Related papers: The Hybrid k-Deck Problem: Reconstructing Sequence…
The equidistant subsequence pattern matching problem is considered. Given a pattern string $P$ and a text string $T$, we say that $P$ is an \emph{equidistant subsequence} of $T$ if $P$ is a subsequence of the text such that consecutive…
A modified $k$-deck of a graph is obtained by removing $k$ edges in all possible ways and adding $k$ (not necessarily new) edges in all possible ways. Krasikov and Roditty used these decks to give an independent proof of M\"uller's result…
Genome rearrangements can be modeled as $k$-breaks, which break a genome at k positions and glue the resulting fragments in a new order. In particular, reversals, translocations, fusions, and fissions are modeled as $2$-breaks, and…
In the $(k,m)$-mappability problem, for a given sequence $T$ of length $n$, the goal is to compute a table whose $i$th entry is the number of indices $j \ne i$ such that the length-$m$ substrings of $T$ starting at positions $i$ and $j$…
We study the problem of finding small trees. Classical network design problems are considered with the additional constraint that only a specified number $k$ of nodes are required to be connected in the solution. A prototypical example is…
The well-known trace reconstruction problem is the problem of inferring an unknown source string $x \in \{0,1\}^n$ from independent "traces", i.e. copies of $x$ that have been corrupted by a $\delta$-deletion channel which independently…
In this paper we study lower bounds for the fundamental problem of text indexing with mismatches and differences. In this problem we are given a long string of length $n$, the "text", and the task is to preprocess it into a data structure…
The problem of reconstructing strings from their substring spectra has a long history and in its most simple incarnation asks for determining under which conditions the spectrum uniquely determines the string. We study the problem of coded…
In this paper we consider the problem to reconstruct a $k$-uniform hypergraph from its line graph. In general this problem is hard. We solve this problem when the number of hyperedges containing any pair of vertices is bounded. Given an…
Let $G$ be a complete edge-weighted graph on $n$ vertices. To each subset of vertices of $G$ assign the cost of the minimum spanning tree of the subset as its weight. Suppose that $n$ is a multiple of some fixed positive integer $k$. The…
A modified $k$-deck of a graph $G$ is obtained by removing $k$ edges of $G$ in all possible ways, and adding $k$ (not necessarily new) edges in all possible ways. Krasikov and Roditty asked if it was possible to construct the usual $k$-edge…
In the k-arc connected subgraph problem, we are given a directed graph G and an integer k and the goal is the find a subgraph of minimum cost such that there are at least k-arc disjoint paths between any pair of vertices. We give a simple…
The high-throughput short-reads RNA-seq protocols often produce paired-end reads, with the middle portion of the fragments being unsequenced. We explore if the full-length fragments can be computationally reconstructed from the sequenced…
Suppose that two independent sets $I$ and $J$ of a graph with $\vert I \vert = \vert J \vert$ are given, and a token is placed on each vertex in $I$. The Sliding Token problem is to determine whether there exists a sequence of independent…
Given an array A of n real numbers, the maximum subarray problem is to find a contiguous subarray which has the largest sum. The k-maximum subarrays problem is to find k such subarrays with the largest sums. For the 1-maximum subarray the…
Finding the longest common subsequence in $k$-length substrings (LCS$k$) is a recently proposed problem motivated by computational biology. This is a generalization of the well-known LCS problem in which matching symbols from two sequences…
We study the following substring suffix selection problem: given a substring of a string T of length n, compute its k-th lexicographically smallest suffix. This a natural generalization of the well-known question of computing the maximal…
The problem called "String reconstruction from substrings" is a mathematical model of sequencing by hybridization that plays an important role in DNA sequencing. In this problem, we are given a blackbox oracle holding an unknown string…
We improve the bound on K\"uhnel's problem to determine the smallest $n$ such that the $k$-skeleton of an $n$-simplex $\Delta_n^{(k)}$ does not embed into a compact PL $2k$-manifold $M$ by showing that if $\Delta_n^{(k)}$ embeds into $M$,…
In this paper we define a new problem, motivated by computational biology, $LCSk$ aiming at finding the maximal number of $k$ length $substrings$, matching in both input strings while preserving their order of appearance. The traditional…