Related papers: The Tandem Duplication Distance Problem is hard ov…
We address the problem of finding the minimal number of block interchanges (exchange of two intervals) required to transform a duplicated linear genome into a tandem duplicated linear genome. We provide a formula for the distance as well as…
In this article, we study the problem of finding the longest common separable pattern between several permutations. We give a polynomial-time algorithm when the number of input permutations is fixed and show that the problem is NP-hard for…
Decision-theoretic troubleshooting is one of the areas to which Bayesian networks can be applied. Given a probabilistic model of a malfunctioning man-made device, the task is to construct a repair strategy with minimal expected cost. The…
Frameshift mutations in protein-coding DNA sequences produce a drastic change in the resulting protein sequence, which prevents classic protein alignment methods from revealing the proteins' common origin. Moreover, when a large number of…
Genome assembly, the process of reconstructing a long genetic sequence by aligning and merging short fragments, or reads, is known to be NP-hard, either as a version of the shortest common superstring problem or in a Hamiltonian-cycle…
Let $S$ and $D$ each be a set of orthogonal line segments in the plane. A line segment $s\in S$ \emph{stabs} a line segment $s'\in D$ if $s\cap s'\neq\emptyset$. It is known that the problem of stabbing the line segments in $D$ with the…
The edit distance is a way of quantifying how similar two strings are to one another by counting the minimum number of character insertions, deletions, and substitutions required to transform one string into the other. A simple dynamic…
An RNA sequence is a string composed of four types of nucleotides, $A, C, G$, and $U$. The goal of the RNA folding problem is to find a maximum cardinality set of crossing-free pairs of the form $\{A,U\}$ or $\{C,G\}$ in a given RNA…
This paper addresses the online exact string matching problem which consists in finding all occurrences of a given pattern p in a text t. It is an extensively studied problem in computer science, mainly due to its direct applications to…
The Closest String Problem is an NP-complete problem which appears more commonly in bioinformatics and coding theory. Less surprisingly, classical approaches have been pursued with two prominent algorithms being the genetic algorithm and…
Cadences are structurally maximal arithmetic progressions of indices corresponding to equal characters in an underlying string. This paper provides a polynomial time detection algorithm for 3-cadences in grammar-compressed binary strings.…
String edit distances have been used for decades in applications ranging from spelling correction and web search suggestions to DNA analysis. Most string edit distances are variations of the Levenshtein distance and consider only…
In this work, we consider a variant of the classical Longest Common Subsequence problem called Doubly-Constrained Longest Common Subsequence (DC-LCS). Given two strings s1 and s2 over an alphabet A, a set C_s of strings, and a function Co…
The computation of genomic distances has been a very active field of computational comparative genomics over the last 25 years. Substantial results include the polynomial-time computability of the inversion distance by Hannenhalli and…
In this paper, we consider the $k$-approximate pattern matching problem under differential privacy, where the goal is to report or count all substrings of a given string $S$ which have a Hamming distance at most $k$ to a pattern $P$, or…
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…
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…
The closest string problem is an NP-hard problem, whose task is to find a string that minimizes maximum Hamming distance to a given set of strings. This can be reduced to an integer program (IP). However, to date, there exists no known…
We study a combinatorial problem arising from microarrays synthesis. The synthesis is done by a light-directed chemical process. The objective is to minimize unintended illumination that may contaminate the quality of experiments.…
If $x$ is a non-empty string then the repetition $xx$ is called a tandem repeat. Similarly, a tandem in a two dimensional array $X$ is a configuration consisting of a same primitive block $W$ that touch each other with one side or corner.…