Genetics

Genotoxicity evaluation of titanium dioxide nanoparticles using the mouse lymphoma assay and the Ames test.

Titanium dioxide nanoparticles (TiO-NPs) are widely used in the cosmetics, health, and food industries, but their safety and genotoxicity remain a matter of debate. We investigated whether TiO-NPs could induce gene mutations in mouse lymphoma L5178Y cells and Salmonella typhimurium strains TA97a, TA98, TA100, TA102, and TA1535. Following preliminary tests, 2 mg/mL for the mouse lymphoma gene mutat...

Label-Free Pathogen Detection by a Deoxyribozyme Cascade with Visual Signal Readout.

A colorimetric nucleic acid based test for label-free pathogen detection has been developed and used for the detection of the Zika virus. The test relies on nucleic acid sequence-based amplification (NASBA) of a viral RNA followed by interrogation of the amplicon by a cascade of deoxyribozymes constituting a visual split deoxyribozyme (vsDz) probe. The probe consists of a split phosphodiesterase d...

Deep learning identifies genome-wide DNA binding sites of long noncoding RNAs.

Long noncoding RNAs (lncRNAs) can exert their function by interacting with the DNA via triplex structure formation. Even though this has been validate...

RNA3DCNN: Local and global quality assessments of RNA 3D structures using 3D deep convolutional neural networks.

Quality assessment is essential for the computational prediction and design of RNA tertiary structures. To date, several knowledge-based statistical p...

Sensitive detection of uracil-DNA glycosylase (UDG) activity based on terminal deoxynucleotidyl transferase-assisted formation of fluorescent copper nanoclusters (CuNCs).

As an important base excision repair (BER) enzyme, uracil-DNA glycosylase (UDG) can repair the uracil-induced DNA lesion and maintain the genomic inte...

A versatile assay for alkaline phosphatase detection based on thymine-Hg-thymine structure generation mediated by TdT.

Alkaline phosphatase (ALP) is a vital hydrolysis enzyme in phosphate metabolism, which catalyzes the hydrolysis of phosphate ester groups in proteins,...

Deleterious Non-Synonymous Single Nucleotide Polymorphism Predictions on Human Transcription Factors.

Transcription factors (TFs) are the major components of human gene regulation. In particular, they bind onto specific DNA sequences and regulate neigh...

Machine Learning Methods as a Tool for Predicting Risk of Illness Applying Next-Generation Sequencing Data.

Next-generation sequencing (NGS) data present an untapped potential to improve microbial risk assessment (MRA) through increased specificity and redef...

Changes in the expression of four ABC transporter genes in response to imidacloprid in Bemisia tabaci Q (Hemiptera: Aleyrodidae).

Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae), a globally invasive species complex that causes serious damage to field crops, has developed resi...

Deep learning architectures for prediction of nucleosome positioning from sequences data.

BACKGROUND: Nucleosomes are DNA-histone complex, each wrapping about 150 pairs of double-stranded DNA. Their function is fundamental for one of the pr...

Bi-stream CNN Down Syndrome screening model based on genotyping array.

BACKGROUND: Human Down syndrome (DS) is usually caused by genomic micro-duplications and dosage imbalances of human chromosome 21. It is associated wi...

Gene Ontology-based function prediction of long non-coding RNAs using bi-random walk.

BACKGROUND: With the development of sequencing technology, more and more long non-coding RNAs (lncRNAs) have been identified. Some lncRNAs have been c...

Deepbinner: Demultiplexing barcoded Oxford Nanopore reads with deep convolutional neural networks.

Multiplexing, the simultaneous sequencing of multiple barcoded DNA samples on a single flow cell, has made Oxford Nanopore sequencing cost-effective f...

Laplacian regularized low-rank representation for cancer samples clustering.

Cancer samples clustering based on biomolecular data has been becoming an important tool for cancer classification. The recognition of cancer types is...

Evaluation of the bias and precision of regression techniques and machine learning approaches in total dissolved solids modeling of an urban aquifer.

TDS is modeled for an aquifer near an unlined landfill in Canada. Canadian Drinking Water Guidelines and other indices are used to evaluate TDS concen...

Molecular prevalence of parvovirus B19 among HIV1-infected patients in Iran.

Different outcomes of parvovirus B19 (B19V) infection in immunocompromised patients, including HIV1-infected persons, may be life-threatening. Consid...

A machine learning approach for reliable prediction of amino acid interactions and its application in the directed evolution of enantioselective enzymes.

Directed evolution is an important research activity in synthetic biology and biotechnology. Numerous reports describe the application of tedious muta...

Prognostic models in primary biliary cholangitis.

Risk prediction modelling is important to better understand the determinants of the course and outcome of PBC and to inform the risk across the diseas...

Modeling and Predicting the Activities of Trans-Acting Splicing Factors with Machine Learning.

Alternative splicing (AS) is generally regulated by trans-splicing factors that specifically bind to cis-elements in pre-mRNAs. The human genome encod...

A Deep Neural Network Model using Random Forest to Extract Feature Representation for Gene Expression Data Classification.

In predictive model development, gene expression data is associated with the unique challenge that the number of samples (n) is much smaller than the ...