相关论文: Finding New Order in Biological Functions from the…
The genome sequence contains the blueprint for governing cellular processes. While the availability of genomes has vastly increased over the last decades, experimental annotation of the various functional, non-coding and regulatory elements…
When designing new molecules with particular properties, it is not only important what to make but crucially how to make it. These instructions form a synthesis directed acyclic graph (DAG), describing how a large vocabulary of simple…
Proteins are essential macromolecules of life and thus understanding their function is of great importance. The number of functionally unclassified proteins is large even for simple and well studied organisms such as baker's yeast. Methods…
We present DINGO (Data INtegration for Grants Ontology), an ontology that provides a machine readable extensible framework to model data for semantically-enabled applications relative to projects, funding, actors, and, notably, funding…
Molecular biologists frequently interpret gene lists derived from high-throughput experiments and computational analysis. This is typically done as a statistical enrichment analysis that measures the over- or under-representation of…
Biological processes underlying the basic functions of a cell involve complex interactions between genes. From a technical point of view, these interactions can be represented through a graph where genes and their connections are,…
Predicting gene functions is a challenge for biologists in the post genomic era. Interactions among genes and their products compose networks that can be used to infer gene functions. Most previous studies adopt a linkage assumption, i.e.,…
Ontology matching (OM) plays an essential role in enabling semantic interoperability and integration across heterogeneous knowledge sources, particularly in the biomedical domain which contains numerous complex concepts related to diseases…
We introduced a methodology to efficiently exploit natural-language expressed biomedical knowledge for repurposing existing drugs towards diseases for which they were not initially intended. Leveraging on developments in Computational…
Unraveling the complexities of Gene Regulatory Networks (GRNs) is crucial for understanding cellular processes and disease mechanisms. Traditional computational methods often struggle with the dynamic nature of these networks. This study…
Graphs are a powerful tool for representing and analyzing unstructured, non-Euclidean data ubiquitous in the healthcare domain. Two prominent examples are molecule property prediction and brain connectome analysis. Importantly, recent works…
Motivation: Ontologies are widely used in biology for data annotation, integration, and analysis. In addition to formally structured axioms, ontologies contain meta-data in the form of annotation axioms which provide valuable pieces of…
We argue that ontology-structured knowledge graphs can play a crucial role in generating predictions about future events. By leveraging the semantic framework provided by Basic Formal Ontology (BFO) and Common Core Ontologies (CCO), we…
A genetic algorithm (GA) is a search method that optimises a population of solutions by simulating natural evolution. Good solutions reproduce together to create better candidates. The standard GA assumes that any two solutions can mate.…
Evolution consists of distinct stages: cosmological, biological, linguistic. Since biology verges on natural sciences and linguistics, we expect that it shares structures and features from both forms of knowledge. Indeed, in DNA we…
At the heart of many contemporary theories of life is the concept of biological self-organisation: organisms have to continuously produce and maintain the conditions of their own existence in order to stay alive. The way in which these…
A biological experiment is the most reliable way of assigning function to a protein. However, in the era of high-throughput sequencing, scientists are unable to carry out experiments to determine the function of every single gene product.…
The human organism is an integrated network where complex physiologic systems, each with its own regulatory mechanisms, continuously interact, and where failure of one system can trigger a breakdown of the entire network. Identifying and…
Ontologies have been known for their semantic representation of knowledge. ontologies cannot automatically evolve to reflect updates that occur in respective domains. To address this limitation, researchers have called for automatic…
In several domains such as linguistics, molecular biology or social sciences, holistic effects are hardly well-defined by modeling with single units, but more and more studies tend to understand macro structures with the help of meaningful…