AIMC Topic: Gene Expression Profiling
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Integrating multiomics analysis and machine learning to refine the molecular subtyping and prognostic analysis of stomach adenocarcinoma.
Scientific reports
Jan 30, 2025
Stomach adenocarcinoma (STAD) is a common malignancy with high heterogeneity and a lack of highly precise treatment options. We downloaded the multiomics data of STAD patients in The Cancer Genome Atlas (TCGA)-STAD cohort, which included mRNA, microR...
Spatially resolved transcriptomics and graph-based deep learning improve accuracy of routine CNS tumor diagnostics.
Nature cancer
Jan 29, 2025
The diagnostic landscape of brain tumors integrates comprehensive molecular markers alongside traditional histopathological evaluation. DNA methylation and next-generation sequencing (NGS) have become a cornerstone in central nervous system (CNS) tum...
scSMD: a deep learning method for accurate clustering of single cells based on auto-encoder.
BMC bioinformatics
Jan 29, 2025
BACKGROUND: Single-cell RNA sequencing (scRNA-seq) has transformed biological research by offering new insights into cellular heterogeneity, developmental processes, and disease mechanisms. As scRNA-seq technology advances, its role in modern biology...
Fluo-Cast-Bright: a deep learning pipeline for the non-invasive prediction of chromatin structure and developmental potential in live oocytes.
Communications biology
Jan 29, 2025
In mammalian oocytes, large-scale chromatin organization regulates transcription, nuclear architecture, and maintenance of chromosome stability in preparation for meiosis onset. Pre-ovulatory oocytes with distinct chromatin configurations exhibit pro...
Unveiling the role of PANoptosis-related genes in breast cancer: an integrated study by multi-omics analysis and machine learning algorithms.
Breast cancer research and treatment
Jan 28, 2025
BACKGROUND: The heterogeneity of breast cancer (BC) necessitates the identification of novel subtypes and prognostic models to enhance patient stratification and treatment strategies. This study aims to identify novel BC subtypes based on PANoptosis-...
Multimodal learning for mapping genotype-phenotype dynamics.
Nature computational science
Jan 28, 2025
How complex phenotypes emerge from intricate gene expression patterns is a fundamental question in biology. Integrating high-content genotyping approaches such as single-cell RNA sequencing and advanced learning methods such as language models offers...
Identification of biomarkers associated with coronary artery disease and non-alcoholic fatty liver disease by bioinformatics analysis and machine learning.
Scientific reports
Jan 28, 2025
The constantly emerging evidence indicates a close association between coronary artery disease (CAD) and non-alcoholic fatty liver disease (NAFLD). However, the exact mechanisms underlying their mutual relationship remain undefined. This study aims t...
Identification of ubiquitination-related key biomarkers and immune infiltration in Crohn's disease by bioinformatics analysis and machine learning.
Scientific reports
Jan 27, 2025
Crohn's disease (CD) is a chronic inflammatory bowel disease with an unknown etiology. Ubiquitination plays a significant role in the pathogenesis of CD. This study aimed to explore the functional roles of ubiquitination-related genes in CD. Differen...
STAIG: Spatial transcriptomics analysis via image-aided graph contrastive learning for domain exploration and alignment-free integration.
Nature communications
Jan 27, 2025
Spatial transcriptomics is an essential application for investigating cellular structures and interactions and requires multimodal information to precisely study spatial domains. Here, we propose STAIG, a deep-learning model that integrates gene expr...
Identification and validation of key autophagy-related genes in lupus nephritis by bioinformatics and machine learning.
PloS one
Jan 27, 2025
INTRODUCTION: Lupus nephritis (LN) is one of the most frequent and serious organic manifestations of systemic lupus erythematosus (SLE). Autophagy, a new form of programmed cell death, has been implicated in a variety of renal diseases, but the relat...
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