Related papers: Reconstructing Mixtures of Coded Strings from Pref…

The problem of reconstructing strings from substring information has found many applications due to its importance in genomic data sequencing and DNA- and polymer-based data storage. One practically important and challenging paradigm…

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…

Motivated by studies of data retrieval in polymer-based storage systems, we consider the problem of reconstructing a multiset of binary strings that have the same length and the same weight from the compositions of their prefixes and…

Motivated by mass-spectrometry protein sequencing, we consider a simply-stated problem of reconstructing a string from the multiset of its substring compositions. We show that all strings of length 7, one less than a prime, or one less than…

Motivated by applications in polymer-based data storage, we study the problem of reconstructing a string from part of its composition multiset. We give a full description of the structure of the strings that cannot be uniquely reconstructed…

The number of zeros and the number of ones in a binary string are referred to as the composition of the string, and the prefix-suffix compositions of a string are a multiset formed by the compositions of the prefixes and suffixes of all…

Motivated by polymer-based data-storage platforms that use chains of binary synthetic polymers as the recording media and read the content via tandem mass spectrometers, we propose a new family of codes that allows for unique string…

This paper studies reconstruction of strings based upon their substrings spectrum. Under this paradigm, it is assumed that all substrings of some fixed length are received and the goal is to reconstruct the string. While many existing works…

The problem of string reconstruction based on its substrings spectrum has received significant attention recently due to its applicability to DNA data storage and sequencing. In contrast to previous works, we consider in this paper a setup…

Synthetic polymer-based storage seems to be a particularly promising candidate that could help to cope with the ever-increasing demand for archival storage requirements. It involves designing molecules of distinct masses to represent the…

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…

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…

This paper studies the problem of encoding messages into sequences which can be uniquely recovered from some noisy observations about their substrings. The observed reads comprise consecutive substrings with some given minimum overlap. This…

We consider the problem of binary string reconstruction from the multiset of its substring compositions, i.e., referred to as the substring composition multiset, first introduced and studied by Acharya et al. We introduce a new algorithm…

Motivated by polymer-based data-storage platforms that use chains of binary synthetic polymers as the recording media and read the content via tandem mass spectrometers, we propose a new family of codes that allows for both unique string…

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…

Graphs are a powerful tool for analyzing large data sets, but many real-world phenomena involve interactions that go beyond the simple pairwise relationships captured by a graph. In this paper we introduce and study a simple combinatorial…

We generalize the problem of reconstructing strings from their substring compositions first introduced by Acharya et al. in 2015 motivated by polymer-based advanced data storage systems utilizing mass spectrometry. Namely, we see strings as…

The problem of reconstructing a sequence from the set of its length-$k$ substrings has received considerable attention due to its various applications in genomics. We study an uncoded version of this problem where multiple random sources…

We study the query complexity of exactly reconstructing a string from adaptive queries, such as substring, subsequence, and jumbled-index queries. Such problems have applications, e.g., in computational biology. We provide a number of new…