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In this paper, we develop a heterogeneous graph neural network, STAMapper, to transfer the cell-type labels from single-cell RNA-sequencing (scRNA-seq) data to single-cell spatial transcriptomics (scST) data. We collect 81 scST datasets consisting of 344 …
Read PDFVascular smooth muscle cells contribute to heritable coronary artery disease risk and undergo complex transitions to multiple disease-related phenotypes. To investigate the genetic basis of these trajectories, we develop a dense timecourse single-cell transcriptomic and …
Read PDFNeuroblastoma (NB) accounts for 10% of pediatric cancer-related deaths, is often highly metastatic at diagnosis, and has a 5-year-survival rate of <50% for patients with high-risk disease. We previously showed that the transcriptional coactivator LMO1 …
Read PDF<h4>Background</h4>Glaucoma Research Foundation's third Catalyst for a Cure team (CFC3) was established in 2019 to uncover new therapies for glaucoma, a leading cause of blindness. In the 2021 meeting "Solving Neurodegeneration," (detailed in Mol Neurodegeneration …
Read PDFBACKGROUND: Cryopreservation of porcine blastocysts remains a significant challenge due to their high lipid content, which can lead to cryoinjury and reduced developmental competence. While liquid nitrogen (LN) vitrification causes significant molecular damage, LHe vitrification …
Read PDFFibroblasts are key potentiators of chronic disease pathophysiology. Despite their established roles in promoting pathological inflammation and tissue remodeling, activated myofibroblasts are generally characterized as a single, homogeneous cell population, obscuring critical functional distinctions. Defining …
Read PDFAmoeboflagellates of the genus <i>Naegleria</i> are free-living protists ubiquitously found in soil and freshwater habitats worldwide. They include the "brain-eating amoeba" <i>Naegleria fowleri</i>, an opportunistic pathogen that causes primary amoebic meningoencephalitis, a rare but fatal …
Read PDFA myelination is essential for neural function in the vertebrate central nervous system, yet the molecular details of how the oligodendrocyte differentiation program has evolved remain poorly understood. Here, we performed a cross-species single-cell transcriptomic …
Read PDFA prevailing hypothesis for the emergence of life on Earth holds that it might have originated in hydrothermal vents, where the environmental conditions, although physically and chemically extreme (acidity, lack of oxygen, high pressure, very …
Read PDFGregarines are a large and diverse subgroup of Apicomplexa, a lineage of obligate animal symbionts including pathogens such as <i>Plasmodium</i>, the malaria parasite. Unlike <i>Plasmodium</i>, however, gregarines are poorly studied, despite the fact that as …
Read PDFThe phylum Rozellomycota has been proposed for a group of early-branching holomycotan lineages representing obligate parasites and hyperparasites of zoosporic fungi, oomycotes or phytoplankton. Given their predominantly intracellular lifestyle, rozellids are typically known from environmental …
Read PDFSingle-cell proteomics (SCP) platforms are widely sought-after biomedical tools to complement existing omics technologies. Here, we present MiProChip, a microfluidic platform that integrates cell capture, lysis, protein digestion, tandem mass tag (TMT) labeling, on-chip pooling, …
Read PDFAntibiotic resistance is a major threat to global public health. It is vital to understand the mechanism of antibiotic resistance development to prevent the emergence of new pan-resistant pathogenic bacteria and to develop new antibiotics. …
Read PDFCell-cell communications are widely explored to understand tissue homeostasis and diseases. Numerous computational tools have been developed to infer cellular interactions from transcriptomic or proteomic expression data. However, proteins often carry post-translational modifications (PTMs) that …
Read PDF<h4>Background</h4>Small cell lung cancer (SCLC) is an aggressive neuroendocrine tumor characterized by rapid progression, early metastasis, and high mortality, with limited effective long-term treatment options. <i>B4GALT1</i>, a β-1,4-galactosyltransferase, has been implicated in the malignant progression …
Read PDFUnderstanding protein distribution patterns across tissue architecture is crucial for deciphering organ function in health and disease. Here we show the application of single-cell Deep Visual Proteomics to perform spatially resolved proteome analysis of individual …
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 PDFBreast cancers are biologically and clinically diverse. While large-scale gene expression analyses have enabled epithelial-centered molecular classifications, studies of the tumor microenvironment (TME) remain limited, especially at the proteome level using tissue-specific resolution. By laser …
Read PDFHere, we introduce Spectral Cruncher, an interactive extension to the PatternLab for Proteomics platform, designed to bridge the gap between manual curation and state-of-the-art computational analysis of proteomic tandem mass spectra. Spectral Cruncher integrates de …
Read PDFAlzheimer's disease (AD) is the most common cause of dementia, yet its molecular causes remain incompletely understood. RNA diversity in part arising from dysregulated splicing may contribute to AD pathogenesis, however the ability to interrogate …
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