Background: Mycosis fungoides (MF) represents the most prevalent entity of cutaneous T cell lymphoma (CTCL). The MF aetiopathogenesis is incompletely understood, due to significant transcriptomic heterogeneity and conflicting views on whether oncolog...
In this perspective, we discuss the current challenges and opportunities in multi-omics, a rapidly evolving approach that integrates multiple molecular layers to advance our understanding of complex biological systems. As biomedical research moves to...
Metabolomics deals with multiple and complex chemical reactions within living organisms and how these are influenced by external or internal perturbations. It lies at the heart of omics profiling technologies not only as the underlying biochemical la...
Background: The precise identification of cancer subtypes through the integration of multi-omics data has emerged as a key research direction in bioinformatics. Among existing multi-omics integration methods, similarity graph-based clustering algorit...
With the growing use of high-throughput technologies, multi-omics data containing various types of high-dimensional omics data is increasingly being generated to explore the association between the molecular mechanism of the host and diseases. In thi...
With the advent of high-throughput technologies, the field of omics has made significant strides in characterizing biological systems at various levels of complexity. Transcriptomics, proteomics, and metabolomics are the three most widely used omics...
Objectives: Cancer, characterized by its profound complexity and heterogeneity, arises from a multitude of molecular disruptions. The pursuit of identifying distinct cancer subtypes is driven by the need to stratify patients into clinically coherent...
Extracellular vesicles (EVs) are membranous structures derived from the endosomal system or generated by plasma membrane shedding. Due to their composition of DNA, RNA, proteins, and lipids, EVs have garnered a lot of attention as an essential mechan...
Thousands of biomarkers have been discovered to solve the mechanisms of cancer, but dynamic alterations in the parameters that affect cancer progression cause complex disease status. Therefore, it is essential when dealing with cancer to analyze all...
High-throughput technologies have been used to generate a large amount of omics data. In the past, single-level analysis has been extensively conducted where the omics measurements at different levels, including mRNA, microRNA, CNV and DNA methylatio...
The recent advancement of omic technologies provides researchers with the possibility to search for disease-associated biomarkers at the system level. The integrative analysis of data from a large number of molecules involved at various layers of the...
Nutritional compounds may have an influence on different OMICs levels, including genomics, epigenomics, transcriptomics, proteomics, metabolomics, and metagenomics. The integration of OMICs data is challenging but may provide new knowledge to explain...
Recent advances in sequencing and biotechnological methodologies have led to the generation of large volumes of molecular data of different omics layers, such as genomics, transcriptomics, proteomics and metabolomics. Integration of these data with c...
Multi-omics is a field that studies the interactions between different biological modalities to obtain a more precise medical understanding of biological phenomena. With recent advances in high-throughput technologies, multi-omics datasets have becom...
This review discusses the transformative potential of integrating multi-omics data and artificial intelligence (AI) in advancing horticultural research, specifically plant phenotyping. The traditional methods of plant phenotyping, while valuable, are...
The rapid advancement of high-throughput technologies has led to the generation of vast amounts of omics data, including genomics, epigenomics, and metabolomics. Integrating these diverse datasets has become essential for gaining comprehensive insigh...
Colorectal cancer (CRC) remains a leading cause of cancer-related mortality worldwide, although advances in molecular profiling and artificial intelligence (AI) are now reshaping precision oncology in ways that promise better patient outcomes. This r...
The integrative personal omics profile (iPOP) is a pioneering study that combines genomics, transcriptomics, proteomics, metabolomics and autoantibody profiles from a single individual over a 14-month period. The observation period includes two episo...
Recent developments in high-throughput technologies have accelerated the accumulation of massive amounts of omics data from multiple sources: genome, epigenome, transcriptome, proteome, metabolome, etc. Traditionally, data from each source (e.g., gen...
Neurodevelopmental disorders (NDDs), including autism spectrum disorder, intellectual disability, and attention-deficit/hyperactivity disorder, are genetically and phenotypically heterogeneous conditions affecting millions worldwide. High-throughput...
High-throughput technologies make it possible to produce a large amount of data representing different biological layers, examples of which are genomics, proteomics, metabolomics and transcriptomics. Omics data have been individually investigated to...
Asthma is a multifactorial inflammatory disorder of the respiratory system characterized by high diversity in clinical manifestations, underlying pathological mechanisms and response to treatment. It is generally established that human microbiota pla...
Advancements in the field of next generation sequencing (NGS) have generated vast amounts of data for the same set of subjects. The challenge that arises is how to combine and reconcile results from different omics studies, such as epigenome and tran...
Combining omics data from different layers using integrative methods provides a better understanding of the biology of a complex disease such as cancer. The discovery of biomarkers related to cancer development or prognosis helps to find more effecti...
Background: Type 1 diabetes (T1D) is a devastating disease with serious health complications. Early T1D biomarkers that could enable timely detection and prevention before the onset of clinical symptoms are paramount but currently unavailable. Despit...
