Multi-omics data integration for topology-based pathway activation assessment and personalized drug ranking

Although multi-omics analysis is popular for revealing diverse physiological effects and biomarkers in many branches of state-of-the-art molecular and cell biology and bioinformatics, there is still…

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MOFNet: a deep learning framework for multi-omics data fusion in cancer subtype classification

Background: cancer exhibits high molecular and clinical heterogeneity, making accurate subtyping essential for personalized treatment. Traditional single-omics approaches often fail to capture this…

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Deep learning methods and applications in single-cell multimodal data integration

The integration of multimodal single-cell omics data is a state-of-art strategy for deciphering cellular heterogeneity and gene regulatory mechanisms. Recent advances in single-cell technologies have…

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Mapping the Helichrysum metabolome: uncovering species-specific chemistry through an AI-guided LC-MS/MS workflow

Helichrysum species, of which 35% are native to South Africa, are renowned for their diverse medicinal properties, yet their chemical composition remains largely unexplored. As such, continuous…

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Global spinal cord peptidome profiling in response to osteoarthritis in rats

Osteoarthritis (OA) is a complex and increasingly prevalent condition, affecting an estimated 600 million people worldwide and significantly reducing quality of life. Understanding OA as both an…

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Mass spectrometry-based profiling of phosphoinositide: advances, challenges, and future directions

Phosphoinositides (PIPs), the phosphorylated derivatives of phosphatidylinositol (PI), are low-abundance yet critical components of eukaryotic membranes. They play pivotal roles in a wide array of…

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Comparative glycomic analysis of hawk (Rupornis magnirostris), caiman (Caiman latirostris) and sea turtle (Caretta caretta) tear films

Glycans are recognized as biomarkers and therapeutic targets. However, these molecules remain a critical blind spot in understanding post-translational modifications, particularly in vertebrate…

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Cytokine-induced memory-like responses in endothelial cells link chronic inflammation to vascular disease risk

Chronic inflammation plays a central role in the progression of both infectious and vascular diseases, yet its impact on endothelial cells (ECs), which form the interface between blood and tissue,…

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DeSciDe: a tool for unbiased literature searching and gene list curation unveils a new role for the acidic patch mutation H2A E92K

Omics analysis has become an indispensable tool for researchers in the life sciences, enabling the study of DNA, RNA, and proteins and how they respond to cellular stimulus. Many methods of data…

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Understanding metabolic alterations in advanced stage chronic kidney disease patients by NMR-based metabolomics

Understanding metabolic alterations in CKD is crucial, as serum creatinine-based diagnosis lacks precision, affecting key clinical decisions. In this study, a 1H NMR-based metabolomics approach was…

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Integrated multi-omic analyses of bovine milk identify biomarkers of negative energy balance

Dairy cows are susceptible to negative energy balance, which can lead to metabolic disorders such as ketosis. Negative energy balance (NEB) often occurs in early lactation, but can also be due to…

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Proteomic and metabolomic dissection of the BRAF V600E mutation-induced cellular state transition in lung epithelial cells

Non-small cell lung cancer (NSCLC) is the most common subtype of lung cancer, and 4% of NSCLC patients are reported to harbor mutations in BRAF, which encodes a serine/threonine kinase capable of…

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POMC-specific modulation of metabolic and immune pathways via melanocortin-3 receptor signaling

This proteomic study provides a nuanced mechanistic understanding of the signaling processes upon agonist binding to the melanocortin-3 receptor (MC3R). Utilizing thermal proteome profiling (TPP)…

pubs.rsc.org

Global spinal cord peptidome profiling in response to osteoarthritis in rats

Osteoarthritis (OA) is a complex and increasingly prevalent condition, affecting an estimated 600 million people worldwide and significantly reducing quality of life. Understanding OA as both an infla...

pubs.rsc.org

Temperature- and time-dependent degradation of mouse tissue proteins: insights into RNA-binding protein stability via mass spectrometry

In proteomics research, samples are frequently stored at −20 °C and −80 °C for extended periods, and assessing protein stability under these conditions is essential. We evaluated protein stability in…

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Advancing colorectal cancer research through lipidomics

Colorectal cancer (CRC) is currently a global health burden, with staggering worldwide prevalence. CRC is ranked as the third most common and second deadliest cancer worldwide. With rising life…

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Transcriptome and proteome analyses reveal the virulence of the Vibrio alginolyticus effector gene vopR

Vibrio alginolyticus is an opportunistic infectious pathogen, and its pathogenicity is related to various virulence factors, with the type III secretion system (T3SS) being one of the important…

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Mammary gland metabolism and its relevance to the fetoplacental expression of cytokine signaling in caveolin-1 null mice

Mice lacking caveolin-1 (Cav1), a major protein of the lipid raft of plasma membrane, show deregulated cellular proliferation of the mammary gland and an abnormal fetoplacental communication during…

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Thioridazine induces phospholipid accumulation and necroptosis in parental and tamoxifen-resistant breast cancer cells

The development of acquired resistance to tamoxifen poses a significant clinical challenge in breast cancer treatment. Tumour heterogeneity has emerged as a primary reason for the clinical…

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PPI network identifies interacting pathogenic signaling pathways in Candida albicans

Candida albicans, an opportunistic and systemic infection causing fungus, causes skin, nail, and mucosal layer lesions in healthy individuals and hospital borne catheter-related and nosocomial…

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Analysis of FAIMS for the study of affinity-purified protein complexes using the orbitrap ascend tribrid mass spectrometer

In this study, we analyzed the combination of affinity purification mass spectrometry (AP-MS) with high-field asymmetric waveform ion mobility spectrometry (FAIMS), integrated between nanoLC-MS and…

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Lipid profiling: proving the geographical origin of strawberries (Fragaria × ananassa) using a non-targeted LC-IM-MS approach

The strawberry, a globally traded fruit, is a prime example of how geographical origin has become an important marketing factor. Significant price differences between countries of origin make…

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Human circulatory proteome interaction, oxidative stress-associated signalling and cardiovascular implications during titanium dioxide nanoparticle (TiO2-NP) exposure

The increasing exposure to nanoparticles raises a concern over their toxicity. Incidentally, reactive oxygen species (ROS) are produced as a result of the nanoparticle's physicochemical…

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Integrating N-glycan and CODEX imaging reveal cell-specific protein glycosylation in healthy human lung

Identifying cell-specific glycan structures in human lungs is critical for understanding the chemistry and mechanisms that guide cell–cell and cell–matrix interactions and determining nuanced…

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A multi-omics machine learning classifier for outgrowth of cow's milk allergy in children

Cow's milk protein allergy (CMA) is one of the most common food allergies in children worldwide. However, it is still not well understood why certain children outgrow their CMA and others do not.…

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