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Cartilage is characterized by a highly specialized extracellular matrix (ECM) secreted by chondrocytes and limited self-regenerative capacity. In vivo investigations of chondrogenesis are limited by difficult and traumatic access, especially in humans. While it is …
Read PDFProteomic and phenotypic cell sensitivity datasets are increasingly important for understanding chemoproteomics and the underlying drug mechanisms of action. Yet, integrating such heterogeneous datasets remains challenging due to inconsistent annotations, incompatible IDs, and variable data …
Read PDF<h4>Background</h4>Endothelial cells express numerous microproteins (miPs) encoded by small open reading frames (smORFs), yet the biological function of most remains unknown. This study set out to characterize a novel 69 amino acid miP encoded within …
Read PDFMitochondrial dysfunction is a prominent hallmark of aging contributing to the decline of metabolic plasticity in late life. While genetic distortions of mitochondrial integrity elicit premature aging, the mechanisms leading to "natural" aging of mitochondria …
Read PDFSpatial biology aims to elucidate cellular organization, function, and interactions within native tissue contexts, offering key insights into both normal physiology and disease. Spatial proteomics complements this by enabling high-resolution mapping of protein localization and …
Read PDFAntimicrobial peptides (AMPs) are natural bioactive peptides produced by all organisms-from plants to insects, microbes and animals-and constitute a first line of defense. As they exhibit a broad spectrum of activity (antibacterial, antiviral, antifungal, antiparasitic, …
Read PDFThe nuclear envelope (NE) is a critical regulatory interface that preserves genome integrity and mediates nucleocytoplasmic transport, yet its compositional and functional landscape in plants remains poorly defined. Here, we present a multiomics atlas of …
Read PDFEarly embryonic development requires tightly regulated molecular programs to coordinate cell division, fate specification, and spatial patterning. While transcriptomic profiling has been widely performed, proteomic analyses of early vertebrate embryos remain limited owing to technical …
Read PDF<h4>Background</h4>Proteins and RNA circulate in plasma and can offer insights into human physiology. Yet, despite their clinical importance, direct comparisons between these analytes remain unexplored.<h4>Methods</h4>Here, we measure and compare plasma cell-free RNA (cfRNA) and protein …
Read PDF<h4>Background</h4>Neurodegenerative diseases remain a central topic in biomedical research, with Alzheimer's disease (AD) being the most extensively studied. Recent advances in multi-omics integration, particularly proteomics-based approaches, have enabled a deeper understanding of AD-related molecular pathways …
Read PDFExercise adaptation depends on overload that is resolved by recovery, yet the same biology becomes maladaptive when immune, endocrine, metabolic, and muscle-centered stress signals fail to normalize. Exercise-induced maladaptation represents a systems-level failure of biological …
Read PDF<h4>Background</h4>Colorectal cancer (CRC) is a major cause of morbidity and mortality, with chronic inflammation from inflammatory bowel disease (IBD) representing a well-established risk factor. Clarifying shared molecular mechanisms may facilitate early detection and prevention strategies.<h4>Methods</h4>Proteomic …
Read PDFIt is now recognized that mitochondria play a crucial role in tumorigenesis; however, it has become clear that tumor metabolism varies significantly between cancer types. The failure of recent clinical trials aimed at directly targeting …
Read PDFMost existing transcriptome wide association studies (TWASs) of Alzheimer's Disease (AD) dementia only use bulk RNA-seq data and a single statistical method. Here, we utilize an omnibus TWAS (TWAS-O) pipeline that leverages multiple complementary statistical …
Read PDFAccurate cell type identification is critical for interpreting single-cell transcriptomic data and understanding complex biological systems. In this review, we discuss how natural language processing and large language models can enhance the accuracy and scalability …
Read PDFAggressive variant prostate cancer (AVPC) is a lethal subtype of prostate cancer characterized by androgen independence, resistance to chemotherapy, and neuroendocrine features that can emerge de novo or via transformation after a prior diagnosis of …
Read PDFThis study presents the first complete mitochondrial genome of <i>Ferula sinkiangensis</i>, a medicinal plant formally recognized in the Chinese Pharmacopoeia since 1977. The assembled mitogenome is 416,958 bp in length, encoding 97 genes, and exhibits …
Read PDFMicroRNAs (miRNAs) are key regulators of gene expression in both health and disease. Their expression and regulatory functions are highly complex and spatiotemporally organized within tissues. In recent years, spatial transcriptomics has made significant progress …
Read PDF<h4>Summary</h4>Long-read RNA-seq uncovers complex transcriptome diversity, opening new avenues for isoform-level expression analysis. Nevertheless, the functional diversity of individual isoforms is still poorly understood. We introduce isoespy, an analysis pipeline for integrating isoform structures, differential …
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