5 citations · 9 across the 10 of their papers we have counts for
14 papers
Characterizations of undirected 2-quasi best match graphs
Annachiara Korchmaros, Guillaume E. Scholz, Peter F. Stadler
Bipartite best match graphs (BMG) and their generalizations arise in mathematical phylogenetics as combinatorial models describing evolutionary relationships among related genes in…
Computing phylogenetic invariants for time-reversible models: from TN93 to its submodels
Marta Casanellas, Jennifer Garbett, Roser Homs +2
Phylogenetic invariants are equations that vanish on algebraic varieties associated with Markov processes that model molecular substitutions on phylogenetic trees. For practical ap…
Automorphisms and quotients of 2-colored quasi best match graphs
Annachiara Korchmaros
2-colored quasi best match graphs (2-qBMGs) are directed graphs that arose in phylogenetics. Investigations of 2-qBMGs have mostly focused on computational issues. However, 2-qBMGs…
Forbidden configurations and dominating bicliques in undirected 2-quasi best match graphs
Annachiara Korchmaros, Peter F. Stadler
2-quasi best match graphs (2-qBMGs) are directed graphs that capture a notion of close relatedness in phylogenetics. Here, we investigate the undirected underlying graph of a 2-qBM…
Forbidden paths and cycles in the undirected underlying graph of a 2-quasi best match graph
Annachiara Korchmaros
The undirected underlying graph of a 2-quasi best match graph (2-qBMG) is proven not to contain any induced graph isomorphic to or . This new feature allows for the inve…
Configurations in the Euclidean space related to the 3D genome reconstruction problem from partially phased data
Annachiara Korchmaros
A motivation for studying the following problems comes from applications to Biology; see \cite{cifuentes20233d}. In the -dimensional Euclidean space , fix six pairwi…
3D genome reconstruction from partially phased Hi-C data
Diego Cifuentes, Jan Draisma, Oskar Henriksson +2
The 3-dimensional (3D) structure of the genome is of significant importance for many cellular processes. In this paper, we study the problem of reconstructing the 3D structure of c…
Quasi-Best Match Graphs
Annachiara Korchmaros, David Schaller, Marc Hellmuth +1
Quasi-best match graphs (qBMGs) are a hereditary class of directed, properly vertex-colored graphs. They arise naturally in mathematical phylogenetics as a generalization of best m…
The Structure of 2-Colored Best Match Graphs
Annachiara Korchmaros
Recent investigations in computational biology have focused on a family of 2-colored digraphs, called 2-colored best match graphs, which naturally arise from rooted phylogenetic tr…
Circles and Paths in 2-Colored Best Match Graphs
Annachiara Korchmaros
Recent investigations in computational biology focus on a family of 2-colored digraphs, called 2-colored best match graphs, which naturally arise from rooted phylogenetic trees. Ac…
Automorphism groups of Cayley graphs generated by block transpositions and regular Cayley maps
Annachiara Korchmaros, István Kovács
This paper deals with the Cayley graph where the generating set consists of all block transpositions. A motivation for the study of these partic…
Combinatorial properties of block transpositions on Symmetric groups
Annachiara Korchmaros
A major problem in the study of combinatorial aspects of permutation groups is to determine the distances in the symmetric group $\Sym_n$ with respect to a generator set. One well-…
Cayley graph on symmetric groups with generating block transposition sets
Annachiara Korchmaros
This paper deals with the Cayley graph $\Cay,$ where the generating set consists of all block transpositions. A motivation for the study of these particular Cayley graphs comes fro…
Upper bound on the block transposition diameter of the symmetric group
Annachiara Korchmaros
Given a generator set of the symmetric group , every permutation is a word (product of elements) of . A positive integer is associat…