Genetics

HRProfiler Detects Homologous Recombination Deficiency in Breast and Ovarian Cancers Using Whole-Genome and Whole-Exome Sequencing Data.

UNLABELLED: Breast and ovarian cancers harboring homologous recombination deficiency (HRD) are sensitive to PARP inhibitors and platinum chemotherapy. Conventionally, detecting HRD involves screening for defects in BRCA1, BRCA2, and other relevant genes. Recent analyses have shown that HRD cancers exhibit characteristic mutational signatures due to the activities of HRD-associated mutational proce...

Leveraging Whole-Exome Sequencing and Mutational Signatures to Detect Homologous Recombination Deficiency in Cancer.

Homologous recombination is a high-fidelity DNA repair mechanism essential for maintaining genome stability. Impairment of this pathway, often due to BRCA1 or BRCA2 inactivation, leads to homologous recombination deficiency (HRD), forcing cells to rely on error-prone mechanisms for repairing DNA double-strand breaks, such as nonhomologous or microhomology-mediated end joining. HRD is a clinically ...

Modeling Gene Expression Distributional Shifts for Unseen Genetic Perturbations

We train a neural network to predict distributional responses in gene expression following genetic perturbations. This is an essential task in early...

DNA-CBIR: DNA Translation Inspired Codon Pattern-Based Deep Image Feature Extraction for Content-Based Image Retrieval.

DNA is emerging as a promising medium for storing huge volumes of data in a confined space that remains intact for thousands of years. Although this t...

MACHINE LEARNING AND BIOINFORMATICS TO IDENTIFY COAGULATION BIOMARKERS IN SEPSIS-RELATED KIDNEY INJURY.

Background: Sepsis-associated acute kidney injury (SA-AKI) is a life-threatening complication with mortality rates exceeding 50%, yet its molecular dr...

A Novel Linear Machine Learning Method Based on DNA Hybridization Reaction Circuit.

DNA hybridization reaction is a significant technology in the field of semi-synthetic biology and holds great potential for use in biological computat...

Innovations in Quail Welfare: Integrating Environmental Enrichment, Nutrition and Genetic Advances for Improved Health and Productivity.

The demand for ethical and sustainable poultry production is driving up the importance of quail welfare. Because quail meat and eggs are in high deman...

Integrative analyses of 16S rDNA sequencing and serum metabolomics demonstrate significant roles for the oral microbiota and serum metabolites in post-kidney transplant diabetes mellitus.

Oral microbiota and serum metabolites play crucial roles in diabetes, but their relationship with post-transplant diabetes mellitus (PTDM), a common c...

Accurate Diagnosis of Colorectal Cancer Using a Combination of Lectin-Induced Recombinase Polymerase Amplification and CRISPR/Cas12a Assay on a Point-of-Care Testing Platform with Deep Learning Assistant.

Specific glycosylation patterns on exosome surfaces represent novel diagnostic biomarkers for cancer liquid biopsy. Lectins can induce exosome aggrega...

Differentiable graph clustering with structural grouping for single-cell RNA-seq data.

MOTIVATION: Clustering cells into subpopulations is one of the most crucial tasks in single-cell RNA sequencing (scRNA-seq) data analysis, which provi...

Personalized medicine for cardiovascular diseases: how next generation epigenetic technologies can contribute?

Advances in DNA methylation and artificial intelligence have led to new methods for assessing risk and diagnosing coronary heart disease (CHD), the le...

Advances in viral vector-based delivery systems for gene therapy: a comprehensive review.

Gene therapy offers a revolutionary approach for treating genetic and acquired disorders by delivering therapeutic genes to target cells. Viral vector...

Integrating AI/ML and multi-omics approaches to investigate the role of TNFRSF10A/TRAILR1 and its potential targets in pancreatic cancer.

Pancreatic ductal adenocarcinoma (PDAC) remains one of the most lethal malignancies, with a five-year survival of under 10 % despite current therapies...

Advances in pancreatic cancer diagnosis: from DNA methylation to AI-assisted imaging.

INTRODUCTION: Pancreatic Cancer (PC) is a highly aggressive tumor that is mainly diagnosed at later stages. Various imaging technologies, such as CT, ...

Improving human brucellosis susceptibility mapping using effective and simultaneously metaheuristic-based feature selection and hyperparameter tuning.

Human Brucellosis, a neglected zoonotic disease, affects 1.6 to 2.1 million people globally each year. In Iran, it has become a significant health con...

Novel robotic tools used for the detection of faecal shedding of Escherichia coli resistant to critically important antimicrobials in healthy dogs.

Escherichia coli recovered from dogs with clinical conditions such as urinary tract infections are often used to assess populations for resistance to ...

Precision medicine applications in dilated cardiomyopathy: Advancing personalized care.

Dilated cardiomyopathy (DCM) is a prevalent cardiac disorder affecting 1 in 250-500 individuals, characterized by ventricular dilation and impaired sy...

Machine learning prediction of pathological complete response to neoadjuvant chemotherapy with peritumoral breast tumor ultrasound radiomics: compare with intratumoral radiomics and clinicopathologic predictors.

PURPOSE: Noninvasive, accurate and novel approaches to predict patients who will achieve pathological complete response (pCR) after neoadjuvant chemot...

Letter to the Editor regarding "Prediction of PFAS bioaccumulation in different plant tissues with machine learning models based on molecular fingerprints" by Song et al. (2024), Sci. Total Environ. 950 175091.

Song et al. (2024), "Prediction of PFAS bioaccumulation in different plant tissues with machine learning models based on molecular fingerprints," empl...

A novel Harris Hawks Optimization-based clustering method for elucidating genetic associations in osteoarthritis and Diverse Cancer Types.

Considering the high incidence of osteoarthritis (OA), especially of the knee and hip, this study explores the possible genetic associations between O...