One common problem in omics data analysis is missing values, which can arise due to various reasons, such as poor tissue quality and insufficient sample volumes. Instead of discarding missing values and related data, imputation approaches offer an al...
As researchers are increasingly able to collect data on a large scale from multiple clinical and omics modalities, multi-omics integration is becoming a critical component of metabolomics research. This introduces a need for increased understanding b...
(1) Background: Single-cell multi-omics is a powerful method for the dissection and detection of complicated immunologic functions and synapses. However, most currently available technologies merge datasets of different omics from separate portions o...
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...
Lipopolysaccharide (LPS) or endotoxin, the major cell wall component of Gram-negative bacteria, plays a pivotal role in the pathogenesis of sepsis. It is able to activate the host defense system through interaction with Toll-like receptor 4, thus tri...
Nonnegative Matrix Factorization (NMF) has acquired a relevant role in the panorama of knowledge extraction, thanks to the peculiarity that non-negativity applies to both bases and weights, which allows meaningful interpretations and is consistent wi...
The underlying causes fof major mental illnesses, including anxiety disorders (ADs), depression, and bipolar disorder (BD), remain insufficiently understood, limiting the availability of effective, patient-friendly treatments and accurate diagnostic...
High-throughput technologies such as RNA-seq and single-cell transcriptomics generate increasingly large and high-dimensional gene expression datasets in which nonlinear dependence structures are common. Because classical methods primarily capture li...
Breast cancer is the most prevalent cancer among women and is challenging to diagnose and treat due to its diverse subtypes and stages. Precision medicine aims to improve early detection, prognosis, and treatment planning by identifying new clinical...
Mycotoxins are well-known secondary metabolites produced by several fungi that grow and occur in different crops during both pre-harvest and post-harvest conditions. The contamination and occurrence of mycotoxins currently represent some of the major...
Background: Rapid advances in biotechnology provide researchers with the opportunity to integrate omics profiles (genomics, epigenomics, transcriptomics, proteomics, etc.) with multiple phenotypes or experimental conditions. In cancers such as acute...
Streptomyces are well-known producers of a range of different secondary metabolites, including antibiotics and other bioactive compounds. Recently, it has been demonstrated that “silent” biosynthetic gene clusters (BGCs) can be activated by heterolog...
(1) Background: Machine learning (ML) methods are rarely used for an omics-based prescription of cancer drugs, due to shortage of case histories with clinical outcome supplemented by high-throughput molecular data. This causes overtraining and high v...
Neuroblastoma is a common malignant tumor in childhood that seriously endangers the health and lives of children, making it essential to find effective prognostic markers to accurately predict their clinical outcomes. The development of high-throughp...
Plant natural products, also known as plant specialized metabolites (SMs) due to their lineage-specific distribution, are small molecules synthesized by plants to adapt to changing environments [...]
High-altitude plants face extreme environments such as low temperature, low oxygen, low nutrient levels, and strong ultraviolet radiation, causing them to adopt complex adaptation mechanisms. Phenotypic variation is the core manifestation of ecologic...
The quick and accurate identification of microorganisms and the study of resistance to antibiotics is crucial in the economic and industrial fields along with medicine. One of the fastest-growing identification methods is the spectrometric approach c...
Radiomics has shown remarkable potential in predicting cancer prognosis by noninvasive and quantitative analysis of tumors through medical imaging. This review summarizes recent advances in the use of radiomics across various cancer types and imaging...
Organophosphate flame retardants (OPFRs) have increasingly replaced polybrominated diphenyl ethers (PBDEs) in various consumer products and raw materials, due to regulatory restrictions on PBDEs. However, concerns about the toxicity and environmental...
A major trend in biomedical research has been an ideological shift away from studying individual components of an organism or biological process in isolation, and towards how those components function collectively, forming the basis of the field now...
There is a growing number of multi-domain genomic datasets for human tumors. Multi-domain data are usually interpreted after separately analyzing single-domain data and integrating the results post hoc. Data fusion techniques allow for the real integ...
Recent advances in developmental biology have been made possible by using multi-omic studies at single cell resolution. However, progress in plants has been slowed, owing to the tremendous difficulty in protoplast isolation from most plant tissues an...
It is imperative to comprehend the mechanisms that underlie drug toxicity in order to enhance the efficacy and safety of novel therapeutic agents. The capacity to identify molecular pathways that contribute to drug-induced toxicity has been significa...
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...
