Protein function prediction plays a crucial role in uncovering the molecular mechanisms underlying life processes in the post-genomic era. However, with the widespread adoption of high-throughput sequencing technologies, the pace of protein function...
Aedes aegypti is a significant vector for many tropical and subtropical flavivirus diseases. Only the female mosquito transmits pathogens, while the male plays a vital role in mating and species continuity. This study explored the total proteomes of...
Protein Language Models (PLMs) are shown to be capable of learning sequence representations useful for various prediction tasks, from subcellular localization, evolutionary relationships, family membership, and more. They have yet to be demonstrated...
The increasing number of OMICs studies demands bioinformatic tools that aid in the analysis of large sets of genes or proteins to understand their roles in the cell and establish functional networks and pathways. In the last decade, over-representati...
Although the integration of sensor-based information into analysis and decision making has been a research topic for many years, semantic interoperability has not yet been reached. The advent of user-generated content for the geospatial domain, Volun...
Gene function prediction is a complicated and challenging hierarchical multi-label classification (HMC) task, in which genes may have many functions at the same time and these functions are organized in a hierarchy. This paper proposed a novel HMC al...
Sustainable manufacturing practices are crucial in job shop scheduling (JSS) to enhance the resilience of production systems against resource shortages and regulatory changes, contributing to long-term operational stability and environmental care. JS...
Its purpose is to prove information law by logic, mathematics and translation. The method involves: the generalized bilingual logic established on both Aristotle’s formal logic and Frege’s mathematical logic, the linkage function established on both...
The concept of an operator is used in a variety of practical and theoretical areas. Operators, as both conceptual and physical entities, are found throughout the world as subsystems in nature, the human mind, and the manmade world. Operators, and wha...
Despite tremendous efforts in genomics, transcriptomics, and proteomics communities, there is still no comprehensive data about the exact number of protein-coding genes, translated proteoforms, and their function. In addition, by now, we lack functio...
The current rate at which new DNA and protein sequences are being generated is too fast to experimentally discover the functions of those sequences, emphasizing the need for accurate Automatic Function Prediction (AFP) methods. AFP has been an active...
High-throughput sequencing generally results in a list of genes. Which functional groups of genes among the DEGs are meaningful underlying factors to the differential biological/biomedical conditions under investigation? The process to find answers t...
The clinical characteristics of clear cell carcinoma (CCC) and endometrioid carcinoma EC) are concomitant with endometriosis (ES), which leads to the postulation of malignant transformation of ES to endometriosis-associated ovarian carcinoma (EAOC)....
Accurate protein function prediction (PFP) is essential for understanding biological systems. However, structure-based graph neural networks often rely on fixed-distance contact maps, which may inadequately capture continuous, multi-scale spatial top...
Conformational protein properties are coupled to protein functionality and could provide a useful parameter for functional annotation of differentially expressed genes in transcriptome studies. The aim was to determine whether predicted intrinsic pro...
Genome-wide, loss-of-function screening can be used to identify novel vulnerabilities upon which specific tumor cells depend for survival. Functional Signature Ontology (FUSION) is a gene expression-based high-throughput screening (GE-HTS) method tha...
Ovarian clear cell carcinoma (OCCC) is the second most common epithelial ovarian carcinoma (EOC). It is refractory to chemotherapy with a worse prognosis after the preliminary optimal debulking operation, such that the treatment of OCCC remains a cha...
Transcription factors are an integral component of the cellular machinery responsible for regulating many biological processes, and they recognize distinct DNA sequence patterns as well as internal/external signals to mediate target gene expression....
Chemicals found in nature have evolved over geological time scales to productively interact with biological molecules, and thus represent an effective resource for pharmaceutical development. Marine-derived bacteria are rich sources of chemically div...
Background: Fish skin mucus contains proteins involved in diverse biological pathways, representing a valuable non-invasive diagnostic of fish health. Methods: Skin mucus from three male and three female barramundi was analysed using liquid chromatog...
In this paper, we present a method that facilitates Internet of Things (IoT) for building a product passport and data exchange enabling the next stage of the circular economy. SmartTags based on printed sensors (i.e., using functional ink) and a modi...
Ion channels and transporters are diverse membrane proteins that regulate ion flux across biological membranes and play essential roles in cellular signaling, homeostasis, and physiological processes. Accurate classification and functional annotation...
Tropomyosin (TPM) is a contractile protein responsible for muscle contraction through its actin-binding activity. The complete sequence of TPM in Haliotis discus hannai (Hdh-TPM) was 2160 bp, encoding 284 amino acids, and contained a TPM signature mo...
Previous studies report that the asymmetric response, observed along the main poplar woody bent root axis, was strongly related to both the type of mechanical forces (compression or tension) and the intensity of force displacement. Despite a large nu...
Background: The Zika virus (ZIKV) is an arbovirus linked to “Congenital Zika Syndrome” and a range of neurodevelopmental disorders (NDDs), with microcephaly as the most severe manifestation. Milder NDDs, such as autism spectrum disorders...
