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<h4>Motivation</h4>Disease models are fundamental tools in drug discovery and early-stage drug development, but they only approximate human disease, and selecting a suitable model is challenging. Quantitative computational methods exist to assess molecular resemblance to human …
Read PDF<h4>Background</h4>Cardiovascular mortality remains predominantly driven by acute myocardial infarction (AMI), necessitating comprehensive elucidation of mechanisms governing cardiomyocyte reprogramming for therapeutic advancement. Characterizing molecular dynamics throughout cardiac repair processes presents substantial methodological challenges.<h4>Methods</h4>We employed a comprehensive …
Read PDFIntegrating single-cell omics data at an atlas scale enhances our understanding of cell types and disease mechanisms. However, the integration of data processed by different normalization methods can lead to biases, such as unexpected batch …
Read PDF<b>Objective:</b> To elucidate the role of cytoskeleton-associated protein 2 (CKAP2) in gastric cancer (GC) progression and evaluate its prognostic and potential protective significance. <b>Methods:</b> The candidate genes for GC were identified using differential expression and …
Read PDF<i>In vitro</i> kidney models play a crucial role in the study of renal development, (patho)physiology, drug development, and potential applications in bioartificial kidneys. Human <i>in vitro</i> kidney models have recently advanced significantly with the development …
Read PDFMacrophages are pivotal in the progression of metabolic dysfunction-associated steatohepatitis (MASH), yet their specific markers remain elusive. Herein, we employed an integrated bioinformatics strategy, combining single-cell and bulk transcriptomic data from human MASH livers, to …
Read PDF<h4>Background</h4>Hepatocellular carcinoma (HCC) is one of the most common types of cancer globally. However, HCC features poor prognosis due to complex pathogenesis and limitations of therapeutic approaches.<h4>Method</h4>To improve the prognosis of HCC patients, we analyzed …
Read PDFSingle-cell sequencing is revolutionizing biological research by enabling unprecedented cellular resolution, yet traditional multi-sample experiments are often constrained by high costs and batch effects. Sample multiplexing offers a critical solution by uniquely tagging individual cells …
Read PDFReconstructing temporal cellular dynamics from static single-cell transcriptomics remains a major challenge. Methods based on RNA velocity are useful, but interpreting their results to learn new biology remains difficult, and their predictive power is limited. …
Read PDF<h4>Background</h4>The surge in single-cell omics data exposes limitations in traditional, manually defined analysis workflows. AI agents offer a paradigm shift, enabling adaptive planning, executable code generation, traceable decisions, and real-time knowledge fusion. However, the lack …
Read PDF<h4>Background</h4>Bladder cancer (BLCA) exhibits a poor prognosis, highlighting the urgent need for reliable prognostic genes. Although succinylation is linked to tumor progression, its role in BLCA remains understudied. This study aimed to identify and validate …
Read PDFSingle-cell optimization objective and trade-off inference (SCOOTI) is a computational framework that integrates bulk and single-cell omics data with genome-scale metabolic modeling to infer metabolic objectives and trade-offs in biological systems. Here, we present a …
Read PDFAmpullary carcinoma (AC) is a rare epithelial cancer, representing around 0.2% of all gastrointestinal malignancies worldwide, with an estimated incidence of 0.73 per 100,000 people. The rarity of AC, combined with the intricate anatomy of …
Read PDFAt the transcriptomic level, several molecular subtyping schemes have been established to elucidate the intrinsic heterogeneity of urothelial carcinoma and to inform prognostic assessment and therapeutic guidance. However, a unified molecular classification scheme characterizing genomic …
Read PDFThe melanoma differentiation-associated gene 5 (MDA5) sensor recognizes double-stranded RNA (dsRNA) produced during viral infections, leading to type I interferon (IFN) production. Host proteins can shield endogenous dsRNA from MDA5 through RNA modifications, such as …
Read PDFProstate cancer (PCa)-related deaths are mainly due to metastasis. The increase in de novo metastatic hormone-naive PCa (mHNPCs) highlights the urgent need for biomarkers and treatment strategies. We report in a cohort of French PCa …
Read PDF<h4>Background</h4>Secondary lymphedema is a common complication of cancer treatment and epidermal changes are recognised as histological hallmarks of secondary lymphedema; however, the role of keratinocytes in the pathophysiology of this disease remains unclear.<h4>Methods</h4>Hyperkeratosis, up-regulation of …
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