Genetics

TEWS: Transformer-empowered weakly supervised prediction of immune score and genetic mutations in liver cancer from whole slide image.

Whole Slide Imaging (WSI) plays a crucial role in predicting immune scores by providing detailed cellular and tissue-level insights, thereby enhancing pathological diagnosis accuracy and biomarker detection. Additionally, WSI contributes essential information for personalized treatment decisions. However, the application of deep learning models to WSI is hindered by two major challenges. First, th...

HeptaTB Dx: a diagnostic model leveraging cuproptosis-ferroptosis crosstalk for distinguishing latent from active tuberculosis.

UNLABELLED: Distinguishing latent tuberculosis infection (LTBI) from active tuberculosis (ATB) remains challenging. The roles of cuproptosis-ferroptosis crosstalk in TB immunopathology and diagnostic potential are unexplored. Transcriptomic data from Gene Expression Omnibus data sets (GSE37250/GSE28623) were analyzed to identify cuproptosis-/ferroptosis-related differentially expressed genes. Bioi...

MetIoR: A meta predictor to predict intrinsic disorder in RNA binding proteins.

Intrinsic disorder in proteins is ubiquitous in nature across various proteomes. The association of intrinsically disordered proteins (IDP) with a lar...

Revealing the anti-tumor mechanisms of aromatic oil from Amomum villosum through integrated network pharmacology, bioinformatics, machine learning, single-cell sequencing, and cell experiments.

The dry fruits of Amomum villosum (Av) are a traditional Chinese medicine used for gastrointestinal disease. Aromatic oil has been reported to have an...

Integrative analysis of transcriptomic data reveals a predictive gene signature for chemoradiotherapy response in rectal cancer.

Locally advanced rectal cancer (LARC) is treated with neoadjuvant chemoradiotherapy (nCRT), but only a minority of patients achieve a pathological com...

Designing prokaryotic gene expression regulatory elements: From genomic mining to artificial intelligence-driven generation.

Gene expression regulatory elements (GEREs) play a pivotal role in the control of gene transcription and translation. The design of GEREs with precise...

NLRP1 as a Novel Pyroptosis Biomarker in Irreversible Pulpitis: A Laboratory Investigation and Animal Model Study.

AIM: Irreversible pulpitis poses a significant clinical burden due to progressive inflammatory pulp damage. While inflammatory mechanisms are central ...

Endocrinology in maternal-fetal synchronization and developmental origins of susceptibility to metabolic diseases.

The biological clock enables organisms to align their intrinsic rhythms with daily environmental cycles thereby maintaining homeostasis and imparting ...

Analysis of PANoptosis-related genes in septic cardiomyopathy by bioinformatics, machine learning and experimental validation.

The mechanisms underlying the pathogenesis of septic cardiomyopathy (SCM) are intricate and incompletely understood. PANoptosis is a novel type of pro...

A Scoping Review of Male Fertility Assessment and Treatment Across Historical and Contemporary Paradigms.

BACKGROUND: Male factor infertility accounts for up to 50% of couples' inability to conceive. Despite this significant burden, perspectives on male fe...

Development and validation of a deep learning-based automatic segmentation and classification of cerebral white matter hyperintensities.

OBJECTIVES: White matter hyperintensities (WMH) represent neuroimaging markers of cerebral small vessel disease. We aimed to develop and validate a de...

Cellular and molecular determinants of lymph node metastasis in papillary thyroid carcinoma: Integrated multi-omics profiling and machine learning models.

The mechanisms underlying lymph node metastasis (LNM) in papillary thyroid carcinoma (PTC) remain elusive. This study integrated single-cell RNA seque...

Structure of the Enterobacter pan-genome is revealed using machine learning.

The growing availability of publicly accessible Enterobacter genomes offers an opportunity to reveal the structure of its pangenome, uncovering the ca...

Optimization of NIRS-based models for predicting quality and gas production traits of fresh alfalfa silage via machine learning.

Near-infrared spectroscopy (NIRS) prediction models offer an expeditious method for assessing the nutritional value of feedstuffs, however, developing...

Interpreting Deep Learning-Based Prediction of the BRAF V600E Mutation Using Diagnostic Whole Slide Images in Skin Cutaneous Melanoma.

Deep learning (DL) models have shown promise in predicting molecular alterations directly from hematoxylin and eosin-stained whole slide images in a v...

Consensus machine learning identifies cell death gene signature for carotid artery stenosis diagnosis.

Carotid artery stenosis (CAS) is a major contributor to ischemic stroke, and molecular tools for its early detection remain limited. To address this n...

A novel multimodal diagnostic framework integrating hyperspectral imaging and deep learning for predicting RET gene mutations in medullary thyroid carcinoma.

BACKGROUND AND OBJECTIVE: Medullary thyroid carcinoma (MTC) is an aggressive malignancy driven predominantly by activating mutations in the RET proto-...

Unveiling Putative Functions of Burkholderia pseudomallei K96243 Hypothetical Proteins Via High-Throughput Characterization of Structural Similarities.

Burkholderia pseudomallei (BP) infections claims tens of thousands of lives worldwide every year. The bacterium's distinctive characteristics include ...

Aspartame promotes ovarian cancer progression: A multi-omics study integrating mendelian randomization, network toxicology, and in vitro validation.

The causal relationship between the artificial sweetener aspartame and ovarian cancer (OC), a highly lethal malignancy, remains unclear. This study, t...

Circadian rhythm: An emerging force for colorectal cancer treatment.

The relationship between circadian rhythm disorder and the occurrence and progression of colorectal cancer (CRC) has received attention. The circadian...