Genetics

Evaluation of genotoxicity after acute and chronic exposure to 2,4-dichlorophenoxyacetic acid herbicide (2,4-D) in rodents using machine learning algorithms.

2,4-Dichlorophenoxyacetic acid (2,4-D) is one of the most widely used herbicides in the world, but its mutagenic and carcinogenic potential is still controversial. We simulated environmental exposure to 2,4-D, with the objective of evaluating the genotoxic effect of acute and chronic exposure to 2,4-D in rodents. We also evaluated the performance of machine learning algorithms in detecting differe...

Revisiting CRISPR/Cas-mediated crop improvement: Special focus on nutrition.

Genome editing (GE) technology has emerged as a multifaceted strategy that instantaneously popularised the mechanism to modify the genetic constitution of an organism. The clustered regularly interspaced short palindromic repeat (CRISPR) and CRISPR-associated (Cas) protein-based genome editing (CRISPR/Cas) approach has huge potential for efficacious editing of genomes of numerous organisms. This f...

Mediated Synthesis of Silver Nanoparticles and Its Evaluation of Antineoplastic Activity to Combat Colorectal Cancer Cell Line.

Several formulations of herbal plants have been extensively applied to treat diseases. ( is an Iranian traditional plant with a wide range of benefit...

Deep learning of the back-splicing code for circular RNA formation.

MOTIVATION: Circular RNAs (circRNAs) are a new class of endogenous RNAs in animals and plants. During pre-RNA splicing, the 5' and 3' termini of exon(...

Machine learning approach to identify a resting-state functional connectivity pattern serving as an endophenotype of autism spectrum disorder.

Endophenotype refers to a measurable and heritable component between genetics and diagnosis, and the same endophenotype is present in both individuals...

iRNAD: a computational tool for identifying D modification sites in RNA sequence.

MOTIVATION: Dihydrouridine (D) is a common RNA post-transcriptional modification found in eukaryotes, bacteria and a few archaea. The modification can...

Biogenesis mechanisms of circular RNA can be categorized through feature extraction of a machine learning model.

MOTIVATION: In recent years, multiple circular RNAs (circRNA) biogenesis mechanisms have been discovered. Although each reported mechanism has been ex...

The analysis of pharmacokinetic and pharmacogenomic impact on gefitinib efficacy in advanced non-small cell lung cancer patients: results from a prospective cohort study.

BACKGROUND: The current study is aimed to examine the impact of pharmacokinetics and gene polymorphisms of enzymes involving in absorption, distributi...

Gene-gene interaction: the curse of dimensionality.

Identified genetic variants from genome wide association studies frequently show only modest effects on the disease risk, leading to the "missing heri...

Machine learning meets genome assembly.

MOTIVATION: With the recent advances in DNA sequencing technologies, the study of the genetic composition of living organisms has become more accessib...

Large-scale comparative assessment of computational predictors for lysine post-translational modification sites.

Lysine post-translational modifications (PTMs) play a crucial role in regulating diverse functions and biological processes of proteins. However, beca...

Functional interpretation of genetic variants using deep learning predicts impact on chromatin accessibility and histone modification.

Identifying functional variants underlying disease risk and adoption of personalized medicine are currently limited by the challenge of interpreting t...

The pan-genome of Saccharomyces cerevisiae.

Understanding genotype-phenotype relationship is fundamental in biology. With the benefit from next-generation sequencing and high-throughput phenotyp...

Risk stratification of cervical lesions using capture sequencing and machine learning method based on HPV and human integrated genomic profiles.

From initial human papillomavirus (HPV) infection and precursor stages, the development of cervical cancer takes decades. High-sensitivity HPV DNA tes...

Machine-learned analysis of the association of next-generation sequencing-based genotypes with persistent pain after breast cancer surgery.

Cancer and its surgical treatment are among the most important triggering events for persistent pain, but additional factors need to be present for th...

Gene Ontology Causal Activity Modeling (GO-CAM) moves beyond GO annotations to structured descriptions of biological functions and systems.

To increase the utility of Gene Ontology annotations for interpretation of genome-wide experimental data, we have developed GO-CAM, a structured frame...

Machine-Learning Classification Suggests That Many Alphaproteobacterial Prophages May Instead Be Gene Transfer Agents.

Many of the sequenced bacterial and archaeal genomes encode regions of viral provenance. Yet, not all of these regions encode bona fide viruses. Gene ...

Interaction Effects of Gene Polymorphisms and Obesity on Nonalcoholic Fatty Liver Disease.

Goat Polyclonal Antibody Against the Sex Determining Region Y to Separate X- and Y-Chromosome Bearing Spermatozoa.

BACKGROUND: Sex selection of sperm by separating X- and Y-chromosome bearing spermatozoa is critical for efficiently obtaining the desired sex of anim...

DL-CNV: A deep learning method for identifying copy number variations based on next generation target sequencing.

Copy number variations (CNVs) play an important role in many types of cancer. With the rapid development of next generation sequencing (NGS) technique...