Genetics

Tumor-preserving Deformable Registration of Longitudinal Breast DCE MRI during Neoadjuvant Chemotherapy.

Purpose To develop a deep learning-based deformable registration method for breast dynamic contrast-enhanced (DCE) MRI that preserves tumor regions while maintaining global anatomic alignment during neoadjuvant chemotherapy (NAC) response assessment. Materials and Methods This retrospective study included internal and external cohorts of patients with breast cancer undergoing NAC. The internal coh...

PlantGFM: A Genomic Foundation Model for Discovery and Creation of Plant Genes.

The artificial intelligence (AI)-driven generation of genetic sequences holds transformative potential for addressing global challenges in agriculture, medicine, and bioenergy. Traditional approaches including hybridization, mutagenesis, and CRISPR-based editing enable targeted modification of endogenous DNA, yet remain constrained by natural sequence diversity. We here introduce PlantGFM, an appl...

Unveiling Viral Escape Mechanisms With Machine Learning: A Transformative Approach to Mutation Analysis for SARS-CoV-2 and Beyond.

Persistent viruses like Influenza, HIV, and Coronavirus exemplify the challenge of viral escape, significantly hindering the development of long-lasti...

Shared diagnostic biomarkers in metabolic syndrome and coronary artery disease identified by integrated bioinformatics and machine learning.

BACKGROUND: Metabolic syndrome (MetS) comprises various complicated metabolic disorders. Coronary artery disease (CAD) is a major cardiovascular disea...

Interpretable deep learning framework for mapping E3-substrate binding interfaces.

E3 ubiquitin ligases recognize substrates through specific interfaces. Accurate delineation of these interfaces is essential, as mutations disrupting ...

Explainable convolutional neural network model provides an alternative genome-wide association perspective on mutations in SARS-CoV-2.

Identifying informative genomic features in SARS-CoV-2 can help clarify patterns of viral evolution. In this study, we developed an explainable convol...

IALA-BPNN: superior house price prediction through multi-strategy optimized Artificial Lemming Algorithm and BP neural network.

Against this backdrop of a global economic downturn, the real estate market exhibits characteristics of both a consumer good and an investment asset, ...

Genetic and immunological determinants of Pemphigus vulgaris: integrative analysis of HLA-DRB1 and FCGR2B variants.

Pemphigus vulgaris (PV) is a rare autoimmune blistering disease mediated by pathogenic autoantibodies. Although both HLA and non-HLA loci contribute t...

Machine learning to predict genotypes and genotype-environment interaction associated with complex traits for genomic selection.

Genomic selection (GS) can accelerate crop breeding and enhance selection efficiency. However, accurately predicting genomic estimated breeding values...

The One Health resistome: Integrating environmental, microbial, and human antimicrobial resistance surveillance and risk analysis in the digital age.

Antimicrobial resistance (AMR) and antibiotic resistance (ABR) represent one of the most pressing global health threats, driven by the complex interpl...

BRPtools: An AutoML-Powered web platform for multiclass disease prediction from bulk blood RNA-seq data.

Blood-based transcriptomic profiling provides a minimally invasive approach for disease diagnosis; however, the integration of large-scale, heterogene...

Machine learning framework for cost effective deep mutational scanning through targeted substitution profiling.

BACKGROUND: Deep mutational scanning (DMS) provides comprehensive maps of protein variant effects but remains experimentally intensive. Machine learni...

Achieving precise m6A RNA modification prediction from nanopore signals through integration with pre-trained foundation model.

While predicting base modification states directly from nanopore electrical signals offers a cost-effective approach to epitranscriptomic profiling, c...

Polystyrene Microplastics Drive Chondrotoxicity in Osteoarthritis through Inducing ER Stress and Apoptosis via NFKB1 Activation.

Polystyrene microplastics (PS-MPs), recognized as widespread environmental contaminants, have been identified within human articular tissues. However,...

SDP-ChroNet: A shared dilated pooling network for chromatin interaction prediction.

A deep understanding of chromatin interactions is crucial for elucidating the mechanisms of gene expression regulation. Although various computational...

Pre-analytical standardization and multi-biofluid harmonization for liquid biopsy biomarkers in lung cancer: From discovery to clinical laboratory implementation.

Lung cancer remains the leading cause of cancer-related mortality worldwide, with early detection being critical for improving survival outcomes. Liqu...

DNA methylation biomarkers-based pan-cancer classifier: predictive modeling for cancer classification.

BACKGROUND: Machine-learning (ML) driven molecular diagnostics based on omics data has a potential to revolutionize personalized medicine. However, im...

Rapid Cas13a-based penA genotyping for cefixime susceptibility in Neisseria gonorrhoeae.

UNLABELLED: Antimicrobial resistance in Neisseria gonorrhoeae is an urgent public health threat. Resistance-guided therapy can assure appropriate trea...

FRDNAC: A Future-Ready DNA Cryptography Paradigm for Secure Cloud Data Transmission Using Deep Learning-Enhanced Key Generation.

The growing reliance upon cloud settings has rendered secure transmission of information essential. This study introduces the future-ready DNA-based c...

APTw CEST MRI in therapy-naive IDH-wildtype glioblastoma: insights into tumor heterogeneity and molecular subtypes.

PURPOSE: Advanced MRI techniques may provide non-invasive insight into the molecular heterogeneity of glioblastoma. Amide proton transfer-weighted (AP...