Genetics

Single-cell and bulk transcriptomic profiling of M2-like tumor-associated macrophages reveals a prognostic signature and an inflammation-metabolism crosstalk program in multiple myeloma.

BACKGROUND: M2-like tumor-associated macrophages (TAMs) contribute to multiple myeloma (MM) progression and treatment resistance, yet their internal heterogeneity remains poorly understood. We used single-cell RNA sequencing (scRNA-seq) with bulk transcriptomic cohorts to resolve MM-specific M2-TAM subpopulations and develop a prognostic signature. METHODS: scRNA-seq data from MM and normal bone m...

Multi-omics integration and machine learning define an iron-sulfur cluster/zinc-binding protein prognostic signature in esophageal squamous cell carcinoma.

Esophageal squamous cell carcinoma (ESCC) is characterized by substantial intratumoral heterogeneity and poor clinical prognosis. Although metalloproteins are well-documented to drive ESCC malignant progression, incomplete functional annotation of this protein family significantly impedes the clinical translation of related research outcomes. This study reports the development and validation of a ...

Correction: Interpretable machine learning for cattle breed classification and SNP prioritization.

Multidimensional 5-hydroxymethylcytosine features in cell-free DNA enable the detection, staging and subtyping of pancreatic ductal adenocarcinoma.

Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal malignant cancer with limited biomarkers for early detection and disease stratification. He...

A Vision-Based Deep Learning Framework enables High-Accuracy Prediction of Geng Rice Eating Quality and Facilitates QTL Mapping.

Northeast China's Geng rice (Oryza sativa subsp. japonica) dominates the high-value rice markets in China due to its superior eating quality. However,...

Machine Learning Analysis of Single-Cell Transcriptomics Identifies a B-Cell-Associated Fibroblast Signature Predictive of Renal Fibrosis Severity.

BACKGROUND: Renal fibrosis represents the final common pathway of chronic kidney disease (CKD); however, both its definitive diagnostic biomarkers and...

CDKN3, PKP2, ADM, MS4A1, FAM83A, and DKK1 Define a Posttranslational Modification (PTM)-Associated Prognostic Model for Lung Adenocarcinoma.

INTRODUCTION: Posttranslational modification (PTM) plays an important role in protein regulation and may influence tumor initiation and progression. H...

An integrated systems biology and machine learning framework for identifying potential biomarkers and pathways in autism spectrum disorder.

BACKGROUND: Autism spectrum disorders (ASD) are a group of neurodevelopmental disorders whose underlying molecular mechanisms and biological processes...

Identification of a novel small-molecule modulator targeting SNX10 to inhibit osteoclastic bone resorption.

Current antiresorptive therapies reduce bone loss by eliminating osteoclasts or inhibiting their formation. However, these approaches could disrupt os...

A Comprehensive Comparative Analysis of Sequence-Based Deep Learning Models for Single-Cell Genomics.

To streamline the application of sequence-based DL methods in single-cell genomics, we established a two-layer CNN as our baseline model. We focus our...

GRASSP: RNA Language Model-Enhanced Graph Attention with Adaptive Gating for RNA-Small Molecule Binding Site Prediction.

MOTIVATION: RNA-small molecule binding site prediction is crucial for targeted drug discovery. Sequence-based methods are efficient but often fail to ...

Apigenin Alleviates Ligamentum Flavum Ossification by Dual-Targeting CA9 and CDK6 and Modulating Calcium/PI3K-Akt Signaling.

While apigenin shows therapeutic potential for bone-related disorders like osteoporosis and osteoarthritis, its mechanisms in regulating ligamentum fl...

Harnessing Yeast Biodiversity for Advanced Industrial Applications.

Budding yeast Saccharomyces cerevisiae and various non-conventional species are widely applied in the production of diverse industrial products, inclu...

Targeting GLS and LPIN2 in renal fibroblasts: potential therapeutic targets for kidney stone disease identified by integrated multi-omics analysis.

Kidney stones (KS) are a common urological condition, the aetiology of which remains incompletely understood. This study aimed to investigate the key ...

Neoantigen in cancer immunotherapy: mechanism, therapeutic strategies and future perspectives.

Neoantigens are tumor-specific antigens resulting from genetic, transcriptomic, and proteomic changes, making them a promising avenue for personalized...

Integrative single-cell and machine-learning analysis identifies LGALS1 as a macrophage-associated diagnostic and prognostic biomarker in hepatocellular carcinoma.

BACKGROUND: Hepatocellular carcinoma (HCC) is characterized by marked heterogeneity and an immunosuppressive microenvironment in which tumor-associate...

Integrative single-cell sequencing and machine learning analyses identify chronic inflammation and cancer-associated fibroblast subsets as drivers of adverse outcomes in ovarian cancer.

BACKGROUND: Ovarian cancer remains the deadliest gynecological malignancy, with neoadjuvant chemotherapy (NACT) often leaving residual fibroblast-enri...

Twin-screw wet granulation in continuous pharmaceutical manufacturing.

Wet granulation is a critical unit operation in the manufacturing of solid dosage forms. However, conventional wet granulation techniques are limited ...

The synergy of artificial intelligence and organ-on-a-chip: building a next-generation intelligent engine for drug development.

Drug development has long been constrained by high costs, lengthy timelines, and low success rates, primarily due to the insufficient human physiologi...

Ensemble DNA methylation clock demonstrates Immune-metabolic Aging signatures associated with Mortality.

Aging is a multifactorial process that is best described in terms of the progressive acquisition of multiple layers of phenotypic changes, such as epi...