Magnaporthe oryzae Oryzae (MoO) pathotype is a devastating fungal pathogen of rice; however, its pathogenic mechanism remains poorly understood. The current research is primarily focused on single-omics data, which is insufficient to capture the...
With innovations and advancements in analytical instruments and computer technology, omics studies based on statistical analysis, such as phytochemical omics, oilomics/lipidomics, proteomics, metabolomics, and glycomics, are increasingly popular in t...
Acute myocardial infarction (AMI) is a leading cause of mortality and morbidity worldwide. This work aims to investigate the translational potential of a multi-omics study (comprising metabolomics, lipidomics, glycomics, and metallomics) in revealing...
Rumen microbial protein synthesis (MPS) provides at least half of the amino acids for the synthesis of milk and meat protein in ruminants. As such, it is fundamental to global food protein security. Estimating microbial protein is central to diet for...
Rapeseed meal (RSM), a major agricultural byproduct, is limited in application due to high anti-nutritional factors like glucosinolates, while microbial fermentation can improve its nutritional and flavor profiles. This study combined physicochemical...
The glutathione shunt is one of the most important contributors to the cellular redox state, with implications across cancer, chronic diseases, diseases of ageing, and autoimmune diseases, including inflammatory bowel disease (IBD). Traditionally, th...
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...
Leishmaniases are a group of vector-borne diseases caused by infection with the protozoan parasites Leishmania spp. Some of them, such as Mediterranean visceral leishmaniasis, are zoonotic diseases transmitted from vertebrate to vertebrate by a hemat...
Over the years, research studies have shown there is a key connection between the microbial community in the gut, genes, and immune system. Understanding this association may help discover the cause of complex chronic idiopathic disorders such as inf...
Genome-scale metabolic models (GEMs) have found numerous applications in different domains, ranging from biotechnology to systems medicine. Herein, we overview the most popular algorithms for the automated reconstruction of context-specific GEMs usin...
Pathogenicity-associated genes are highly host-specific and contribute to host-specific virulence. We tailored the traditional Koch’s postulates with integrative omics by hypothesizing that the effector genes associated with host-pathogenicity...
The International Association for Intelligent Biology and Medicine (IAIBM) is a nonprofit organization that promotes intelligent biology and medical science. It hosts an annual International Conference on Intelligent Biology and Medicine (ICIBM), whi...
The use of microorganisms in industry has enabled the (over)production of various compounds (e.g., primary and secondary metabolites, proteins and enzymes) that are relevant for the production of antibiotics, food, beverages, cosmetics, chemicals and...
Cancer is a major health issue worldwide for many years and has been increasing significantly. Among the different types of cancer, breast cancer (BC) remains the leading cause of cancer-related deaths in women being a disease caused by a combination...
Chronic kidney disease is a global public health concern, representing a critical global public health challenge with increasing morbidity and mortality rates. The disease is a long-term condition characterized by the progressive loss of renal functi...
Plant endophytes can regulate host plant growth, improve stress resistance, and facilitate the biosynthesis of secondary metabolites, with great research value and application potential. However, traditional approaches for the isolation, cultivation...
Biomolecular and multi-omics approaches have transformed archaeology and heritage science, yet they are still widely conceptualized as ancillary techniques that refine narratives built on artifacts, architecture, and texts. This Perspective argues in...
Obesity in the 21st century has become a global epidemic owing to its heterogeneous aetiology and clinical presentation, as well as the development of associated comorbidities such as cardiovascular disease, type2 diabetes, hypertension, dyslipidaemi...
Conventional male reproductive toxicity testing relies on rodent bioassays and two-dimensional cultures, which are limited by species extrapolation, low throughput, and weak mechanistic resolution. Testicular and seminiferous-tubule organoids partial...
The number of researchers using multi-omics is growing. Though still expensive, every year it is cheaper to perform multi-omic studies, often exponentially so. In addition to its increasing accessibility, multi-omics reveals a view of systems biology...
Nanoparticles (NPs) in biomedical applications have benefits owing to their small size. However, their intricate and sensitive nature makes an evaluation of the adverse effects of NPs on health necessary and challenging. Since there are limitations t...
Investigators often face ultra-high dimensional multi-omics data, where identifying significant genes and omics within a gene is of interest. In such data, each gene forms a group consisting of its multiple omics. Moreover, some genes may also be hig...
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...
Lung adenocarcinoma (LUAD) is a common and very lethal cancer. Accurate staging is a prerequisite for its effective diagnosis and treatment. Therefore, improving the accuracy of the stage prediction of LUAD patients is of great clinical relevance. Pr...
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: 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...
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