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Tamarindus indica is the sole member of the genus Tamarindus of the Leguminosae family. It is a multipurpose horticultural plant, with every part of the plant finding importance in food, medicine, and other industries. To …
Read PDF<h4>Background</h4>Pattern matching is a fundamental challenge in bioinformatics, especially in the fields of genomics, transcriptomics and proteomics. Efficient indexing structures, such as suffix arrays, are critical for searching large datasets. A sparse suffix array (SSA) …
Read PDFWhole-genome duplication is a major evolutionary force, with salmonids providing a key model system. In this study, we generated a high-quality masu salmon genome using PacBio HiFi, ONT ultra-long and Hi-C sequencing technologies. The final …
Read PDFWe present a high-quality chromosome-scale genome assembly for the Orange Baboon Tarantula (Pterinochilus murinus). The 4.7 Gb genome is organized into 22 chromosomes and demonstrates 96.32% completeness based on BUSCO analysis (-m genome) using the …
Read PDFGynostemma guangxiense X. X. Chen & D. H. Qin, belonging to the family Cucurbitaceae, is a perennial creeping herbaceous plant endemic to China with potential medicinal and health value. Here, we report the high-quality chromosome-level …
Read PDF<h4>Motivation</h4>Short-read sequencing data can be affected by alignment artifacts in certain genomic regions. Removing reads overlapping these exclusion regions, previously known as Blacklists, help to potentially improve biological signal. Alternatively, "sponge" or decoy sequences have …
Read PDF<h4>Motivation</h4>Advances in sequencing technologies have enabled researchers to sequence whole genomes rapidly and cheaply. However, despite improvements in genome assembly, structural genome annotation (i.e. the identification of protein-coding genes) remains challenging, particularly for eukaryotic genomes. …
Read PDFHomarid lobsters are notable for their remarkable immunity and longevity, with lifespans reaching up to 80 years in the wild. A reference genome is available for the American lobster (Homarus americanus), but not for the …
Read PDFAntibodies produced by B cells aid in the recognition and clearance of pathogens and are the cornerstone of vaccination strategies. Humans produce nine different antibody isotypes, and their effector functions differ according to the type …
Read PDFSpondyloarthritis (SpA) and psoriatic arthritis (PsA) are interrelated, immune-mediated inflammatory diseases characterized by significant clinical heterogeneity. Early differential diagnosis, accurate disease activity assessment, and the development of personalized treatment strategies remain significant clinical challenges. Single-omics …
Read PDF<h4>Background/aim</h4>Cancer stem cells (CSCs) play key roles in hepatocellular carcinoma (HCC) initiation, progression, therapeutic resistance, and recurrence, yet their cellular and spatial heterogeneity remains poorly understood. This study aimed to systematically characterize HCC-associated CSCs and …
Read PDFReconstructing the 3D spatial organization of transcription from 2D spatial data is a fundamental challenge in genomics. Here, we introduce Cytocraft, a computational framework that addresses this problem by inferring a shared, cell-type-specific 3D configuration …
Read PDF[This corrects the article DOI: 10.3389/fonc.2025.1588514.].
Read PDF<h4>Introduction</h4>Pressure overload-induced myocardial hypertrophy is associated with complex spatial and temporal remodeling of cardiac cell populations. However, the spatial organization of these changes and their dynamic transcriptional programs remain incompletely understood. Integrating spatial transcriptomics with …
Read PDF<h4>Background</h4>Epstein-Barr virus (EBV)-positive nodal T/NK-cell lymphoma (EBV<sup>+</sup> nTNKL) has recently been delineated in the WHO-HAEM5 classification as a distinct and exceptionally rare entity. Its biology and clinical trajectory remain obscure relative to Extranodal NK/T-cell lymphoma …
Read PDFMedicinal plants synthesize an immense diversity of specialized metabolites that play crucial roles in ecological interactions and serve as valuable pharmaceutical resources. However, the biosynthetic pathways responsible for this chemical diversity remain largely uncharacterized. These …
Read PDFBACKGROUND: Prostate cancer (PCa) is a heterogeneous disease characterised by a highly complex cellular ecosystem within its tumour microenvironment (TME). However, the crosstalk patterns between tumour and immune cells remain poorly understood. METHODS: Single cell …
Read PDFSpatial transcriptomics (ST) technologies are revolutionizing our ability to investigate the spatial organization of complex tissues. While ST has significantly advanced our understanding of tissue architecture, most analytical approaches remain restricted to 2D sections, limiting …
Read PDF[This corrects the article DOI: 10.1371/journal.pone.0322026.].
Read PDFModern cancer care and precision medicine increasingly rely on high quality human tissue yet tissue preservation practices in many healthcare systems remain outdated. Traditional formalin-fixed paraffin-embedded (FFPE) tissues while long established, is poorly suited to …
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