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Transcriptome analyses are widely used for biological research. Gene ontology (GO) enrichment analysis is often used for effectively analyzing large data matrices. However, various software and methods can be used for performing GO enrichment analyses, …
Read PDFIdentifying and functionally validating the causal variants at genome-wide association study (GWAS) loci is very challenging and has only been achieved for very few variants. Here, we validate a single-nucleotide polymorphism (SNP) associated with increased …
Read PDFTriple-negative breast cancer (TNBC) is a subtype of breast cancer (BC) and constitutes approximately 15-20% of all BC cases. This subtype has the most aggressive behavior and the worst prognosis. Numerous studies have been conducted …
Read PDFExtrachromosomal circular DNA (eccDNA) has emerged as a pivotal contributor to cancer progression, facilitating oncogene amplification, dysregulated gene expression, and tumor heterogeneity. Despite its significance in cancer, the interplay between eccDNA and key epigenetic regulators …
Read PDFBacterial small RNA are important context-sensitive regulators of gene expression, especially in highly pathogenic bacteria, often controlling virulence. The number of predicted small RNA (sRNA) entries in public repositories has grown exponentially, contrasting with the …
Read PDF<b>Introduction:</b> MicroRNAs (miRNAs) play central roles in cancer pathogenesis by modulating oncogenic and tumor-suppressive pathways. The microRNA-29 (miR-29) family, known to inhibit matrix metalloproteinase-2 (MMP-2), represents a key regulatory axis in tumor invasion. This study …
Read PDF<h4>Background</h4>RNA-based fusion panels using targeted next-generation sequencing of formalin-fixed paraffin-embedded tumour tissue specimens are used for various tumour types to detect rearrangements/fusions. Using bioinformatic approaches, the data obtained from RNA sequencing (RNA-Seq) can also be …
Read PDFTranscriptome profiling is a cornerstone of functional genomics, enabling the detailed characterization of gene expression in health and disease. Bulk RNA sequencing (bulk RNAseq) remains the most widely used approach in clinical and large-cohort studies …
Read PDF<h4>Background</h4>Xylem development is a dynamic, continuous process fundamental to secondary growth in woody plants and to biomass accumulation on earth. While single-cell RNA sequencing (scRNA-seq) enables reconstruction of early xylem differentiation trajectories, its reliance on …
Read PDF<h4>Introduction</h4>Non-small cell lung cancer (NSCLC) remains a leading cause of cancer-related mortality worldwide. Nanovesicles have been demonstrated to be important mediators of intercellular communication in NSCLC. Plant-derived nanovesicles contain lipids, proteins, nucleic acids, and pharmacologically …
Read PDFRNA editing is a post-transcriptional source of protein diversity and occurs across the animal kingdom. Given the complete profile of mRNA targets and their editing rate in individual cells is unclear, single-cell RNA transcriptomes obtained …
Read PDFParkinson's disease (PD) is a complex neurodegenerative disorder where environmental factors play a predominant role in sporadic cases. While environmental toxins are implicated in PD pathogenesis via epigenetic pathways, the specific alterations in chromatin accessibility …
Read PDFThis article reports transcriptomic dataset generated by rationalized sequencing of the 3' ends of messenger RNAs (3' mRNA-Seq) in porcine samples. Libraries were prepared from whole blood, plasma, serum, and exosome-enriched fractions derived from plasma …
Read PDFIntegration of multimodal, multi-omics data is critical for advancing precision medicine, yet its application is frequently limited by incomplete datasets where one or more modalities are missing. To address this challenge, we developed a generative …
Read PDFCaddisflies (Trichoptera) are among the most diverse groups of freshwater animals with more than 16 000 described species. They play a fundamental role in freshwater ecology and environmental engineering in streams, rivers and lakes. Because …
Read PDFTerrestriality, the adaptation to life on land, is one of the key evolutionary transitions, occurring numerous times across the tree of life. Within Arthropoda, there have been several independent transitions: in hexapods, myriapods, arachnids and …
Read PDFThe latest animal phylum to be discovered, Micrognathozoa, constitutes a rare group of limnic meiofauna. These microscopic 'jaw animals' are among the smallest metazoans yet possess highly complex jaw structures. The single species of Micrognathozoa, …
Read PDFDinoflagellates are an abundant and diverse group of protists representing a wealth of unique biology and ecology. While many dinoflagellates are photosynthetic or mixotrophic, many taxa are heterotrophs, often with complex feeding strategies. Compared to …
Read PDFCompared to plastid genomes, plant mitochondrial genomes have been less frequently used for species discrimination and phylogenetic studies due to assembly challenges, lower substitution rates and rapid structural evolution. However, this study demonstrates that mitochondrial …
Read PDFEvolution is reticulate. Reticulation increases diversity and complexity on the different levels of the evolutionary hierarchy. In addition to the tendency for diversity and complexity to increase in unchecked evolutionary systems by ongoing divergence ('Zero-Force …
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