相关论文: Orthologs from maxmer sequence context

Many of the commonly used methods for orthology detection start from mutually most similar pairs of genes (reciprocal best hits) as an approximation for evolutionary most closely related pairs of genes (reciprocal best matches). This…

Genome-scale orthology assignments are usually based on reciprocal best matches. In the absence of horizontal gene transfer (HGT), every pair of orthologs forms a reciprocal best match. Incorrect orthology assignments therefore are always…

A wide variety of problems in computational biology, most notably the assessment of orthology, are solved with the help of reciprocal best matches. Using an evolutionary definition of best matches that captures the intuition behind the…

Orthology is a central concept in evolutionary and comparative genomics, used to relate corresponding genes in different species. In particular, orthologs are needed to infer species trees. In this chapter, we introduce the fundamental…

Ontology matching is a core task when creating interoperable and linked open datasets. In this paper, we explore a novel structure-based mapping approach which is based on knowledge graph embeddings: The ontologies to be matched are…

Orthologous genes, which arise through speciation, play a key role in comparative genomics and functional inference. In particular, graph-based methods allow for the inference of orthology estimates without prior knowledge of the underlying…

Reconstructing the evolutionary past of a family of genes is an important aspect of many genomic studies. To help with this, simple operations on a set of sequences called orthology relations may be employed. In addition to being…

Ontology alignment (a.k.a ontology matching (OM)) plays a critical role in knowledge integration. Owing to the success of machine learning in many domains, it has been applied in OM. However, the existing methods, which often adopt ad-hoc…

Large Language Models (LLMs) are increasingly being integrated into various components of Ontology Matching pipelines. This paper investigates the capability of LLMs to perform ontology matching directly on ontology modules and generate the…

Constructing comprehensive knowledge graphs requires the use of multiple ontologies in order to fully contextualize data into a domain. Ontology matching finds equivalences between concepts interconnecting ontologies and creating a cohesive…

Ortholog detection (OD) is a critical step for comparative genomic analysis of protein-coding sequences. In this paper, we begin with a comprehensive comparison of four popular, methodologically diverse OD methods: MultiParanoid, Blat,…

Inconsistency handling is an important issue in knowledge management. Especially in ontology engineering, logical inconsistencies may occur during ontology construction. A natural way to reason with an inconsistent ontology is to utilize…

Ontology matching is the process of automatically determining the semantic equivalences between the concepts of two ontologies. Most ontology matching algorithms are based on two types of strategies: terminology-based strategies, which…

Most genes are part of larger families of evolutionary related genes. The history of gene families typically involves duplications and losses of genes as well as horizontal transfers into other organisms. The reconstruction of detailed gene…

The biological literature is rich with sentences that describe causal relations. Methods that automatically extract such sentences can help biologists to synthesize the literature and even discover latent relations that had not been…

Phylogenetic reconstruction aims at finding plausible hypotheses of the evolutionary history of genes or species based on genomic sequence information. The distinction of orthologous genes (genes that having a common ancestry and diverged…

Biomedical ontologies, which comprehensively define concepts and relations for biomedical entities, are crucial for structuring and formalizing domain-specific information representations. Biomedical code mapping identifies similarity or…

Ontology alignment process is overwhelmingly cited in Knowledge Engineering as a key mechanism aimed at bypassing heterogeneity and reconciling various data sources, represented by ontologies, i.e., the the Semantic Web cornerstone. In such…

THIS IS A CORRECTED VERSION INCLUDING AN APPENDED CORRIGENDUM. Best match graphs arise naturally as the first processing intermediate in algorithms for orthology detection. Let $T$ be a phylogenetic (gene) tree $T$ and $\sigma$ an…

We consider a novel approach of measuring the homology of DNA sequences based of the variety of optimal alignments in the longest common subsequence sense. The proposed approach is compared with BLAST in measuring the homology of four…