Genetics

Genetic Bee Colony (GBC) algorithm: A new gene selection method for microarray cancer classification.

Naturally inspired evolutionary algorithms prove effectiveness when used for solving feature selection and classification problems. Artificial Bee Colony (ABC) is a relatively new swarm intelligence method. In this paper, we propose a new hybrid gene selection method, namely Genetic Bee Colony (GBC) algorithm. The proposed algorithm combines the used of a Genetic Algorithm (GA) along with Artifici...

Analysis of strand-specific RNA-seq data using machine learning reveals the structures of transcription units in Clostridium thermocellum.

Identification of transcription units (TUs) encoded in a bacterial genome is essential to elucidation of transcriptional regulation of the organism. To gain a detailed understanding of the dynamically composed TU structures, we have used four strand-specific RNA-seq (ssRNA-seq) datasets collected under two experimental conditions to derive the genomic TU organization of Clostridium thermocellum us...

Human pulmonary artery endothelial cells in the model of mucopolysaccharidosis VI present a prohypertensive phenotype.

BACKGROUND: Mucopolysaccharidosis type VI (MPS VI) is an autosomal recessive lysosomal disorder caused by a deficient activity of N-acetylgalactosamin...

Lung cancer prediction using neural network ensemble with histogram of oriented gradient genomic features.

This paper reports an experimental comparison of artificial neural network (ANN) and support vector machine (SVM) ensembles and their "nonensemble" va...

A semi-supervised learning approach for RNA secondary structure prediction.

RNA secondary structure prediction is a key technology in RNA bioinformatics. Most algorithms for RNA secondary structure prediction use probabilistic...

HPOSim: an R package for phenotypic similarity measure and enrichment analysis based on the human phenotype ontology.

BACKGROUND: Phenotypic features associated with genes and diseases play an important role in disease-related studies and most of the available methods...

Computationally predicting protein-RNA interactions using only positive and unlabeled examples.

Protein-RNA interactions (PRIs) are considerably important in a wide variety of cellular processes, ranging from transcriptional and post-transcriptio...

Identifying DNA-binding proteins by combining support vector machine and PSSM distance transformation.

BACKGROUND: DNA-binding proteins play a pivotal role in various intra- and extra-cellular activities ranging from DNA replication to gene expression c...

Multifactor dimensionality reduction analysis to elucidate the cross-talk between one-carbon and xenobiotic metabolic pathways in multi-disease models.

Putatively functional polymorphisms of one-carbon and xenobiotic metabolic pathways influence susceptibility for wide spectrum of diseases. The curren...

Universal Memcomputing Machines.

We introduce the notion of universal memcomputing machines (UMMs): a class of brain-inspired general-purpose computing machines based on systems with ...

16S classifier: a tool for fast and accurate taxonomic classification of 16S rRNA hypervariable regions in metagenomic datasets.

The diversity of microbial species in a metagenomic study is commonly assessed using 16S rRNA gene sequencing. With the rapid developments in genome s...

Pharmacokinetics of single and repeat doses of icatibant.

PURPOSE: Icatibant is a bradykinin-2 receptor antagonist approved to treat acute hereditary angioedema attacks in adults. To-date, no thorough investi...

EcoliNet: a database of cofunctional gene network for Escherichia coli.

During the past several decades, Escherichia coli has been a treasure chest for molecular biology. The molecular mechanisms of many fundamental cellul...

Prediction of success for polymerase chain reactions using the Markov maximal order model and support vector machine.

Polymerase chain reaction (PCR) is hailed as one of the monumental scientific techniques of the twentieth century, and has become a common and often i...

Scene recognition by manifold regularized deep learning architecture.

Scene recognition is an important problem in the field of computer vision, because it helps to narrow the gap between the computer and the human being...

Genome-wide association data classification and SNPs selection using two-stage quality-based Random Forests.

BACKGROUND: Single-nucleotide polymorphisms (SNPs) selection and identification are the most important tasks in Genome-wide association data analysis....

Construction of a fuzzy and Boolean logic gates based on DNA.

Logic gates are devices that can perform logical operations by transforming a set of inputs into a predictable single detectable output. The hybridiza...

Semantic similarity measurement between gene ontology terms based on exclusively inherited shared information.

Quantifying the semantic similarities between pairs of terms in the Gene Ontology (GO) structure can help to explore the functional relationships betw...

RNA splicing. The human splicing code reveals new insights into the genetic determinants of disease.

To facilitate precision medicine and whole-genome annotation, we developed a machine-learning technique that scores how strongly genetic variants affe...

Classification of lung cancer using ensemble-based feature selection and machine learning methods.

Lung cancer is one of the leading causes of death worldwide. There are three major types of lung cancers, non-small cell lung cancer (NSCLC), small ce...