Genetics

Afann: bias adjustment for alignment-free sequence comparison based on sequencing data using neural network regression.

Alignment-free methods, more time and memory efficient than alignment-based methods, have been widely used for comparing genome sequences or raw sequencing samples without assembly. However, in this study, we show that alignment-free dissimilarity calculated based on sequencing samples can be overestimated compared with the dissimilarity calculated based on their genomes, and this bias can signifi...

Machine learning approach to single nucleotide polymorphism-based asthma prediction.

Machine learning (ML) is poised as a transformational approach uniquely positioned to discover the hidden biological interactions for better prediction and diagnosis of complex diseases. In this work, we integrated ML-based models for feature selection and classification to quantify the risk of individual susceptibility to asthma using single nucleotide polymorphism (SNP). Random forest (RF) and r...

The integrative knowledge base for miRNA-mRNA expression in colorectal cancer.

"miRNA colorectal cancer" (https://mirna-coadread.omics.si/) is a freely available web application for studying microRNA and mRNA expression and their...

TSLRF: Two-Stage Algorithm Based on Least Angle Regression and Random Forest in genome-wide association studies.

One of the most important tasks in genome-wide association analysis (GWAS) is the detection of single-nucleotide polymorphisms (SNPs) which are relate...

CDSeq: A novel complete deconvolution method for dissecting heterogeneous samples using gene expression data.

Quantifying cell-type proportions and their corresponding gene expression profiles in tissue samples would enhance understanding of the contributions ...

RNA secondary structure prediction using an ensemble of two-dimensional deep neural networks and transfer learning.

The majority of our human genome transcribes into noncoding RNAs with unknown structures and functions. Obtaining functional clues for noncoding RNAs ...

Machine Learning Approaches for the Prioritization of Genomic Variants Impacting Pre-mRNA Splicing.

Defects in pre-mRNA splicing are frequently a cause of Mendelian disease. Despite the advent of next-generation sequencing, allowing a deeper insight ...

Point-of-care cervical cancer screening using deep learning-based microholography.

Most deaths (80%) from cervical cancer occur in regions lacking adequate screening infrastructures or ready access to them. In contrast, most develope...

DualWMDR: Detecting epistatic interaction with dual screening and multifactor dimensionality reduction.

Detecting epistatic interaction is a typical way of identifying the genetic susceptibility of complex diseases. Multifactor dimensionality reduction (...

Machine learning with multiparametric magnetic resonance imaging of the breast for early prediction of response to neoadjuvant chemotherapy.

In patients with locally advanced breast cancer undergoing neoadjuvant chemotherapy (NAC), some patients achieve a complete pathologic response (pCR),...

ImaGene: a convolutional neural network to quantify natural selection from genomic data.

BACKGROUND: The genetic bases of many complex phenotypes are still largely unknown, mostly due to the polygenic nature of the traits and the small eff...

A 21‑gene Support Vector Machine classifier and a 10‑gene risk score system constructed for patients with gastric cancer.

Gastric cancer (GC) ranks fifth in terms of incidence and third in terms of tumor mortality worldwide. The present study was designed to construct a S...

The Hearing Impairment Ontology: A Tool for Unifying Hearing Impairment Knowledge to Enhance Collaborative Research.

Hearing impairment (HI) is a common sensory disorder that is defined as the partial or complete inability to detect sound in one or both ears. This di...

Unsupervised feature selection algorithm for multiclass cancer classification of gene expression RNA-Seq data.

This paper presents a Grouping Genetic Algorithm (GGA) to solve a maximally diverse grouping problem. It has been applied for the classification of an...

Artificial intelligence in genetic services delivery: Utopia or apocalypse?

Artificial intelligence (AI) technologies have a long history, with increasing presence and potential in society and medicine. Much of the medical lit...

Ranking of non-coding pathogenic variants and putative essential regions of the human genome.

A gene is considered essential if loss of function results in loss of viability, fitness or in disease. This concept is well established for coding ge...

The complete chloroplast genome of , an important tropical crop.

(Willd. ex Spreng.) K. Schum., an economically important tree in the family Malvaceae, is native to the Amazonian region of South America and it is w...

AGONOTES: A Robot Annotator for Argonaute Proteins.

The argonaute protein (Ago) exists in almost all organisms. In eukaryotes, it functions as a regulatory system for gene expression. In prokaryotes, it...

Machine learning-based quantitative texture analysis of conventional MRI combined with ADC maps for assessment of IDH1 mutation in high-grade gliomas.

PURPOSE: To assess the performance of texture analysis of conventional magnetic resonance imaging (MRI) and apparent diffusion coefficient (ADC) maps ...

Effect of bacterial endotoxin lipopolysaccharide treatment on duck Leydig cells.

This study aimed to investigate the effects of bacterial endotoxin lipopolysaccharide (LPS) on hormone production and gene expression in duck Leydig c...