112 citations · 135 across the 11 of their papers we have counts for
15 papers
Orthology and Near-Cographs in the Context of Phylogenetic Networks
Anna Lindeberg, Guillaume E. Scholz, Nicolas Wieseke +1
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 o…
Relative Timing Information and Orthology in Evolutionary Scenarios
David Schaller, Tom Hartmann, Manuel Lafond +3
Evolutionary scenarios describing the evolution of a family of genes within a collection of species comprise the mapping of the vertices of a gene tree to vertices and edges of…
Indirect Identification of Horizontal Gene Transfer
David Schaller, Manuel Lafond, Peter F. Stadler +2
Several implicit methods to infer Horizontal Gene Transfer (HGT) focus on pairs of genes that have diverged only after the divergence of the two species in which the genes reside.…
Complete Edge-Colored Permutation Graphs
Tom Hartmann, Max Bannach, Martin Middendorf +3
We introduce the concept of complete edge-colored permutation graphs as complete graphs that are the edge-disjoint union of "classical" permutation graphs. We show that a graph $G=…
Phylogenomics with Paralogs
Marc Hellmuth, Nicolas Wieseke, Marcus Lechner +3
Phylogenomics heavily relies on well-curated sequence data sets that consist, for each gene, exclusively of 1:1-orthologous. Paralogs are treated as a dangerous nuisance that has t…
Reconstructing Gene Trees From Fitch's Xenology Relation
Manuela Geiß, John Anders, Peter F. Stadler +2
Two genes are xenologs in the sense of Fitch if they are separated by at least one horizontal gene transfer event. Horizonal gene transfer is asymmetric in the sense that the trans…
Partial Homology Relations - Satisfiability in terms of Di-Cographs
Nikolai Nøjgaard, Nadia El-Mabrouk, Daniel Merkle +2
Directed cographs (di-cographs) play a crucial role in the reconstruction of evolutionary histories of genes based on homology relations which are binary relations between genes. A…
From event labeled gene trees to species trees
Maribel Hernandez-Rosales, Marc Hellmuth, Nicolas Wieseke +3
Background: Tree reconciliation problems have long been studied in phylogenetics. A particular variant of the reconciliation problem for a gene tree T and a species tree S assumes…
Forbidden Time Travel: Characterization of Time-Consistent Tree Reconciliation Maps
Nikolai Nøjgaard, Manuela Geiß, Peter F. Stadler +3
In the absence of horizontal gene transfer it is possible to reconstruct the history of gene families from empirically determined orthology relations, which are equivalent to event…
The Mathematics of Xenology: Di-cographs, Symbolic Ultrametrics, 2-structures and Tree-representable Systems of Binary Relations
Marc Hellmuth, Peter F. Stadler, Nicolas Wieseke
The concepts of orthology, paralogy, and xenology play a key role in molecular evolution. Orthology and paralogy distinguish whether a pair of genes originated by speciation or dup…
Construction of Gene and Species Trees from Sequence Data incl. Orthologs, Paralogs, and Xenologs
Marc Hellmuth, Nicolas Wieseke
Phylogenetic reconstruction aims at finding plausible hypotheses of the evolutionary history of genes or species based on genomic sequence information. The distinction of orthologo…
Techniques for the Cograph Editing Problem: Module Merge is equivalent to Editing P4s
Marc Hellmuth, Adrian Fritz, Nicolas Wieseke +1
Cographs are graphs in which no four vertices induce a simple connected path . Cograph editing is to find for a given graph a set of at most edge additions and…
On Tree Representations of Relations and Graphs: Symbolic Ultrametrics and Cograph Edge Decompositions
Marc Hellmuth, Nicolas Wieseke
Tree representations of (sets of) symmetric binary relations, or equivalently edge-colored undirected graphs, are of central interest, e.g.\ in phylogenomics. In this context symbo…
On Symbolic Ultrametrics, Cotree Representations, and Cograph Edge Decompositions and Partitions
Marc Hellmuth, Nicolas Wieseke
Symbolic ultrametrics define edge-colored complete graphs K_n and yield a simple tree representation of K_n. We discuss, under which conditions this idea can be generalized to find…
Unifying Parsimonious Tree Reconciliation
Nicolas Wieseke, Matthias Bernt, Martin Middendorf
Evolution is a process that is influenced by various environmental factors, e.g. the interactions between different species, genes, and biogeographical properties. Hence, it is int…