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DNA storage has emerged as an important area of research. The reliability of DNA storage system depends on designing the DNA strings (called DNA codes) that are sufficiently dissimilar. In this work, we introduce DNA codes that satisfy a…
An RNA molecule is structured on several layers. The primary and most obvious structure is its sequence of bases, i.e. a word over the alphabet {A,C,G,U}. The higher structure is a set of one-to-one base-pairings resulting in a…
Quasiperiodicity in strings was introduced almost 30 years ago as an extension of string periodicity. The basic notions of quasiperiodicity are cover and seed. A cover of a text $T$ is a string whose occurrences in $T$ cover all positions…
Double-stranded DNA `overstretches' at a pulling force of about 65 pN, increasing in length by a factor of 1.7. The nature of the overstretched state is unknown, despite its considerable importance for DNA's biological function and…
A \emph{binary tanglegram} is a drawing of a pair of rooted 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, it is essential…
The last decade brought a significant increase in the amount of data and a variety of new inference methods for reconstructing the detailed evolutionary history of various cancers. This brings the need of designing efficient procedures for…
The paper investigates the computational problem of predicting RNA secondary structures. The general belief is that allowing pseudoknots makes the problem hard. Existing polynomial-time algorithms are heuristic algorithms with no…
A matching is said to be disconnected if the saturated vertices induce a disconnected subgraph and induced if the saturated vertices induce a 1-regular graph. The disconnected and induced matching numbers are defined as the maximum…
We study approximation algorithms for variants of the \emph{median string} problem, which asks for a string that minimizes the sum of edit distances from a given set of $m$ strings of length $n$. Only the straightforward $2$-approximation…
In the usual trace reconstruction problem, the goal is to exactly reconstruct an unknown string of length $n$ after it passes through a deletion channel many times independently, producing a set of traces (i.e., random subsequences of the…
Approximate pattern matching is a natural and well-studied problem on strings: Given a text $T$, a pattern $P$, and a threshold $k$, find (the starting positions of) all substrings of $T$ that are at distance at most $k$ from $P$. We…
The genome rearrangement problem computes the minimum number of operations that are required to sort all elements of a permutation. A block-interchange operation exchanges two blocks of a permutation which are not necessarily adjacent and…
Binary embedding is a nonlinear dimension reduction methodology where high dimensional data are embedded into the Hamming cube while preserving the structure of the original space. Specifically, for an arbitrary $N$ distinct points in…
We consider DNA codes based on the nearest-neighbor (stem) similarity model which adequately reflects the "hybridization potential" of two DNA sequences. Our aim is to present a survey of bounds on the rate of DNA codes with respect to a…
String matching is a fundamental problem in computer science, with critical applications in text retrieval, bioinformatics, and data analysis. Among the numerous solutions that have emerged for this problem in recent decades,…
An RNA sequence is a word over an alphabet on four elements $\{A,C,G,U\}$ called bases. RNA sequences fold into secondary structures where some bases match one another while others remain unpaired. Pseudoknot-free secondary structures can…
DNA sequencing is the process of determining the exact order of the nucleotide bases of an individual's genome in order to catalogue sequence variation and understand its biological implications. Whole-genome sequencing techniques produce…
The edit distance (a.k.a. the Levenshtein distance) between two strings is defined as the minimum number of insertions, deletions or substitutions of symbols needed to transform one string into another. The problem of computing the edit…
Duplicate question detection is an ongoing challenge in community question answering because semantically equivalent questions can have significantly different words and structures. In addition, the identification of duplicate questions can…
Approximating a definite integral of product of cosines to within an accuracy of n binary digits where the integrand depends on input integers x[k] given in binary radix, is equivalent to counting the number of equal-sum partitions of the…