Genetics

Characterizing yield through wheat's perception of chronological progression: a multi-omics plant-time warping approach.

To address challenges in food security, a better understanding of crop performance under varying and changing environmental conditions is required. Plant Time Warping (PTW) is a deep learning model that integrates high-throughput field phenotyping data with genomic and environmental information to predict wheat yield. PTW leverages image time series, genetic markers, and environmental covariates t...

Methane cycling microbes are important predictors of methylmercury accumulation in rice paddies.

Microbial production of methylmercury from inorganic mercury in rice paddies poses health risks to consumers of this essential dietary staple. Although mercury-methylating communities are well characterized, the microbial guilds contributing to methylmercury accumulation in rice paddies remain unclear. Here, we collected paddy soils across a mercury concentration gradient throughout the rice-growi...

Machine learning algorithms for predicting colchicine resistance in familial Mediterranean fever.

OBJECTIVES: Familial Mediterranean Fever (FMF) is a genetic autoinflammatory condition marked by recurrent fever and serositis. Colchicine is the main...

ERBB2 as a Prognostic Biomarker in Prostate Cancer: Integration of Single-Cell Transcriptomics, Deep Learning, and Immunohistochemical Validation.

Biochemical recurrence (BCR) is a critical factor affecting the prognosis of prostate cancer (PCa) patients, while T cell exhaustion and metastatic pr...

The accuracy of carbon-13 NMR magnetic-shielding tensors calculated using periodic DFT: a case study on the distinction of crystalline serine phases.

Carbon-13 nuclear magnetic resonance (NMR) spectroscopic fingerprints enable the unambiguous identification of a chemical compound. Ab initio calculat...

DRfold2 is a deep learning-based tool that enables efficient and accurate RNA structure prediction.

RNA structures are essential for understanding their biological functions and developing RNA-targeted therapeutics. However, accurate RNA structure pr...

MENDELSEEK: An algorithm that predicts mendelian genes and elucidates what makes them special.

Although individual Mendelian diseases-those caused by a single gene-are rare, their collective disease burden is substantial. Identifying the causal ...

EnDeep4mC predicts DNA N 4-methylcytosine sites using a dual-adaptive feature encoding framework in deep ensembles.

DNA N 4-methylcytosine (4mC), a key epigenetic modification regulating DNA repair and replication, requires efficient computational detection methods ...

Characterising processing conditions that artifactually bias human brain tissue transcriptomes.

Autopsy-derived brain tissue analysis is crucial for understanding neurobiology, but post-mortem handling can introduce artifacts. We studied adult hu...

Machine learning-based cfDNA fragmentation profiling using automated capillary electrophoresis for early detection of hepatocellular carcinoma.

BACKGROUND: Early detection of hepatocellular carcinoma (HCC) remains a significant clinical challenge due to the limited sensitivity of current surve...

Germline Pathogenic Variant Prediction Model for Tumor-Only Sequencing Based on Japanese Clinicogenomic Database.

PURPOSE: Germline pathogenic variants (GPV) are frequently identified as secondary findings in cancer gene panel testing. Due to limited data on germl...

Diethyl Phthalate (DEP) as a potential osteosarcoma risk factor: a multi-omics study integrating network Toxicology, single-cell RNA sequencing, and molecular docking.

Diethyl phthalate (DEP), a common plasticiser and endocrine disruptor, has been linked to cancer, but its role in osteosarcoma (OS) remains unclear. T...

The 487-gene expression profile test guides systemic therapy selection to improve outcomes for patients with atopic dermatitis: Results from a prospective trial.

BACKGROUND: Current atopic dermatitis (AD) therapy selection does not account for molecular drivers of disease, contributing to inadequate disease con...

Advances and challenges in the application of metagenomic sequencing for the diagnosis and treatment of infectious diseases: from pathogen spectrum identification to personalized antimicrobial strategies.

Infectious diseases remain a major global public health concern, demanding rapid and accurate identification of pathogens. Although conventional diagn...

Cross-modal attention deep learning reveals how transformation products inherit life-cycle risks from parent antibiotics: Insights for environmental, ecological, health, and AMR risks.

The environmental, ecological, antimicrobial resistance (AMR), and human health risks of antibiotic transformation products (TPs) in aquatic environme...

Predictors of sensitivity to immune therapies in classic Hodgkin lymphoma.

Immune checkpoint blockade, particularly programmed cell death protein 1 inhibition, has redefined the management of classic Hodgkin lymphoma (cHL), a...

Exploring estrogen synthesis and metabolism related markers and immune dynamics in osteoporosis-insights from single-cell RNA sequencing and Mendelian randomization.

BACKGROUND: Osteoporosis (OP) is characterized by decreased bone mineral density and an increased fracture risk, often due to declining sex hormone le...

DoBSeqWF: a framework for sensitive detection of individual genetic variation in pooled sequencing data.

Population screening for rare genetic diseases has the potential to increase early diagnosis and treatment, but the high cost of next-generation seque...

Coordinated DNA methyltransferase 3A and methyltransferase-like 7A activity reprograms the tumor microenvironment through discoidin domain receptor 1 signaling.

OBJECTIVE: Breast cancer is the most common malignancy in women and is characterized by a high recurrence rate that severely impacts patient survival....

Advancements and challenges in CAR-NK cell therapy for cancer treatment.

Chimeric antigen receptor natural killer (CAR-NK) cell therapy is an emerging cancer treatment offering advantages over CAR-T therapy, including reduc...