BioData Mining

Competing endogenous RNAs play key roles in cellular molecular mechanisms through cross-talk in post-transcriptional interactions. Studies on ceRNA cross-talk, which is particularly dependent on the abundance of free transcripts, generally involve large- and small-scale studies involving the integration of transcriptomic data from tissues and correlation analyses. This abundance-dependent nature of ceRNA interactions suggests that tissue- and condition-specific ceRNA dynamics may fluctuate. However, there are no comprehensive studies investigating the ceRNA interactions in normal tissue, ceRNAs that are lost and/or appear in cancerous tissues or their interactions...

BACKGROUND: Gene network information is believed to be beneficial for disease module and pathway identification, but has not been explicitly utilized in the standard random forest (RF) algorithm for gene expression data analysis. We investigate the performance of a network-guided RF where the network information is summarized into a sampling probability of predictor variables which is further used in the construction of the RF. RESULTS: Our simulation results suggest that network-guided RF does not provide better disease prediction than the standard RF...

BACKGROUND: Integrating multi-omics data is emerging as a critical approach in enhancing our understanding of complex diseases. Innovative computational methods capable of managing high-dimensional and heterogeneous datasets are required to unlock the full potential of such rich and diverse data. METHODS: We propose a Multi-Omics integration framework with auxiliary Classifiers-enhanced AuToencoders (MOCAT) to utilize intra- and inter-omics information comprehensively...

BACKGROUND: Breast cancer is the most common malignancy among women worldwide. Despite advances in treating breast cancer over the past decades, drug resistance and adverse effects remain challenging. Recent therapeutic progress has shifted toward using drug combinations for better treatment efficiency. However, with a growing number of potential small-molecule cancer inhibitors, in silico strategies to predict pharmacological synergy before experimental trials are required to compensate for time and cost restrictions...

PURPOSE: Epistasis, the interaction between two or more genes, is integral to the study of genetics and is present throughout nature. Yet, it is seldom fully explored as most approaches primarily focus on single-locus effects, partly because analyzing all pairwise and higher-order interactions requires significant computational resources. Furthermore, existing methods for epistasis detection only consider a Cartesian (multiplicative) model for interaction terms. This is likely limiting as epistatic interactions can evolve to produce varied relationships between genetic loci, some complex and not linearly separable...

BACKGROUND: Previous studies have shown an association between gut microbiota and cardiovascular diseases (CVDs). However, the underlying causal relationship remains unclear. This study aims to elucidate the causal relationship between gut microbiota and CVDs and to explore the pathogenic role of gut microbiota in CVDs. METHODS: In this two-sample Mendelian randomization study, we used genetic instruments from publicly available genome-wide association studies, including single-nucleotide polymorphisms (SNPs) associated with gut microbiota (n = 14,306) and CVDs (n = 2,207,591)...

BACKGROUND: Prioritizing candidate drugs based on genome-wide expression data is an emerging approach in systems pharmacology due to its holistic perspective for preclinical drug evaluation. In the current study, a network-based approach was proposed and applied to prioritize plant polyphenols and identify potential drug combinations in breast cancer. We focused on MEK5/ERK5 signalling pathway genes, a recently identified potential drug target in cancer with roles spanning major carcinogenesis processes...

BACKGROUND: 1-methyladenosine (m1A) is a variant of methyladenosine that holds a methyl substituent in the 1st position having a prominent role in RNA stability and human metabolites. OBJECTIVE: Traditional approaches, such as mass spectrometry and site-directed mutagenesis, proved to be time-consuming and complicated. METHODOLOGY: The present research focused on the identification of m1A sites within RNA sequences using novel feature development mechanisms...

BACKGROUND: Non-linear relationships at the genotype level are essential in understanding the genetic interactions of complex disease traits. Genome-wide association Studies (GWAS) have revealed statistical association of the SNPs in many complex diseases. As GWAS results could not thoroughly reveal the genetic background of these disorders, Genome-Wide Interaction Studies have started to gain importance. In recent years, various statistical approaches, such as entropy-based methods, have been suggested for revealing these non-additive interactions between variants...

BACKGROUND: Nowadays, the chance of discovering the best antibody candidates for predicting clinical malaria has notably increased due to the availability of multi-sera data. The analysis of these data is typically divided into a feature selection phase followed by a predictive one where several models are constructed for predicting the outcome of interest. A key question in the analysis is to determine which antibodies  should be included in the predictive stage and whether they should be included in the original or a transformed scale (i...

