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An ELIXIR scoping review on domain-specific evaluation metrics for synthetic data in life sciences
Synthetic data (SD) has become an increasingly important asset in the life sciences, helping address data scarcity, privacy concerns, and barriers to data access. Creating artificial datasets that mirror the characteristics of real data allows …
Read PDFUnraveling TIME: CD8+ T cell- and CXCL11-driven endocrine resistance in breast cancer
A major unmet need in estrogen receptor-positive (ER+) breast cancer is understanding the mechanisms that underlie resistance to endocrine therapy. Although accumulating evidence suggests an association between the tumor immune microenvironment (TIME) and endocrine response, …
Read PDFCBX3:IL1RN Reflects Distinct Cellular States That Defines the Clinical Outcome of Oral Squamous Cell Carcinoma
<h4>Background</h4>Oral squamous cell carcinoma (OSCC) exhibits heterogeneous therapeutic outcomes owing to various tumor microenvironments (TMEs). Previous studies have classified OSCC according to its molecular characteristics; however, clinical practice is limited by technical complexity.<h4>Methods</h4>A total of …
Read PDFAssessing current capabilities for incorporating lipidomics in multiomics data integration
Comprehensive analyses of multiple biological components including nucleic acids, proteins, metabolites, and lipids (i.e. "multiomics") provide unique insights into complex biological processes. Combining insights from these components through multiomics data integration enhances the depth and …
Read PDFIntegrated cross-species translation and biophysical multi-scale modeling links molecular signatures and locomotory phenotypes in spaceflight-induced sarcopenia
Age-related skeletal muscle deterioration, referred to as sarcopenia, poses significant risks to astronaut health and mission success during spaceflight, yet its multisystem drivers remain poorly understood. While terrestrial sarcopenia manifests gradually through aging, spaceflight induces …
Read PDFSex‐specific metabolic and vascular brain aging in preclinical models of dementia
No abstract available.
Read PDFIntegrating biocomputational techniques for vaccine development for glioblastoma multiforme: a possible way of enhancing precision
Glioblastoma multiforme (GBM) is the most aggressive primary brain tumor in adults, with poor survival despite multimodal therapy. Tumor heterogeneity, immune evasion, and recurrence limit the effectiveness of current treatments, necessitating novel therapeutic strategies. Vaccine-based …
Read PDFSecreted phospholipase PLA2G5 acts as a hemolytic factor in sepsis
Sepsis is a systemic response to infection with life-threatening consequences such as hemolysis, a predictor of mortality risks for the disease. Here, by measuring organism-wide changes in gene expression, we discovered that the secreted phospholipase …
Read PDFOrganoids glimpse: the nexus for diverse tumor heterogeneity
Intratumor, intertumor and temporal heterogeneity shapes capricious therapeutic response and complicates personalized treatment. It reflects interacting genetic, epi-genetic, transcriptional, and microenvironmental variation. Patient derived organoids (PDOs) are three-dimensional, patient anchored cultures that preserve key tumor …
Read PDFMulti-omics reveals the immune and metabolic characteristics and associations in non-mucinous ovarian cancer
BACKGROUND: The complex metabolic and immune characteristics of ovarian cancer and their interconnections can promote tumor immune evasion, ultimately leading to immunotherapy failure. A comprehensive understanding of these relationships can inform the development of diagnostic …
Read PDFCastl: robust identification of spatially variable genes in spatial transcriptomics via an ensemble-based framework
Spatially variable genes (SVGs) are essential for elucidating tissue organization within spatially resolved transcriptomics. While a number of computational methods have been developed for SVG identification, their reliance on algorithm-specific assumptions, such as predefined kernel …
Read PDFConstruction of Rheumatoid Arthritis-Associated Interstitial Lung Disease diagnostic model and identification of biomarkers based on a multi-omics integration strategy of machine learning
<h4>Objective</h4>This study aimed to develop and validate a machine learning model integrating multi-omics and radiomics data to improve diagnostic accuracy and identify potential biomarkers for Rheumatoid Arthritis-Associated Interstitial Lung Disease (RA-ILD).<h4>Methods</h4>A total of 278 patients …
Read PDFAPOE4 driven splicing defects disrupt neurite projection in excitatory neurons
No abstract available.
Read PDFTopography-aware optimal transport for alignment of spatial omics data
Recent advances in spatial omics technologies have provided unprecedented insight into tissue spatial organization, but challenges remain in aligning spatial slices and integrating complementary single-cell and spatial data. Here, we propose TOAST (topography-aware optimal alignment …
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