Genetics

Continuous Distributed Representation of Biological Sequences for Deep Proteomics and Genomics.

We introduce a new representation and feature extraction method for biological sequences. Named bio-vectors (BioVec) to refer to biological sequences in general with protein-vectors (ProtVec) for proteins (amino-acid sequences) and gene-vectors (GeneVec) for gene sequences, this representation can be widely used in applications of deep learning in proteomics and genomics. In the present paper, we ...

Evaluation of data discretization methods to derive platform independent isoform expression signatures for multi-class tumor subtyping.

BACKGROUND: Many supervised learning algorithms have been applied in deriving gene signatures for patient stratification from gene expression data. However, transferring the multi-gene signatures from one analytical platform to another without loss of classification accuracy is a major challenge. Here, we compared three unsupervised data discretization methods--Equal-width binning, Equal-frequency...

An Enhanced Differential Evolution Algorithm Based on Multiple Mutation Strategies.

Differential evolution algorithm is a simple yet efficient metaheuristic for global optimization over continuous spaces. However, there is a shortcomi...

Changes in brain ribonuclease (BRB) messenger RNA in granulosa cells (GCs) of dominant vs subordinate ovarian follicles of cattle and the regulation of BRB gene expression in bovine GCs.

Brain ribonuclease (BRB) is a member of the ribonuclease A superfamily that is constitutively expressed in a range of tissues and is the functional ho...

Characteristics of pellets with immobilized activated sludge and its performance in increasing nitrification in sequencing batch reactors at low temperatures.

Immobilized pellets obtained by means of entrapping activated sludge in waterborne polyurethane were successfully adapted in ammonium (NH4(+)-N) synth...

Ontology-Based Search of Genomic Metadata.

The Encyclopedia of DNA Elements (ENCODE) is a huge and still expanding public repository of more than 4,000 experiments and 25,000 data files, assemb...

Codon bias and gene ontology in holometabolous and hemimetabolous insects.

The relationship between preferred codon use (PCU), developmental mode, and gene ontology (GO) was investigated in a sample of nine insect species wit...

The identification of cis-regulatory elements: A review from a machine learning perspective.

The majority of the human genome consists of non-coding regions that have been called junk DNA. However, recent studies have unveiled that these regio...

Prevalence and Viral Load of Human Parvovirus B19 (B19V) Among Blood Donors in South-East Brazil.

The infection of human parvovirus B19 (B19V) is a common event in the general population, including volunteer blood donors. In some cases it can be as...

A-DaGO-Fun: an adaptable Gene Ontology semantic similarity-based functional analysis tool.

SUMMARY: Gene Ontology (GO) semantic similarity measures are being used for biological knowledge discovery based on GO annotations by integrating biol...

Genome-Wide Detection and Analysis of Multifunctional Genes.

Many genes can play a role in multiple biological processes or molecular functions. Identifying multifunctional genes at the genome-wide level and stu...

Characterization and machine learning prediction of allele-specific DNA methylation.

A large collection of Single Nucleotide Polymorphisms (SNPs) has been identified in the human genome. Currently, the epigenetic influences of SNPs on ...

Effect of MRP2 and MRP3 Polymorphisms on Anastrozole Glucuronidation and MRP2 and MRP3 Gene Expression in Normal Liver Samples.

Anastrozole is an aromatase inhibitor (AI) used as adjuvant therapy for breast cancer. Anastrozole is subject to direct glucuronidation catalyzed by U...

A Framework for Identifying Genotypic Information from Clinical Records: Exploiting Integrated Ontology Structures to Transfer Annotations between ICD Codes and Gene Ontologies.

Although some methods are proposed for automatic ontology generation, none of them address the issue of integrating large-scale heterogeneous biomedic...

Genetic Learning Particle Swarm Optimization.

Social learning in particle swarm optimization (PSO) helps collective efficiency, whereas individual reproduction in genetic algorithm (GA) facilitate...

An ensemble approach to accurately detect somatic mutations using SomaticSeq.

SomaticSeq is an accurate somatic mutation detection pipeline implementing a stochastic boosting algorithm to produce highly accurate somatic mutation...

Sparse Markov chain-based semi-supervised multi-instance multi-label method for protein function prediction.

Automated assignment of protein function has received considerable attention in recent years for genome-wide study. With the rapid accumulation of gen...

Knockdown of NADPH-cytochrome P450 reductase results in reduced resistance to buprofezin in the small brown planthopper, Laodelphax striatellus (fallén).

NADPH-cytochrome P450 reductase (CPR) plays an important role in cytochrome P450 function, and CPR knockdown in several insects leads to increased sus...

Seq-ing improved gene expression estimates from microarrays using machine learning.

BACKGROUND: Quantifying gene expression by RNA-Seq has several advantages over microarrays, including greater dynamic range and gene expression estima...

Networks that learn the precise timing of event sequences.

Neuronal circuits can learn and replay firing patterns evoked by sequences of sensory stimuli. After training, a brief cue can trigger a spatiotempora...