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<h4>Motivation</h4>Aberrant DNA methylation is a fundamental epigenetic hallmark of cancer. However, existing resources often lack technological diversity and comprehensive cancer coverage. Furthermore, most platforms fail to achieve deep multi-omics integration and tend to ignore cancer-type-specific …
Read PDF<h4>Motivation</h4>Illumina DNA methylation arrays have evolved rapidly, expanding genomic coverage while introducing backward incompatibilities by removing many CpG sites present in earlier versions. These changes result in systematic missing values when integrating data across array …
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 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 PDF<b>Background</b>: Diabetic vascular complications are a major cause of poor prognosis in patients with diabetes mellitus (DM). Mitophagy activation is a potential therapeutic target for type 2 diabetes mellitus (T2DM), but the role of low-intensity …
Read PDF<h4>Motivation</h4>Single-cell Hi-C (scHi-C) technologies have significantly advanced our understanding of the 3D genome organization. However, scHi-C data are often sparse and noisy, leading to substantial computational challenges in downstream analyses.<h4>Results</h4>In this study, we introduce SHICEDO, …
Read PDFLung adenocarcinoma (LUAD), the most common subtype of nonsmall cell lung cancer, exhibits substantial molecular heterogeneity, complicating subtype classification, progression assessment, and treatment decision-making. Advances in high-throughput sequencing enable multi-omics analysis to reveal cancer mechanisms …
Read PDFBACKGROUND: The nectin cell adhesion molecule 4 (NECTIN4) has been implicated in tumor progression and immune evasion, yet its role and translational targeted imaging potential in lung cancer remain unclear. Therefore, this study aims to …
Read PDF<h4>Motivation</h4>Molecular dynamics (MD) simulations provide detailed atomistic insights into biomolecular processes, but comparing independent trajectories remains challenging due to stochastic divergence. Misaligned simulations can obscure shared mechanisms or exaggerate differences, limiting reproducibility and mechanistic interpretation. …
Read PDF<h4>Motivation</h4>Chromatin 3D folding creates numerous DNA interactions, participating in gene expression regulation. Single-cell chromatin-accessibility assays now profile hundreds of thousands of cells, challenging existing methods for mapping cis-regulatory interactions.<h4>Results</h4>We present CIRCE, a fast and scalable …
Read PDF<h4>Motivation</h4>Modern genomic research is driven by next-generation sequencing experiments such as ChIP-seq, CUT&Tag, and CUT&RUN that generate coverage files for transcription factor binding, as well as ATAC-seq that yield coverage files for chromatin accessibility. Due …
Read PDF<h4>Motivation</h4>N6-methyladenine (6 mA) is an important epigenetic modification of DNA that regulates biological processes such as gene expression, transcription, replication, DNA repair, and cell cycle without altering the DNA sequence. It also plays a key …
Read PDF<h4>Motivation</h4>Global population aging has led to a rapid increase in neurodegenerative disorders such as Alzheimer's disease (AD). Although existing drugs can temporarily alleviate symptoms, none have been proven to delay or prevent disease progression. Acetylcholinesterase …
Read PDFMetabolic syndrome and excessive alcohol consumption (MetALD) result in liver injury and fibrosis, which are driven by increased collagen production by activated hepatic stellate cells (HSCs). Our previous studies demonstrated that LARP6, an RNA-binding protein, …
Read PDFThe rapid and accurate diagnosis of rare diseases is paramount in directing clinical management. In recent years, the integration of multi-omics approaches has emerged as a potential strategy to overcome diagnostic hurdles. This review examines …
Read PDFBladder cancer (BC) is one of the most prevalent types of cancer in developed countries. BC is characterized by its highly heterogeneous and dynamic nature, with significantly higher morbidity and mortality rates in men compared …
Read PDFSpatial omics integrates molecular profiling with spatial tissue context, enabling high-resolution analysis of gene expression, protein interactions, and epigenetic modifications. This approach provides critical insights into disease mechanisms and therapeutic responses, with applications in cancer, …
Read PDFRNA methylation, particularly N6-methyladenosine (m<sup>6</sup>A) and 5-methylcytosine (m<sup>5</sup>C), functions as a pivotal post-transcriptional regulatory mechanism and plays a central role in plant growth, development, and stress responses. This review provides a systematic summary of recent …
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