Middle Aged Humans Neural Networks, Computer Machine Learning Twins, Monozygotic Saliva High-Throughput Nucleotide Sequencing CpG Islands Forensic Genetics Epigenomics DNA Methylation DNA
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Sensitive fluorescent detection of DNA methyltransferase using nicking endonuclease-mediated multiple primers-like rolling circle amplification.

Biosensors & bioelectronics Dec 30, 2016
Sensitive and reliable detection of DNA methyltransferase (MTase) is of great significance for both early tumor diagnosis and therapy. In this study, a simple, label-free and sensitive DNA MTase-sensing method was developed on the basis of a nicking ...
Endonucleases Humans G-Quadruplexes DNA Primers DNA-Cytosine Methylases DNA (Cytosine-5-)-Methyltransferases Biosensing Techniques Nucleic Acid Amplification Techniques HeLa Cells MCF-7 Cells HEK293 Cells DNA DNA (Cytosine-5-)-Methyltransferase 1 Spectrometry, Fluorescence Enzyme Assays
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An ensemble micro neural network approach for elucidating interactions between zinc finger proteins and their target DNA.

BMC genomics Dec 22, 2016
BACKGROUND: The ability to engineer zinc finger proteins binding to a DNA sequence of choice is essential for targeted genome editing to be possible. Experimental techniques and molecular docking have been successful in predicting protein-DNA interac...
Binding Sites Zinc Fingers DNA Neural Networks, Computer Models, Molecular Algorithms DNA-Binding Proteins Protein Binding Molecular Conformation
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acdc - Automated Contamination Detection and Confidence estimation for single-cell genome data.

BMC bioinformatics Dec 20, 2016
BACKGROUND: A major obstacle in single-cell sequencing is sample contamination with foreign DNA. To guarantee clean genome assemblies and to prevent the introduction of contamination into public databases, considerable quality control efforts are put...
DNA Quality Control Genome DNA Contamination Single-Cell Analysis Sequence Analysis, DNA Cluster Analysis Machine Learning
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Combining transcription factor binding affinities with open-chromatin data for accurate gene expression prediction.

Nucleic acids research Nov 29, 2016
The binding and contribution of transcription factors (TF) to cell specific gene expression is often deduced from open-chromatin measurements to avoid costly TF ChIP-seq assays. Thus, it is important to develop computational methods for accurate TF b...
Histones Binding Sites Primary Cell Culture Chromatin Chromatin Assembly and Disassembly Human Embryonic Stem Cells Hepatocytes Gene Expression Regulation Organ Specificity K562 Cells Principal Component Analysis DNA CD4-Positive T-Lymphocytes Humans Machine Learning Protein Binding Algorithms Transcription Factors Cell Line, Tumor Hep G2 Cells Cell Line
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PACE: Probabilistic Assessment for Contributor Estimation- A machine learning-based assessment of the number of contributors in DNA mixtures.

Forensic science international. Genetics Nov 24, 2016
The deconvolution of DNA mixtures remains one of the most critical challenges in the field of forensic DNA analysis. In addition, of all the data features required to perform such deconvolution, the number of contributors in the sample is widely cons...
Models, Statistical Humans DNA Machine Learning Probability Algorithms DNA Fingerprinting
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Development of amino functionalized carbon coated magnetic nanoparticles and their application to electrochemical detection of hybridization of nucleic acids.

Talanta Nov 11, 2016
In our study, the development of amino functionalized carbon coated magnetic nanoparticles (NH-CC-MNPs) and their usage for electrochemical detection of hybridization of nucleic acids have been aimed. Firstly, NH-CC-MNPs were prepared by coating of p...
Nucleic Acid Hybridization Carbon Electrochemistry DNA Guanine Magnetite Nanoparticles Electrodes Nanotechnology
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Transfer String Kernel for Cross-Context DNA-Protein Binding Prediction.

IEEE/ACM transactions on computational biology and bioinformatics Sep 15, 2016
Through sequence-based classification, this paper tries to accurately predict the DNA binding sites of transcription factors (TFs) in an unannotated cellular context. Related methods in the literature fail to perform such predictions accurately, sinc...
Animals Protein Binding Mice Computational Biology Models, Statistical DNA DNA-Binding Proteins Humans Machine Learning Algorithms
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