BACKGROUND: Although the 2019 EULAR/ACR classification criteria for systemic lupus erythematosus (SLE) has required at least a positive anti-nuclear antibody (ANA) titer (≥ 1:80), it remains challenging for clinicians to identify patients with SLE. This study aimed to develop a machine learning (ML) approach to assist in the detection of SLE patients using genomic data and electronic health records. METHODS: Participants with a positive ANA (≥ 1:80) were enrolled from the Taiwan Precision Medicine Initiative cohort...

OBJECTIVES: The elderly are disproportionately affected by age-related hearing loss (ARHL). Despite being a well-known tool for ARHL evaluation, the Hearing Handicap Inventory for the Elderly Screening version (HHIE-S) has only traditionally been used for direct screening using self-reported outcomes. This work uses a novel integration of machine learning approaches to improve the predicted accuracy of the HHIE-S tool for ARHL in older adults. METHODS: We employed a dataset that was gathered between 2016 and 2018 and included 1,526 senior citizens from several Taipei City Hospital branches...

DNA N6-adenine methylation (N6-methyladenine, 6mA) plays a key regulating role in the cellular processes. Precisely recognizing 6mA sites is of importance to further explore its biological functions. Although there are many developed computational methods for 6mA site prediction over the past decades, there is a large root left to improve. We presented a cross validation-based stacking ensemble model for 6mA site prediction, called 6mA-StackingCV. The 6mA-StackingCV is a type of meta-learning algorithm, which uses output of cross validation as input to the final classifier...

BACKGROUND: Discrimination between patients affected by inflammatory bowel diseases and healthy controls on the basis of endoscopic imaging is an challenging problem for machine learning models. Such task is used here as the testbed for a novel deep learning classification pipeline, powered by a set of solutions enhancing characterising elements such as reproducibility, interpretability, reduced computational workload, bias-free modeling and careful image preprocessing. RESULTS: First, an automatic preprocessing procedure is devised, aimed to remove artifacts from clinical data, feeding then the resulting images to an aggregated per-patient model to mimic the clinicians decision process...

BACKGROUND AND OBJECTIVE: The classification of glioma subtypes is essential for precision therapy. Due to the heterogeneity of gliomas, the subtype-specific molecular pattern can be captured by integrating and analyzing high-throughput omics data from different genomic layers. The development of a deep-learning framework enables the integration of multi-omics data to classify the glioma subtypes to support the clinical diagnosis. RESULTS: Transcriptome and methylome data of glioma patients were preprocessed, and differentially expressed features from both datasets were identified...

BACKGROUND: The governance of health systems is complex in nature due to several intertwined and multi-dimensional factors contributing to it. Recent challenges of health systems reflect the need for innovative approaches that can minimize adverse consequences of policies. Hence, there is compelling evidence of a distinct outlook on the health ecosystem using artificial intelligence (AI). Therefore, this study aimed to investigate the roles of AI and its applications in health system governance through an interpretive scoping review of current evidence...

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BACKGROUND: Patients with Type 2 Diabetes Mellitus (T2DM) are at a higher risk of polypharmacy and more susceptible to irrational prescriptions; therefore, pharmacological therapy patterns are important to be monitored. The primary objective of this study was to highlight current prescription patterns in T2DM patients and compare them with existing Standards of Medical Care in Diabetes. The second objective was to analyze whether age and gender affect prescription patterns. METHOD: This cross-sectional study was conducted using the Iran Health Insurance Organization (IHIO) prescription database...

Automatic segmentation of skin lesions is a critical step in Computer Aided Diagnosis (CAD) of melanoma. However, due to the blurring of the lesion boundary, uneven color distribution, and low image contrast, resulting in poor segmentation result. Aiming at the problem of difficult segmentation of skin lesions, this paper proposes an Attention-based Dual-path Feature Fusion Network (ADFFNet) for automatic skin lesion segmentation. Firstly, in the spatial path, a Boundary Refinement (BR) module is designed for the output of low-level features to filter out irrelevant background information and retain more boundary details of the lesion area...

Squiggle data is the numerical output of DNA and RNA sequencing by the Nanopore next generation sequencing platform. Nanopore sequencing offers expanded applications compared to previous sequencing techniques but produces a large amount of data in the form of current measurements over time. The analysis of these segments of current measurements require more complex and computationally intensive algorithms than previous sequencing technologies. The purpose of this study is to investigate in principle the potential of using quantum computers to speed up Nanopore data analysis...