Related papers: Genome Halving by Block Interchange
A permutation graph can be defined as an intersection graph of segments whose endpoints lie on two parallel lines $l_1$ and $l_2$, one on each. A bipartite permutation graph is a permutation graph which is bipartite. In this paper we study…
The repeat content and heterozygosity rate of a target genome are important factors in determining the feasibility of achieving a complete telomere-to-telomere assembly. The mathematical relationship between the required coverage and read…
2D display is a fast and economical way of visualizing polymorphism and comparing genomes, which is based on the separation of DNA fragments in two steps, according first to their size and then to their sequence composition. In this paper,…
Distributed quantum computing has been well-known for many years as a system composed of a number of small-capacity quantum circuits. Limitations in the capacity of monolithic quantum computing systems can be overcome by using distributed…
An applied problem facing all areas of data science is harmonizing data sources. Joining data from multiple origins with unmapped and only partially overlapping features is a prerequisite to developing and testing robust, generalizable…
A linear optical probabilistic scheme for the optimal cloning of a pair of orthogonally-polarized photons is devised, based on single- and two-photon interferences. It consists in a partial symmetrization device, realized with a modified…
Covering alignment problems arise from recent developments in genomics; so called pan-genome graphs are replacing reference genomes, and advances in haplotyping enable full content of diploid genomes to be used as basis of sequence…
This paper considers a base station that delivers packets to multiple receivers through a sequence of coded transmissions. All receivers overhear the same transmissions. Each receiver may already have some of the packets as side…
On the string of finite length, a (genomic) transposition is defined as the operation of exchanging two consecutive substrings. The minimum number of transpositions needed to transform one into the other is the transposition distance, that…
The problem of diagonalizing a class of complicated matrices, to be called ultrametric matrices, is investigated. These matrices appear at various stages in the description of disordered systems with many equilibrium phases by the technique…
We examine LDPC codes decoded using linear programming (LP). Four contributions to the LP framework are presented. First, a new method of tightening the LP relaxation, and thus improving the LP decoder, is proposed. Second, we present an…
In this paper, we study how to quickly compute the <-minimal monomial interpolating basis for a multivariate polynomial interpolation problem. We address the notion of "reverse" reduced basis of linearly independent polynomials and design…
A Genome rearrangement problem studies large-scale mutations on a set of DNAs in living organisms. Various rearrangements like reversals, transpositions, translocations, fissions, fusions, and combinations and different variations have been…
Locating recombination hotspots in genomic data is an important but difficult task. Current methods frequently rely on estimating complicated models at high computational cost. In this paper we develop an extremely fast, scalable method for…
In this research, we consider a mixture of genome fragments of a certain bacteria set. The problem of mixture separation is studied under the assumption that all the genomes present in the mixture are completely sequenced or are close to…
It is an open question whether there exists a polynomial-time algorithm for computing the rotation distances between pairs of extended ordered binary trees. The problem of computing the rotation distance between an arbitrary pair of trees,…
We consider the reconstruction of a phylogeny from multiple genes under the multispecies coalescent. We establish a connection with the sparse signal detection problem, where one seeks to distinguish between a distribution and a mixture of…
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…
Genomic data I used in many fields but, it has become known that most of the platforms used in the sequencing process produce significant errors. This means that the analysis and inferences generated from these data may have some errors…
We study a minimal model for genome evolution whose elementary processes are single site mutation, duplication and deletion of sequence regions and insertion of random segments. These processes are found to generate long-range correlations…