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09/19/2023
On the Realisability of Chemical Pathways
The exploration of pathways and alternative pathways that have a specifi...
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09/12/2023
Chemically inspired Erdős-Rényi oriented hypergraphs
High-order structures have been recognised as suitable models for system...
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06/12/2023
Fitch Graph Completion
Horizontal gene transfer is an important contributor to evolution. Accor...
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04/24/2023
The Theory of Gene Family Histories
Most genes are part of larger families of evolutionary related genes. Th...
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03/28/2023
Optimisation via encodings: a renormalisation group perspective
The traditional way of tackling discrete optimization problems is by usi...
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12/05/2022
Relative Timing Information and Orthology in Evolutionary Scenarios
Evolutionary scenarios describing the evolution of a family of genes wit...
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04/28/2022
Clustering Systems of Phylogenetic Networks
Rooted acyclic graphs appear naturally when the phylogenetic relationshi...
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12/11/2021
The Past as a Stochastic Process
Historical processes manifest remarkable diversity. Nevertheless, schola...
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12/01/2021
Orientation of Fitch Graphs and Detection of Horizontal Gene Transfer in Gene Trees
Horizontal gene transfer events partition a gene tree T and thus, its le...
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10/18/2021
Planar Median Graphs and Cubesquare-Graphs
Median graphs are connected graphs in which for all three vertices there...
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07/07/2021
Defining Autocatalysis in Chemical Reaction Networks
Autocatalysis is a deceptively simple concept, referring to the situatio...
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07/05/2021
Combining Orthology and Xenology Data in a Common Phylogenetic Tree
A rooted tree T with vertex labels t(v) and set-valued edge labels λ(e) ...
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06/30/2021
A Simple Linear-Time Algorithm for the Common Refinement of Rooted Phylogenetic Trees on a Common Leaf Set
Background. The supertree problem, i.e., the task of finding a common re...
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04/29/2021
Compatibility of Partitions, Hierarchies, and Split Systems
The question whether a partition 𝒫 and a hierarchy ℋ or a tree-like spli...
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03/11/2021
From Modular Decomposition Trees to Rooted Median Graphs
The modular decomposition of a symmetric map δ X× X →Υ (or, equivalently...
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03/11/2021
Arc-Completion of 2-Colored Best Match Graphs to Binary-Explainable Best Match Graphs
Best match graphs (BMGs) are vertex-colored digraphs that naturally aris...
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03/10/2021
Heuristic Algorithms for Best Match Graph Editing
Best match graphs (BMGs) are a class of colored digraphs that naturally ...
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01/18/2021
Least resolved trees for two-colored best match graphs
2-colored best match graphs (2-BMGs) form a subclass of sink-free bi-tra...
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12/16/2020
Indirect Identification of Horizontal Gene Transfer
Several implicit methods to infer Horizontal Gene Transfer (HGT) focus o...
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11/01/2020
Best Match Graphs with Binary Trees
Best match graphs (BMG) are a key intermediate in graph-based orthology ...
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06/30/2020
Complexity of Modification Problems for Best Match Graphs
Best match graphs (BMGs) are vertex-colored directed graphs that were in...
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06/03/2020
Complete Characterization of Incorrect Orthology Assignments in Best Match Graphs
Genome-scale orthology assignments are usually based on reciprocal best ...
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04/15/2020
Complete Edge-Colored Permutation Graphs
We introduce the concept of complete edge-colored permutation graphs as ...
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04/14/2020
Hierarchical and Modularly-Minimal Vertex Colorings
Cographs are exactly the hereditarily well-colored graphs, i.e., the gra...
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01/16/2020
Generalized Fitch Graphs III: Symmetrized Fitch maps and Sets of Symmetric Binary Relations that are explained by Unrooted Edge-labeled Trees
Binary relations derived from labeled rooted trees play an import role i...
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11/18/2019
Generalized Fitch Graphs II: Sets of Binary Relations that are explained by Edge-labeled Trees
Fitch graphs G=(X,E) are digraphs that are explained by {∅, 1}-edge-labe...
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11/18/2019
Generalized Fitch Relations II: Sets of Binary Relations that are explained by Edge-labeled Trees
Fitch graphs G=(X,E) are digraphs that are explained by {∅, 1}-edge-labe...
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07/20/2019
Complexity of Modification Problems for Reciprocal Best Match Graphs
Reciprocal best match graphs (RBMGs) are vertex colored graphs whose ver...
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04/26/2019
Best Match Graphs and Reconciliation of Gene Trees with Species Trees
A wide variety of problems in computational biology, most notably the as...
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11/19/2018
Forman-Ricci Curvature for Hypergraphs
In contrast to graph-based models for complex networks, hypergraphs are ...
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10/09/2018
Alignments as Compositional Structures
Alignments, i.e., position-wise comparisons of two or more strings or or...
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12/25/2017
Topological Representation of the Transit Sets of k-Point Crossover Operators
k-point crossover operators and their recombination sets are studied fro...
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12/18/2017
Phylogenomics with Paralogs
Phylogenomics heavily relies on well-curated sequence data sets that con...
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12/07/2017
Chemical Transformation Motifs - Modelling Pathways as Integer Hyperflows
We present an elaborate framework for formally modelling pathways in che...
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12/05/2017
A Short Note on Undirected Fitch Graphs
The symmetric version of Fitch's xenology relation coincides with class ...
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11/06/2017