The ontological categorization of the cellular elements of the brain was proposed over a century ago by Santiago Ramón y Cajal (neurons, astroglia) and Pío del Río-Hortega (oligodendroglia, microglia). It combines histochemical o...
Serous carcinoma (SC) is the most common and lethal subtype of epithelial ovarian carcinoma; immunotherapy is a potential treatment for SC, however, the global immunological functions of SC as well as their change during the progression of SC have no...
Phase-separation proteins (PSPs) are a class of proteins that play a role in the process of liquid–liquid phase separation, which is a mechanism that mediates the formation of membranelle compartments in cells. Identifying phase separation prot...
Ontologies in artificial intelligence systems are an effective way to represent and integrate knowledge and data. The property of such structures is that any subject area is accurately described in formal language. There is a problem in the research...
Elucidating the biological and biochemical roles of proteins, and subsequently determining their interacting partners, can be difficult and time consuming using in vitro and/or in vivo methods, and consequently the majority of newly sequenced protein...
GIGANTEA (GI) is a gene involved in multiple biological functions, which have been analysed and are partially conserved in a series of mono- and dicotyledonous plant species. The identified biological functions include control over the circadian rhyt...
Diabetic kidney disease (DKD) is the leading cause of end-stage renal disease worldwide. This study’s goal was to identify the signaling drivers and pathways that modulate glomerular endothelial dysfunction in DKD via artificial intelligence-en...
The saprophytic soil fungus Aspergillus flavus infects crops and produces aflatoxin. Pichia anomala, which is a biocontrol yeast and produces the major volatile 2-phenylethanol (2-PE), is able to reduce growth of A. flavus and aflatoxin production wh...
Biological interpretability is a key requirement for the output of microarray data analysis pipelines. The most used pipeline first identifies a gene signature from the acquired measurements and then uses gene enrichment analysis as a tool for functi...
Ovarian hyperstimulation syndrome (OHSS) is often a complication of polycystic ovarian syndrome (PCOS), the most frequent disorder of the endocrine system, which affects women in their reproductive years. The etiology of OHSS is multifactorial, thoug...
While wheat (Triticum aestivum L.) is a widely grown and enjoyed crop, the diverse and complex global situation and climate are exacerbating the instability of its supply. In particular, pre-harvest sprouting (PHS) is one of the major abiotic stresse...
Long non-coding RNAs (lncRNAs) are emerging as key regulators in many biological processes. The dysregulation of lncRNA expression has been associated with many diseases, including cancer. Mounting evidence suggests lncRNAs to be involved in cancer i...
In this paper, we introduce a novel method to formally represent elements of control engineering knowledge in a suitable data structure. To this end, we first briefly review existing representation methods (RDF, OWL, Wikidata, ORKG). Based on this, w...
This paper presents and discusses Simon Evnine’s hylomorphic account of fictional characters and proposes some amendments to it with the aim of explaining the functioning of fictional characters. The paper does so by relying on a case study, vi...
Biomimetics aims to learn from living systems to develop innovative technical artefacts. As it transcends disciplinary boundaries and needs to integrate both biological and technological knowledge, a domain ontology for biomimetics would be highly de...
Lipidomics has emerged as a transformative discipline in biomedical research, providing high-resolution insights into metabolic signaling and disease pathophysiology. The R programming language provides a widely adopted framework for extensible analy...
Membrane transporters play a crucial role in any cell. Identifying the substrates they translocate across membranes is important for many fields of research, such as metabolomics, pharmacology, and biotechnology. In this study, we leverage recent adv...
Genome sequencing of a diverse array of arthropod genomes is already underway, and these genomes will be used to study human health, agriculture, biodiversity, and ecology. These new genomes are intended to serve as community resources and provide th...
In recent years, perinatal stem cells, such as human amniotic epithelial cells (hAECs), have attracted increasing interest as a novel tool of stem cell-based high-throughput drug screening. In the present study, we investigated the bioactivities of s...
Catalysis research is complex and interdisciplinary, involving diverse physical effects and challenging data practices. Research data often captures only selected aspects, such as specific reactants and products, limiting its utility for machine lear...
Web systems evolve by adding new functionalities or modifying them to meet users’ requirements. Web systems require retesting to ensure that existing functionalities are according to users’ expectations. Retesting a web system is challenging due to h...
The intelligent management of built cultural heritage, including heritage buildings, requires common semantics in the form of standardized ontologies to achieve semantic interoperability. Foundational ontologies should be reused when building new ont...
This paper presents OntologyFixer, a web-based tool that supports a methodology to build, assess, and improve the quality of ontology web language (OWL) ontologies. Using our software, knowledge engineers are able to fix low-quality OWL ontologies (s...
We present a three–dimensional field ontology for Bohmian mechanics in which the single-particle wave functions defined in ordinary physical space are taken as ontological elements alongside particle positions. In this view, each particle is as...
This study investigates the design, development, and practical exploitation of an educational ontology for classical guitar instruction, within a semantically driven and application-oriented framework. The proposed approach aims to bridge the gap bet...
of 43