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Complement Submodular Information Measures for Balanced and Robust Data Selection A Proof of a Conjecture on Positive and Negative Square Energies of Unicyclic Graphs Laplacian Spectrum of the Weakly Zero-Divisor Graph of a Finite Commutative Ring An identity for second Eulerian numbers via lattice-point counting $t$-tone edge coloring of graphs Constructing Maximal Bumpless Pipedreams for Double Grothendieck Polynomials Mubayi's Polynomial-Ideal Conjecture and Cover-Ideal Turán Methods Implicit Binarization via Complex Phase Dynamics in Combinatorial Optimization The limits of Schur multipliers in Pólya conversion problems for the $q$-permanent function Universality theorems for generalized splines Framing Triangulations for Arbitrary Integer Flow Polytopes On the Common Generalization of Gentle Algebras and Framed Directed Acyclic Graphs The complexity of frugal digraph homomorphisms Chaotic and periodic behavior of jeu de taquin on infinite Young tableaux Enumerating Pattern Avoiding Parking Functions Incidence toric ideals and three-point functions Unique Winning Opening Move in Three-Row Chomp Strong majority colorings of graphs A Balancing Theorem for Spanning Trees of Rectangular Grid Graphs Spectral radius and edge-disjoint connected factors of graphs New invariants for rank metric codes, with applications to the classification of rank two semifields of order 256 Flexible DP-4-coloring of planar graphs without 4-cycles and intersecting triangles Balanced intersection size distributions in projective planes List Reconstruction Problem with List Size Two Is Dimensionality a Barrier for Retrieval Models? The INIEP: Irreducible and Positive Realizations The number of Pfaffian orientations on punctured polygonally cellulated surfaces Explicit Construction of Polytopes whose Ehrhart Polynomials Realize any Given Sign Pattern Finite-state enumeration of adjacency-constrained 132-avoiding permutations AMDS and quantum AMDS Constacyclic codes of length $4p^ς$ over $\mathbb{F}_{{p}^{m}}$
Rearrangement Events on Circular Genomes
Joshua Stevenson, Venta Terauds, Jeremy Sumner · 2022-02-04 · via math.CO updates on arXiv.org

Early literature on genome rearrangement modelling views the problem of computing evolutionary distances as an inherently combinatorial one. In particular, attention was given to estimating distances using the minimum number of events required to transform one genome into another. In hindsight, this approach is analogous to early methods for inferring phylogenetic trees from DNA sequences such as maximum parsimony -- both are motivated by the principle that the true distance minimises evolutionary change, and both are effective if this principle is a true reflection of reality. Recent literature considers genome rearrangement under statistical models, continuing this parallel with DNA-based methods; the goal here is to use model-based methods (for example maximum likelihood techniques) to compute distance estimates that incorporate the large number of rearrangement paths that can transform one genome into another. Crucially, this approach requires one to decide upon a set of feasible rearrangement events and, in this paper, we focus on characterising well-motivated models for signed, uni-chromosomal circular genomes, where the number of regions remains fixed. Since rearrangements are often mathematically described using permutations, we isolate the sets of permutations representing rearrangements that are biologically reasonable in this context, for example inversions and translocations. We provide precise mathematical expressions for these rearrangements, and then describe them in terms of the set of cuts made in the genome when they are applied. We directly compare cuts to breakpoints, and use this concept to count the distinct rearrangement actions which apply a given number of cuts. Finally, we provide some examples of rearrangement models, and include a discussion of some questions that arise when defining plausible models.