Related papers: Genome Halving by Block Interchange
We prove a lower and an upper bound on the number of block moves necessary to sort a permutation. We put our results in contrast with existing results on sorting by block transpositions, and raise some open questions.
The Genome Median Problem is an important problem in phylogenetic reconstruction under rearrangement models. It can be stated as follows: given three genomes, find a fourth that minimizes the sum of the pairwise rearrangement distances…
In the evolution of a genome, the gene sequence is sometimes rearranged, for example by transposition of two adjacent gene blocks. In biocombinatorics, one tries to reconstruct these rearrangement incidents from the resulting permutation.…
This paper provides a short and transparent solution for the covering cost of white-grey trees which play a crucial role in the algorithm of Bergeron {\it et al.}\ to compute the rearrangement distance between two multichromosomal genomes…
This paper discusses various types of constraints, difficulties and solutions to overcome the challenges regarding university course allocation problem. A hybrid evolutionary algorithm has been defined combining Local Repair Algorithm and…
The partial transpose of a block matrix M is the matrix obtained by transposing the blocks of M independently. We approach the notion of partial transpose from a combinatorial point of view. In this perspective, we solve some basic…
In computational biology, tandem duplication is an important biological phenomenon which can occur either at the genome or at the DNA level. A tandem duplication takes a copy of a genome segment and inserts it right after the segment - this…
In medicine, visualizing chromosomes is important for medical diagnostics, drug development, and biomedical research. Unfortunately, chromosomes often overlap and it is necessary to identify and distinguish between the overlapping…
In this paper, we study the problem of sorting unichromosomal linear genomes by prefix double-cut-and-joins (or DCJs) in both the signed and the unsigned settings. Prefix DCJs cut the leftmost segment of a genome and any other segment, and…
This paper studies the 1-2-1 half-duplex network model, where two half-duplex nodes can communicate only if they point `beams' at each other; otherwise, no signal can be exchanged or interference can be generated. The main result of this…
Breakpoint graphs are ubiquitous structures in the field of genome rearrangements. Their cycle decomposition has proved useful in computing and bounding many measures of (dis)similarity between genomes, and studying the distribution of…
We propose an approach to the problem of global reconstruction of an orientation field. The method is based on a geometric model called "bisector line fields", which maps a pair of vector fields to an orientation field, effectively…
We present a genetic algorithm for the atomistic design and global optimisation of substitutionally disordered bulk materials and surfaces. Premature convergence which hamper conventional genetic algorithms due to problems with…
This work provides a complete characterization of the solutions of a linear interpolation problem for vector polynomials. The interpolation problem consists in finding n scalar polynomials such that an equation involving a linear…
Motivated by charge balancing constraints for rank modulation schemes, we introduce the notion of balanced permutations and derive the capacity of balanced permutation codes. We also describe simple interleaving methods for permutation code…
We study the complexity of the following cell connection and separation problems in segment arrangements. Given a set of straight-line segments in the plane and two points $a$ and $b$ in different cells of the induced arrangement: (i)…
Motivation: The comparison of diverse genomic datasets is fundamental to understanding genome biology. Researchers must explore many large datasets of genome intervals (e.g., genes, sequence alignments) to place their experimental results…
We describe a new algorithm to compute the geometric intersection number between two curves, given as edge vectors on an ideal triangulation. Most importantly, this algorithm runs in polynomial time in the bit-size of the two edge vectors.…
We present algorithms performing sparse univariate polynomial interpolation with errors in the evaluations of the polynomial. Based on the initial work by Comer, Kaltofen and Pernet [Proc. ISSAC 2012], we define the sparse polynomial…
A "genome structure" is a labeled directed graph with vertices of degree 1 or 2. A set of operations over such graphs is fixed, and each of the operations has a certain cost, a strictly positive number. The transformation problem consists…