Related papers: Sorting Genomes by Prefix Double-Cut-and-Joins
In this paper, we propose an alternative method to the disjoint principal component analysis. The method consists of a principal component analysis with constraints, which allows us to determine disjoint components that are linear…
Huffman coding finds an optimal prefix code for a given probability mass function. Consider situations in which one wishes to find an optimal code with the restriction that all codewords have lengths that lie in a user-specified set of…
We describe an implementation of a genetic algorithm on partially commutative groups and apply it to the double coset search problem on a subclass of groups. This transforms a combinatorial group theory problem to a problem of combinatorial…
There has been surprisingly little work on algorithms for sorting strings on distributed-memory parallel machines. We develop efficient algorithms for this problem based on the multi-way merging principle. These algorithms inspect only…
This paper studies the relationship between undirected (unrooted) and directed (rooted) phylogenetic networks. We describe a polynomial-time algorithm for deciding whether an undirected nonbinary phylogenetic network, given the locations of…
Several modern genomic technologies, such as DNA-Methylation arrays, measure spatially registered probes that number in the hundreds of thousands across multiplechromosomes. The measured probes are by themselves less interesting…
A matching cut of a graph is a partition of its vertex set in two such that no vertex has more than one neighbor across the cut. The Matching Cut problem asks if a graph has a matching cut. This problem, and its generalization d-cut, has…
When applying automatic analysis of fluorescence or histopathological images of cells, it is necessary to partition, or de-clump, partially overlapping cell nuclei. In this work, I describe a method of partitioning partially overlapping…
DNA codes have garnered significant interest due to their utilization in digital media storage, cryptography, and DNA computing. In this paper, we first extend the results of constructing reversible group codes \cite{Cengellenmis} and…
We show how to transform any set of prioritized propositional defaults into an equivalent set of parallel (i.e., unprioritized) defaults, in circumscription. We give an algorithm to implement the transform. We show how to use the transform…
We introduce the boundary length and point spectrum, as a joint generalization of the boundary length spectrum and boundary point spectrum in arXiv:1307.0967. We establish by cut-and-join methods that the number of partial chord diagrams…
Unexpected stimuli induce "error" or "surprise" signals in the brain. The theory of predictive coding promises to explain these observations in terms of Bayesian inference by suggesting that the cortex implements variational inference in a…
This paper is concerned with algorithms for prediction of discrete sequences over a finite alphabet, using variable order Markov models. The class of such algorithms is large and in principle includes any lossless compression algorithm. We…
A simple and fast analysis method to sort large data sets into groups with shared distinguishing characteristics is described, and applied to single molecular break junction conductance versus electrode displacement data. The method, based…
Convolutions of independent random variables often arise in a natural way in many applied problems. In this article, we compare convolutions of two sets of gamma (negative binomial) random variables in the convolution order and the usual…
We consider the problem of efficiently designing sets (codes) of equal-length DNA strings (words) that satisfy certain combinatorial constraints. This problem has numerous motivations including DNA computing and DNA self-assembly. Previous…
Due to the increased availability of large datasets of biological sequences, the tools for sequence comparison are now relying on efficient alignment-free approaches to a greater extent. Most of the alignment-free approaches require the…
This paper introduces a new family of reconstruction codes which is motivated by applications in DNA data storage and sequencing. In such applications, DNA strands are sequenced by reading some subset of their substrings. While previous…
Alignment of large genomic sequences is a fundamental task in computational genome analysis. Most methods for genomic alignment use high-scoring local alignments as {\em anchor points} to reduce the search space of the alignment procedure.…
A central problem in comparative genomics consists in computing a (dis-)similarity measure between two genomes, e.g. in order to construct a phylogeny. All the existing measures are defined on genomes without duplicates. However, we know…