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BACKGROUND Acute lung injury (ALI) after liver transplantation (LT) is a critical complication negatively affecting transplant outcomes and patient survival. However, effective biomarkers for early diagnosis remain unidentified. This study aimed to identify hub biomarkers …
Read PDF<h4>Background</h4>Ionizing radiation (IR) induces profound bone marrow (BM) injury by disrupting hematopoietic stem cell (HSC) homeostasis, leading to acute myelosuppression and long-term hematopoietic dysfunction. Although transcriptome-wide analyses have advanced our understanding of radiation responses, the …
Read PDF<h4>Motivation</h4>Experimentally generated drug-induced transcriptomic signatures are valuable resources to infer candidate drugs for unseen transcriptomes. The Connectivity Map (CMap) includes over 720 000 compound-induced signatures and has been widely used in drug repurposing. However, the …
Read PDF<h4>Motivation</h4>Current software packages to mine key transcription factors (TFs) regulating the differentially expressed genes (DEGs) have not been satisfactorily utilized.<h4>Results</h4>Here, we present TransPilot, a web server that identifies key TFs from transcriptome data via weighted …
Read PDF<h4>Background</h4>Endometriosis (EMs) is a common gynecological disorder associated with impaired fertility and reduced quality of life. This study investigated abnormal spindle-like microcephaly-associated protein (ASPM), identified as a hub gene in EMs pathogenesis, and explored its …
Read PDFBACKGROUND: In recent years, Piwi-interacting RNAs (piRNAs) have been found to be involved in different biological roles beyond their initially identified role in protecting the germline genome. However, there is a lack of robust computational …
Read PDF<h4>Summary</h4>Whereas transcriptomic and spatial profiling offer static snapshots of tissue structure, mechanistic models use biological rules to predict how tissues evolve. We present the BioInformatics WalkThrough (BIWT) software to directly initialize spatial agent-based models from …
Read PDF<h4>Background</h4>The incidence of papillary thyroid cancer (PTC) has risen sharply over the past several decades. Early identification of high-risk PTC is crucial to mitigate the societal burden associated with its overdiagnosis. ER-phagy, a selective form …
Read PDFBACKGROUND: N6-methyladenosine ([Formula: see text]) plays a crucial role in enriching RNA functional and genetic information. While deep learning has advanced [Formula: see text] site identification, current state-of-the-art methods, particularly those based on large-scale Pre-trained …
Read PDF<h4>Motivation</h4>High-dimensional sequencing data, such as RNA-Seq for gene expression and ATAC-Seq for chromatin accessibility, are widely used in studying systems biology. Accessible chromatin allows transcription factors and regulatory elements to bind to DNA, thereby regulating …
Read PDFBACKGROUND: Diabetic nephropathy (DN) has been pathophysiologically associated with macrophage activity; however, the molecular mechanisms underlying this relationship remain unclear. This study aimed to explore the regulatory mechanisms linking DN and macrophages using integrated bioinformatics …
Read PDFBACKGROUND: Single-cell RNA sequencing (scRNA-seq) is considered a revolution in gene expression studies and offers significant benefits across various fields of biomedical or clinical applications. However, a high proportion of technical dropouts in scRNA-seq data …
Read PDFParaquat, a highly toxic herbicide, frequently causes acute poisoning, predominantly inducing pulmonary injury and fibrosis with high mortality, and no specific antidote is available. This study aimed to explore its pathogenesis using a paraquat-induced mouse …
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Read PDFThis study aims to utilize multiomics and bioinformatics techniques to investigate the expression of the connection enzyme inhibitor Ras1 1 (CNKSR1) in ovarian cancer (OC) and its mechanism of action in the processes of tumor …
Read PDF<h4>Motivation</h4>Dysregulation of Ca<sup>2+</sup>-signaling genes has been shown in some types of cancer; however, it is virtually unknown in hepatitis B-derived hepatocellular carcinoma (HBV-HCC). Here, we evaluate the transcriptional and epigenetic regulation of Ca<sup>2+</sup>-signaling genes in …
Read PDFH-SPAR DB is a comprehensive database designed to support space health research by providing a unified platform for data integration, analysis, and interpretation. The database simplifies the complex workflows associated with spaceflight-related biology studies by …
Read PDFBACKGROUND: Hypertension (HTN) results from intricate molecular mechanisms, making clinical remission difficult to achieve. This study explores the molecular pathways through which cannabidiol (CBD) may influence HTN. METHODS: Several RNA sequencing datasets related to HTN …
Read PDF<h4>Motivation</h4>MicroRNAs (miRNAs) play a central role in controlling gene expression, and their abnormal activity is frequently linked to disease. Despite advancements in transcriptomic technologies, elucidating miRNA-mediated mechanisms remains challenging due to methodological limitations and a …
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