Related papers: Algebraic double cut and join -- A group-theoretic…

Using state-of-the-art techniques combining imaging methods and high-throughput genomic mapping tools leaded to the significant progress in detailing chromosome architecture of various organisms. However, a gap still remains between the…

The reconstruction of the history of evolutionary genome-wide events among a set of related organisms is of great biological interest. A simplified model that captures only content modifying operations was introduced recently. It allows the…

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…

Double-strand breaks (DSBs) in DNA are naturally occurring destructive events in all organisms that may lead to genome instability. Cells employ various repair methods known as non-homologous end joining (NHEJ), microhomology mediated end…

Practical image segmentation tasks concern images which must be reconstructed from noisy, distorted, and/or incomplete observations. A recent approach for solving such tasks is to perform this reconstruction jointly with the segmentation,…

Two successful approaches for the segmentation of biomedical images are (1) the selection of segment candidates from a merge-tree, and (2) the clustering of small superpixels by solving a Multi-Cut problem. In this paper, we introduce a…

Detection of double JPEG compression is important to forensics analysis. A few methods were proposed based on convolutional neural networks (CNNs). These methods only accept inputs from pre-processed data, such as histogram features and/or…

We show that the theory of sorting by reversals fits into the well-established theory of circuit partitions of 4-regular multigraphs (which also involves the combinatorial structures of circle graphs and delta-matroids). In this way, we…

DNA rearrangement processes recombine gene segments that are organized on the chromosome in a variety of ways. The segments can overlap, interleave or one may be a subsegment of another. We use directed graphs to represent segment…

Objective. Dual-energy computed tomography (DECT) has the potential to improve contrast, reduce artifacts and the ability to perform material decomposition in advanced imaging applications. The increased number or measurements results with…

Rearrangements of bacterial chromosomes can be studied mathematically at several levels, most prominently at a local, or sequence level, as well as at a topological level. The biological changes involved locally are inversions, deletions,…

Biclustering, also called co-clustering, block clustering, or two-way clustering, involves the simultaneous clustering of both the rows and columns of a data matrix into distinct groups, such that the rows and columns within a group display…

During the course of evolution, an organism's genome can undergo changes that affect the large-scale structure of the genome. These changes include gene gain, loss, duplication, chromosome fusion, fission, and rearrangement. When gene gain…

Of the many modern approaches to calculating evolutionary distance via models of genome rearrangement, most are tied to a particular set of genomic modelling assumptions and to a restricted class of allowed rearrangements. The "position…

In this paper, we examine the computational complexity of enumeration in certain genome rearrangement models. We first show that the Pairwise Rearrangement problem in the Single Cut-and-Join model (Bergeron, Medvedev, & Stoye, J. Comput.…

The BCJ duality between color and kinematics brings two advantages to calculating multi-loop scattering amplitudes. First the number of ordered cuts that need to be performed to fix the integrand to a gauge theory is minimal -- reducing the…

We study complexity of rearrangement problems in the generalized breakpoint model and settle several open questions. The model was introduced by Tannier et al. (2009) who showed that the median problem is solvable in polynomial time in the…

We construct a cubic cut-and-join operator description for the partition function of the Chekhov-Eynard-Orantin topological recursion for a local spectral curve with simple ramification points. In particular, this class contains partition…

The edit distance under the DCJ model can be computed in linear time for genomes with equal content or with Indels. But it becomes NP-Hard in the presence of duplications, a problem largely unsolved especially when Indels are considered. In…

We describe an algorithm for comparing two RNA secondary structures coded in the form of trees that introduces two new operations, called node fusion and edge fusion, besides the tree edit operations of deletion, insertion, and relabeling…