Related papers: Minimum Segmentation for Pan-genomic Founder Recon…
Given a planar graph G on n vertices and an integer parameter r<n, an r-division of G with few holes is a decomposition of G into O(n/r) regions of size at most r such that each region contains at most a constant number of faces that are…
We introduce a compact pangenome representation based on an optimal segmentation concept that aims to reconstruct founder sequences from a multiple sequence alignment (MSA). Such founder sequences have the feature that each row of the MSA…
In this article, we investigate different parsimony-based approaches towards finding recombination breakpoints in a multiple sequence alignment. This recombination detection task is crucial in order to avoid errors in evolutionary analyses…
Given natural limitations on the length DNA sequences, designing phylogenetic reconstruction methods which are reliable under limited information is a crucial endeavor. There have been two approaches to this problem: reconstructing partial…
We introduce a new variant of the $k$-deck problem, which in its traditional formulation asks for determining the smallest $k$ that allows one to reconstruct any binary sequence of length $n$ from the multiset of its $k$-length…
We initiate the study of the shortest reconfiguration problem for independent sets under the adjacency relation derived from the independent set polytope. Given a graph and two independent sets, the problem asks for a shortest sequence…
The problem of reconstructing a sequence of independent and identically distributed symbols from a set of equal size, consecutive, fragments, as well as a dependent reference sequence, is considered. First, in the regime in which the…
We consider the phylogenetic tree reconstruction problem with insertions and deletions (indels). Phylogenetic algorithms proceed under a model where sequences evolve down the model tree, and given sequences at the leaves, the problem is to…
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…
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…
We present the first sub-quadratic time algorithm that with high probability correctly reconstructs phylogenetic trees for short sequences generated by a Markov model of evolution. Due to rapid expansion in sequence databases, such very…
We consider the Minimum Steiner Cut problem on undirected planar graphs with non-negative edge weights. This problem involves finding the minimum cut of the graph that separates a specified subset $X$ of vertices (terminals) into two parts.…
Monotonicity is a simple yet significant qualitative characteristic. We consider the problem of segmenting a sequence in up to K segments. We want segments to be as monotonic as possible and to alternate signs. We propose a quality metric…
A primary challenge in metagenomics is reconstructing individual microbial genomes from the mixture of short fragments created by sequencing. Recent work leverages the sparsity of the assembly graph to find $r$-dominating sets which enable…
Pattern matching on graphs has been widely studied lately due to its importance in genomics applications. Unfortunately, even the simplest problem of deciding if a string appears as a subpath of a graph admits a quadratic lower bound under…
We study the reconstruction problem of permutation sequences from their $k$-minors, which are subsequences of length $k$ with entries renumbered by $1,2,\ldots,k$ preserving order. We prove that the minimum number $k$ such that any…
We consider the following problem: from a given set of gene families trees on a set of genomes, find a first speciation, that splits these genomes into two subsets, that minimizes the number of gene duplications that happened before this…
Multi-segment reconstruction (MSR) problem consists of recovering a signal from noisy segments with unknown positions of the observation windows. One example arises in DNA sequence assembly, which is typically solved by matching short reads…
Motivated by applications to DNA storage, we study reconstruction and list-reconstruction schemes for integer vectors that suffer from limited-magnitude errors. We characterize the asymptotic size of the intersection of error balls in…
We present algorithms for length-constrained maximum sum segment and maximum density segment problems, in particular, and the problem of finding length-constrained heaviest segments, in general, for a sequence of real numbers. Given a…