Integrating proteomic and metabolomic data remains challenging due to the many-to-many relationships between metabolites and proteins and the spatial constraints of cellular compartmentalization. To address this, we developed PMconv, a web-based appl...
Despite recent advances in chronic obstructive pulmonary disease (COPD) research, few studies have identified the potential therapeutic targets systematically by integrating multiple-omics datasets. This project aimed to develop a systems biology pip...
Intensive yak fattening in cold alpine regions requires essential long-term high-concentration feeding, which disrupts rumen microbial homeostasis and causes inefficient digestion of nutrients. Lactobacillus may have probiotic potential for ruminants...
This study focuses on the systematization and integration of ovarian cancer multi-omics data, revealing patterns in the application of different omics-based approaches and assessing factors that affect the identification of potential biomarkers. An i...
Animal venoms offer a valuable source of potent new drug leads, but their mechanisms of action are largely unknown. We therefore developed a novel network pharmacology approach based on multi-omics functional data integration to predict how stingray...
High-throughput technologies produce large-scale omics datasets, and their integration facilitates biomarker discovery and predictive modeling. However, challenges such as data heterogeneity, high dimensionality, and block-wise missing data complicat...
The definitive diagnosis and early treatment of many immune-mediated inflammatory diseases (IMIDs) is hindered by variable and overlapping clinical manifestations. Psoriatic arthritis (PsA), which develops in ~30% of people with psoriasis, is a key e...
High-grade serous ovarian cancer (HGSOC) is characterized by a complex genomic landscape, with both genetic and epigenetic diversity contributing to its pathogenesis, disease course, and response to treatment. To better understand the association bet...
Gene-environment (G×E) interaction is critical for understanding the genetic basis of complex disease beyond genetic and environment main effects. In addition to existing tools for interaction studies, penalized variable selection emerges as a...
Technological advances in next-generation sequencing (NGS) have made it possible to uncover extensive and dynamic alterations in diverse molecular components and biological pathways across healthy and diseased conditions. Large amounts of multi-omics...
The identification of cancer subtypes is crucial to cancer diagnosis and treatments. A number of methods have been proposed to identify cancer subtypes by integrating multi-omics data in recent years. However, the existing methods rarely consider the...
Background/Objectives: Population aging necessitates a shift from disease-focused paradigms to a holistic characterization of biological aging processes. While chronological age remains the primary metric, it poorly captures inter-individual variabil...
The recent development of high-throughput technology has allowed us to accumulate vast amounts of multi-omics data. Because even single omics data have a large number of variables, integrated analysis of multi-omics data suffers from problems such as...
Background and Objectives: The burst of high-throughput omics technologies has given rise to a new era in systems biology, offering an unprecedented scenario for deriving meaningful biological knowledge through the integration of different layers of...
Technological advances in information-processing capacity have enabled integrated analyses (multi-omics) of different omics data types, improving target discovery and clinical diagnosis. This study proposes novel artificial intelligence (AI) learning...
Early diagnosis of lung cancer to increase the survival rate, which is currently at a low range of mid-30%, remains a critical need. Despite this, multi-omics data have rarely been applied to non-small-cell lung cancer (NSCLC) diagnosis. We developed...
Mortality attributed to lung cancer accounts for a large fraction of cancer deaths worldwide. With increasing mortality figures, the accurate prediction of prognosis has become essential. In recent years, multi-omics analysis has emerged as a useful...
The rapid advancements in high-throughput technologies have led to a dramatic increase in diverse -omics data types, enabling comprehensive analyses, especially for complex diseases like cancer. Despite the development of multi-omics approaches, the...
Cancer, as a complex disease with high heterogeneity, is gradually shifting from standardization to individualization. Current research indicates that integrating multi-omics data, including genome, transcriptome, and epigenome, can more comprehensiv...
Precisely identifying cancer drivers helps us to understand the molecular mechanisms of cancer, offering critical targets for early diagnosis. Despite the increasing application of graph neural networks in predicting cancer driver genes, existing app...
Mining interspecies interactions remain a challenge due to the complex nature of microbial communities and the need for computational power to handle big data. Our meta-analysis indicates that genetic potential alone does not resolve all issues invol...
In this paper, we consider the extremal trace problem for the coupled Laplacian on the sets homeomorphic to the Stiefel manifold defined on the complex Euclidean space. The study is implemented via various mathematical methods, including topological...
Background: Epigenomics has emerged as an essential field in modern molecular biology, providing a critical layer of gene regulation. DNA methylation, histone modifications and alterations to the chromatin accessibility of DNA have been widely associ...
Subgingival microbiome dysbiosis promotes the development of periodontitis, an irreversible chronic inflammatory disease associated with metabolic diseases. However, studies regarding the effects of a hyperglycemic microenvironment on host–micr...
In dairy production, the fermentation process is a complex biochemical system that plays a significant role in determining the quality criteria of the final product. Traditional methods for controlling fermentation rely on limited and non-standard pr...
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