相关论文: Complete Characterization of Incorrect Orthology A…
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…
Reciprocal best matches play an important role in numerous applications in computational biology, in particular as the basis of many widely used tools for orthology assessment. Nevertheless, very little is known about their mathematical…
Best match graphs (BMG) are a key intermediate in graph-based orthology detection and contain a large amount of information on the gene tree. We provide a near-cubic algorithm to determine whether a BMG is binary-explainable, i.e., whether…
Orthology and paralogy relations are often inferred by methods based on gene similarity, which usually yield a graph depicting the relationships between gene pairs. Such relation graphs are known to frequently contain errors, as they cannot…
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…
Best match graphs (BMGs) are a class of colored digraphs that naturally appear in mathematical phylogenetics and can be approximated with the help of similarity measures between gene sequences, albeit not without errors. The corresponding…
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…
Context-dependent identification of orthologs customarily relies on conserved gene order or whole-genome sequence alignment. It is shown here that short-range context--as short as single maximal matches--also provides an effective means to…
Best match graphs (BMGs) are vertex-colored directed graphs that were introduced to model the relationships of genes (vertices) from different species (colors) given an underlying evolutionary tree that is assumed to be unknown. In…
Best match graphs (BMGs) are vertex-colored digraphs that naturally arise in mathematical phylogenetics to formalize the notion of evolutionary closest genes w.r.t. an a priori unknown phylogenetic tree. BMGs are explained by unique least…
Reciprocal best match graphs (RBMGs) are vertex colored graphs whose vertices represent genes and the colors the species where the genes reside. Edges identify pairs of genes that are most closely related with respect to an underlying…
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…
Horizontal gene transfer is an important contributor to evolution. According to Walter M.\ Fitch, two genes are xenologs if they are separated by at least one HGT. More formally, the directed Fitch graph has a set of genes is its vertices,…
Past studies on the local limit of maximal weight matchings in edge-weighted large random graphs rely fundamentally on the assumption that the weights are atomless, which ensures that the maximal weight matching is unique. This excludes de…
2-colored best match graphs (2-BMGs) form a subclass of sink-free bi-transitive graphs that appears in phylogenetic combinatorics. There, 2-BMGs describe evolutionarily most closely related genes between a pair of species. They are…
Random graph matching refers to recovering the underlying vertex correspondence between two random graphs with correlated edges; a prominent example is when the two random graphs are given by Erd\H{o}s-R\'{e}nyi graphs $G(n,\frac{d}{n})$.…
The fractional perfect b-matching polytope of an undirected graph G is the polytope of all assignments of nonnegative real numbers to the edges of G such that the sum of the numbers over all edges incident to any vertex v is a prescribed…
Horizontal gene transfer events partition a gene tree $T$ and thus, its leaf set into subsets of genes whose evolutionary history is described by speciation and duplication events alone. Indirect phylogenetic methods can be used to infer…
Graph matching, also known as network alignment, refers to finding a bijection between the vertex sets of two given graphs so as to maximally align their edges. This fundamental computational problem arises frequently in multiple fields…
Bipartite best match graphs (BMG) and their generalizations arise in mathematical phylogenetics as combinatorial models describing evolutionary relationships among related genes in a pair of species. In this work, we characterize the class…