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One of the main challenges in Computational Biology is to find the evolutionary distance between two organisms. In the field of comparative genomics, one way to estimate such distance is to find a minimum cost sequence of rearrangements…
Unbalanced translocations are among the most frequent chromosomal alterations, accounted for 30\% of all losses of heterozygosity, a major genetic event causing inactivation of tumor suppressor genes. Despite of their central role in…
Given two strings $A[1..n]$ and $B[1..m]$, and a set of operations allowed to edit the strings, the edit distance between $A$ and $B$ is the minimum number of operations required to transform $A$ into $B$. Sequentially, a standard Dynamic…
Sorting by reversals is an important problem in inferring the evolutionary relationship between two genomes. The problem of sorting unsigned permutation has been proven to be NP-hard. The best guaranteed error bounded is the 3/2-…
A classical problem in comparative genomics is to compute the rearrangement distance, that is the minimum number of large-scale rearrangements required to transform a given genome into another given genome. While the most traditional…
This paper introduces the \emph{$d$-distance $b$-matching problem}, in which we are given a bipartite graph $G=(S,T;E)$ with $S=\{s_1,\dots,s_n\}$, a weight function on the edges, an integer $d\in\mathbb{Z}_+$ and a degree bound function…
A binary tanglegram is a pair <S,T> of binary trees whose leaf sets are in one-to-one correspondence; matching leaves are connected by inter-tree edges. For applications, for example in phylogenetics or software engineering, it is required…
In this paper we consider the $p$-Norm Hamming Centroid problem which asks to determine whether some given binary strings have a centroid with a bound on the $p$-norm of its Hamming distances to the strings. Specifically, given a set of…
The current paper investigates the bounded distance decoding (BDD) problem for ensembles of lattices whose generator matrices have sub-Gaussian entries. We first prove that, for these ensembles the BDD problem is NP-hard in the worst case.…
Motivated by applications in in-vivo DNA storage, we study codes for correcting duplications. A reverse-complement duplication of length $k$ is the insertion of the reversed and complemented copy of a substring of length $k$ adjacent to its…
In this paper we study a variant of string pattern matching which deals with tuples of strings known as \textit{multi-track strings}. Multi-track strings are a generalisation of strings (or \textit{single-track strings}) that have primarily…
Consensus problems for strings and sequences appear in numerous application contexts, ranging from bioinformatics over data mining to machine learning. Closing some gaps in the literature, we show that several fundamental problems in this…
The coverage depth problem in DNA data storage is about computing the expected number of reads needed to recover all encoded strands. Given a generator matrix of a linear code, this quantity equals the expected number of randomly drawn…
Gibbons and Korach studied a fundamental problem in 1997: given an observed sequence of reads and writes of a multi-threaded program, does there exist an interleaving which is sequentially consistent? Apart from applications in testing…
Bound propagation is an important Artificial Intelligence technique used in Constraint Programming tools to deal with numerical constraints. It is typically embedded within a search procedure ("branch and prune") and used at every node of…
An elastic-degenerate (ED) string $T$ is a sequence of $n$ sets $T[1],\ldots,T[n]$ containing $m$ strings in total whose cumulative length is $N$. We call $n$, $m$, and $N$ the length, the cardinality and the size of $T$, respectively. The…
Charge transfer in a DNA duplex chain is studied by constructing a system with virtual electrodes connected at the ends of each DNA strand. The systeym is described by the tight-binding model and its transport is analyzed by the transfer…
Crossover is the process of recombining the genetic features of two parents. For many applications where crossover is applied to permutations, relevant genetic features are pairs of adjacent elements, also called edges in the permutation…
The problem of finding longest common subsequence (LCS) is one of the fundamental problems in computer science, which finds application in fields such as computational biology, text processing, information retrieval, data compression etc.…
String consensus problems aim at finding a string that minimizes some given distance with respect to an input set of strings. In particular, in the Closest string problem, we are given a set of strings of equal length and a radius $d$. The…