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Found 14 papers, 1 papers with code
On the Realisability of Chemical Pathways
The exploration of pathways and alternative pathways that have a specific function is of interest in numerous chemical contexts.
Unstable Cores are the source of instability in chemical reaction networks
In biochemical networks, complex dynamical features such as superlinear growth and oscillations are classically considered a consequence of autocatalysis.
The Theory of Gene Family Histories
Most genes are part of larger families of evolutionary related genes.
Optimisation via encodings: a renormalisation group perspective
Difficult, in particular NP-complete, optimization problems are traditionally solved approximately using search heuristics.
Relative Timing Information and Orthology in Evolutionary Scenarios
The relative timing information of gene and species divergences is captured by three colored graphs that have the extant genes as vertices and the species in which the genes are found as vertex colors: the equal-divergence-time (EDT) graph, the later-divergence-time (LDT) graph and the prior-divergence-time (PDT) graph, which together form an edge partition of the complete graph.
Clustering Systems of Phylogenetic Networks
The main results are correspondences of classes of networks and clustering system of the following form: If $N$ is a network of type $\mathbb{X}$, then $\mathcal{C}_N$ satisfies $\mathbb{Y}$, and conversely if $\mathscr{C}$ is a clustering system satisfying $\mathbb{Y}$ then there is network $N$ of type $\mathbb{X}$ such that $\mathscr{C}\subseteq\mathscr{C}_N$. This, in turn, allows us to investigate the mutual dependencies between the distinct types of networks in much detail.
What makes a reaction network "chemical"?
In particular, these realizations can be chosen such that any two species have distinct sum formulas, unless $\mathbf{S}$ implies that they are "obligatory isomers".
Defining Autocatalysis in Chemical Reaction Networks
Given a chemical reaction network, however, it is not at all straightforward to identify species that are autocatalytic in the sense that there is a sub-network that takes $X$ as input and produces more than one copy of $X$ as output.
Arc-Completion of 2-Colored Best Match Graphs to Binary-Explainable Best Match Graphs
For the special case of two-colored BMGs, this leads to a characterization of the least resolved trees (LRTs) of binary-explainable trees and a simple, polynomial-time algorithm for the minimum cardinality completion of the arc set of a BMG to reach a BMG that can be explained by a binary tree.
Data Structures and Algorithms Discrete Mathematics Combinatorics Populations and Evolution
From Modular Decomposition Trees to Rooted Median Graphs
The modular decomposition of a symmetric map $\delta\colon X\times X \to \Upsilon$ (or, equivalently, a set of symmetric binary relations, a 2-structure, or an edge-colored undirected graph) is a natural construction to capture key features of $\delta$ in labeled trees.
Combinatorics Discrete Mathematics
Least resolved trees for two-colored best match graphs
Introducing the concept of support vertices we derive an $O(|V|+|E|\log^2|V|)$-time algorithm to recognize 2-BMGs and to construct its LRT.
Indirect Identification of Horizontal Gene Transfer
An edge in an LDT graph implies that the two corresponding genes are separated by at least one HGT event.
