Related papers: Genome Halving by Block Interchange
We consider a refinement of the partition function of graph homomorphisms and present a quasi-polynomial algorithm to compute it in a certain domain. As a corollary, we obtain quasi-polynomial algorithms for computing partition functions…
De novo assembly is the process of reconstructing the genome sequence of an organism from sequencing reads. Genome sequences are essential to biology, and assembly has been a central problem in bioinformatics for four decades. Until…
Identifying palindromes in sequences has been an interesting line of research in combinatorics on words and also in computational biology, after the discovery of the relation of palindromes in the DNA sequence with the HIV virus. Efficient…
In this paper, we give a polynomial (O(n^8)) algorithm for finding a longest common pattern between two permutations of size n given that one is separable. We also give an algorithm for general permutations whose complexity depends on the…
Blockmodeling of a given problem represented by an $N\times N$ adjacency matrix can be found by swapping rows and columns of the matrix (i.e. multiplying matrix from left and right by a permutation matrix). Although classical matrix…
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…
Consider a system evolving according to an absorbing discrete-time Markov chain with known transition matrix. The state of the system is observed at two points in time, separated by an unknown number of generations. We are interested in…
Many problems of interest for cyber-physical network systems can be formulated as Mixed-Integer Linear Programs in which the constraints are distributed among the agents. In this paper we propose a distributed algorithmic framework to solve…
The scheme of divided differences is widely used in many approximation and interpolation problems. Computing the Newton coefficients of the interpolating polynomial is the first step of the Bj\"{o}rck and Pereyra algorithm for solving…
The paper is devoted to the problem of multivariate polynomial interpolation and its application to quantum secret sharing. We show that using quantum Fourier transform one can produce the protocol for quantum secret sharing distribution.
Many high dimensional integrals can be reduced to the problem of finding the relative measures of two sets. Often one set will be exponentially larger than the other, making it difficult to compare the sizes. A standard method of dealing…
Charge transfer along the base-pair stack in DNA is modeled in terms of thermally-assisted tunneling between adjacent base pairs. Central to our approach is the notion that tunneling between fluctuating pairs is rate-limited by the…
We consider a problem of dispersing points on disjoint intervals on a line. Given n pairwise disjoint intervals sorted on a line, we want to find a point in each interval such that the minimum pairwise distance of these points is maximized.…
Rotation distance between rooted binary trees measures the number of simple operations it takes to transform one tree into another. There are no known polynomial-time algorithms for computing rotation distance. We give an efficient,…
DNA renaturation is the recombination of two complementary single strands to form a double helix. It is experimentally known that renaturation proceeds through the formation of a double stranded nucleus of several base pairs (the rate…
Sorting a permutation by reversals is a famous problem in genome rearrangements. Since 1997, quite some biological evidence were found that in many genomes the reversed regions are usually flanked by a pair of inverted repeats. This type of…
A distributed computing system is a collection of processors that communicate either by reading and writing from a shared memory or by sending messages over some communication network. Most prior biologically inspired distributed computing…
Multiple genome alignment remains a challenging problem. Effects of recombination including rearrangement, segmental duplication, gain, and loss can create a mosaic pattern of homology even among closely related organisms. We describe a…
We present a simplification of the recursive algorithm for the evaluation of intersection numbers for differential $n$-forms, by combining the advantages emerging from the choice of delta-forms as generators of relative twisted cohomology…
A difficult step in the process of karyotyping is segmenting chromosomes that touch or overlap. In an attempt to automate the process, previous studies turned to Deep Learning methods, with some formulating the task as a semantic…