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The Gene Ontology (GO) provides biologists with a controlled terminology that describes how genes are associated with functions and how functional terms are related to each other. These term-term relationships encode how scientists conceive…

Gene Ontology (GO) is the most important resource for gene function annotation. It provides a way to unify biological knowledge across different species via a dynamic and controlled vocabulary. GO is now widely represented in the Semantic…

The Gene Ontology (GO) project is the largest resource for cataloguing gene function. The combination of solid conceptual underpinnings and a practical set of features have made the GO a widely adopted resource in the research community and…

The Gene Ontology (GO) is a major bioinformatics ontology that provides structured controlled vocabularies to classify gene and proteins function and role. The GO and its annotations to gene products are now an integral part of functional…

The Gene Ontology (GO) is a formidable resource but there are several considerations about it that are essential to understand the data and interpret it correctly. The GO is sufficiently simple that it can be used without deep understanding…

The last decade has seen the advent and consolidation of ontology based tools for the identification and biological interpretation of classes of genes, such as the Gene Ontology. The information accumulated time-by-time and included in the…

One of the basic questions of phylogenomics is how gene function evolves, whether among species or inside gene families. In this chapter, we provide a brief overview of the problems associated with defining gene function in a manner which…

Increasingly used high throughput experimental techniques, like DNA or protein microarrays give as a result groups of interesting, e.g. differentially regulated genes which require further biological interpretation. With the systematic…

Gene Ontology (GO) is the primary gene function knowledge base that enables computational tasks in biomedicine. The basic element of GO is a term, which includes a set of genes with the same function. Existing research efforts of GO mainly…

The study of human genes and diseases is very rewarding and can lead to improvements in healthcare, disease diagnostics and drug discovery. In this paper, we further our previous study on gene disease relationship specifically with the…

The increasing availability of high throughput data arising from gene expression studies leads to the necessity of methods for summarizing the available information. As annotation quality improves it is becoming common to rely on the Gene…

Evolution has fascinated quantitative and physical scientists for decades: how can the random process of mutation, recombination, and duplication of genetic information generate the diversity of life? What determines the rate of evolution?…

Cell growth and gene expression, essential elements of all living systems, have long been the focus of biophysical interrogation. Advances in single-cell methods have invigorated theoretical studies into these processes. However, until…

Gene expression is a central process to any form of life. It involves multiple temporal and functional scales that extend from specific protein-DNA interactions to the coordinated regulation of multiple genes in response to intracellular…

Query optimization has been studied using machine learning, reinforcement learning, and, more recently, graph-based convolutional networks. Ontology, as a structured, information-rich knowledge representation, can provide context,…

Ontologies are built on systems that conceptually evolve over time. In addition, techniques and languages for building ontologies evolve too. This has led to numerous studies in the field of ontology versioning and ontology evolution. This…

We applied machine learning to predict whether a gene is involved in axon regeneration. We extracted 31 features from different databases and trained five machine learning models. Our optimal model, a Random Forest Classifier with 50…

The SemanticWeb emerged as an extension to the traditional Web, towards adding meaning to a distributed Web of structured and linked data. At its core, the concept of ontology provides the means to semantically describe and structure…

Gene expression is a biochemical process, where stochastic binding and un-binding events naturally generate fluctuations and cell-to-cell variability in gene dynamics. These fluctuations typically have destructive consequences for proper…

Gene finding is the task of identifying the locations of coding sequences within the vast amount of genetic code contained in the genome. With an ever increasing quantity of raw genome sequences, gene finding is an important avenue towards…