AIMC Topic: Sequence Analysis, DNA

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FF-QuantSC: accurate quantification of fetal fraction by a neural network model.

Molecular genetics & genomic medicine Apr 13, 2020
BACKGROUND: Noninvasive prenatal testing (NIPT) is one of the most commonly employed clinical measures for screening of fetal aneuploidy. Fetal Fraction (ff) has been demonstrated to be one of the key factors affecting the performance of NIPT. Accura...
Neural Networks, Computer Software Pregnancy Humans Sensitivity and Specificity Sequence Analysis, DNA Noninvasive Prenatal Testing Female Adult
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Machine Learning Techniques for Classifying the Mutagenic Origins of Point Mutations.

Genetics Mar 19, 2020
There is increasing interest in developing diagnostics that discriminate individual mutagenic mechanisms in a range of applications that include identifying population-specific mutagenesis and resolving distinct mutation signatures in cancer samples....
Machine Learning Sequence Analysis, DNA Mutagens Nucleotide Motifs Animals Mice Point Mutation Ethylnitrosourea
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Machine Learning-Guided Prediction of Antigen-Reactive In Silico Clonotypes Based on Changes in Clonal Abundance through Bio-Panning.

Biomolecules Mar 8, 2020
c-Met is a promising target in cancer therapy for its intrinsic oncogenic properties. However, there are currently no c-Met-specific inhibitors available in the clinic. Antibodies blocking the interaction with its only known ligand, hepatocyte growth...
Antigens Chickens Machine Learning Sequence Analysis, DNA Animals Avian Proteins Single-Chain Antibodies Cloning, Molecular
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Second-Generation Sequencing with Deep Reinforcement Learning for Lung Infection Detection.

Journal of healthcare engineering Feb 22, 2020
Recently, deep reinforcement learning, associated with medical big data generated and collected from medical Internet of Things, is prospective for computer-aided diagnosis and therapy. In this paper, we focus on the application value of the second-g...
Sequence Analysis, DNA Lung Diseases Diagnosis, Computer-Assisted Deep Learning Prospective Studies Gene Expression Profiling Humans
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iEnhancer-ECNN: identifying enhancers and their strength using ensembles of convolutional neural networks.

BMC genomics Dec 24, 2019
BACKGROUND: Enhancers are non-coding DNA fragments which are crucial in gene regulation (e.g. transcription and translation). Having high locational variation and free scattering in 98% of non-encoding genomes, enhancer identification is, therefore, ...
Sequence Analysis, DNA Neural Networks, Computer Enhancer Elements, Genetic
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Evaluation of colorectal cancer subtypes and cell lines using deep learning.

Life science alliance Dec 2, 2019
Colorectal cancer (CRC) is a common cancer with a high mortality rate and a rising incidence rate in the developed world. Molecular profiling techniques have been used to better understand the variability between tumors and disease models such as cel...
Mutation Models, Biological DNA Copy Number Variations Neoplasm Proteins Cell Line, Tumor Sequence Analysis, DNA Machine Learning Colorectal Neoplasms Gene Expression Profiling Deep Learning Biomarkers, Tumor Humans
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ReorientExpress: reference-free orientation of nanopore cDNA reads with deep learning.

Genome biology Nov 29, 2019
We describe ReorientExpress, a method to perform reference-free orientation of transcriptomic long sequencing reads. ReorientExpress uses deep learning to correctly predict the orientation of the majority of reads, and in particular when trained on a...
DNA, Complementary Nanopore Sequencing Deep Learning Sequence Analysis, DNA Software
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Splice sites detection using chaos game representation and neural network.

Genomics Nov 5, 2019
A novel method is proposed to detect the acceptor and donor splice sites using chaos game representation and artificial neural network. In order to achieve high accuracy, inputs to the neural network, or feature vector, shall reflect the true nature ...
Humans Neural Networks, Computer Sequence Analysis, DNA RNA Splice Sites Software Nonlinear Dynamics
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D-GPM: A Deep Learning Method for Gene Promoter Methylation Inference.

Genes Oct 14, 2019
Whole-genome bisulfite sequencing generates a comprehensive profiling of the gene methylation levels, but is limited by a high cost. Recent studies have partitioned the genes into landmark genes and target genes and suggested that the landmark gene e...
Sequence Analysis, DNA DNA Methylation Gene Expression Deep Learning Computational Biology Gene Expression Regulation Promoter Regions, Genetic Linear Models CpG Islands Machine Learning Gene Expression Profiling Humans
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Identification of prokaryotic promoters and their strength by integrating heterogeneous features.

Genomics Aug 19, 2019
The promoter is a regulatory DNA region and important for gene transcriptional regulation. It is located near the transcription start site (TSS) upstream of the corresponding gene. In the post-genomics era, the availability of data makes it possible ...
Genome, Bacterial Genome, Archaeal Sequence Analysis, DNA Promoter Regions, Genetic Software Deep Learning
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