Related papers: Duplication Distance to the Root for Binary Sequen…
Cyclic codes are the most studied subclass of linear codes and widely used in data storage and communication systems. Many cyclic codes have optimal parameters or the best parameters known. They are divided into simple-root cyclic codes and…
Recall that a binary linear code of length $n$ is a linear subspace $\mathcal{C} = \{x\in\mathbb{F}_2^n\mid Ax=0\}$. Here the parity check matrix $A$ is a binary $m\times n$ matrix of rank $m$. We say that $\mathcal{C}$ has rate $R=1-\frac…
The majority of the human genome consists of repeated sequences. An important type of repeated sequences common in the human genome are tandem repeats, where identical copies appear next to each other. For example, in the sequence…
Binary cyclic codes have been a hot topic for many years, and significant progress has been made in the study of this types of codes. As is well known, it is hard to construct infinite families of binary cyclic codes [n, n+1/2] with good…
We answer the following question of R. L. Graham: What is the discrepancy of the lexicographically-least binary de Bruijn sequence? Here, "discrepancy" refers to the maximum (absolute) difference between the number of ones and the number of…
The ability to store data in the DNA of a living organism has applications in a variety of areas including synthetic biology and watermarking of patented genetically-modified organisms. Data stored in this medium is subject to errors…
The problem of reconstructing a sequence from the set of its length-$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…
Three standard subtree transfer operations for binary trees, used in particular for phylogenetic trees, are: tree bisection and reconnection ($TBR$), subtree prune and regraft ($SPR$) and rooted subtree prune and regraft ($rSPR$). For a…
Given a Galton-Watson process conditioned to have total progeny equal to $n$, we study the asymptotic probability that this conditioned Galton-Watson process has distance to the border bigger or equal than $k$, as the number of nodes $n…
Tandem duplication is the process of inserting a copy of a segment of DNA adjacent to the original position. Motivated by applications that store data in living organisms, Jain et al. (2017) proposed the study of codes that correct tandem…
Aperiodic autocorrelation is an important indicator of performance of sequences used in communications, remote sensing, and scientific instrumentation. Knowing a sequence's autocorrelation function, which reports the autocorrelation at…
We study codes that can correct backtracking errors during nanopore sequencing. In this channel, a sequence of length $n$ over an alphabet of size $q$ is being read by a sliding window of length $\ell$, where from each window we obtain only…
Recently, binary cyclic codes with parameters $[n,(n\pm1)/2,\geq \sqrt{n}]$ have been a hot topic since their minimum distances have a square-root bound. In this paper, we construct four classes of binary cyclic codes…
The merit factor problem is of practical importance to manifold domains, such as digital communications engineering, radars, system modulation, system testing, information theory, physics, chemistry. However, the merit factor problem is…
Binary self-dual codes with large minimum distances, such as the extended Hamming code and the Golay code, are fascinating objects in the coding theory. They are closely related to sporadic simple groups, lattices and invariant theory. A…
We introduce and investigate the approximability of the maximum binary tree problem (MBT) in directed and undirected graphs. The goal in MBT is to find a maximum-sized binary tree in a given graph. MBT is a natural variant of the…
The merit factor of a $\{-1, 1\}$ binary sequence measures the collective smallness of its non-trivial aperiodic autocorrelations. Binary sequences with large merit factor are important in digital communications because they allow the…
In parametric sequence alignment, optimal alignments of two sequences are computed as a function of the penalties for mismatches and spaces, producing many different optimal alignments. Here we give a 3/(2^{7/3}\pi^{2/3})n^{2/3} +O(n^{1/3}…
Motivated by applications in DNA storage, we study a setting in which strings are affected by tandem-duplication errors. In particular, we look at two settings: disjoint tandem-duplication errors, and equal-length tandem-duplication errors.…
Rotation distance between rooted binary trees measures the number of simple operations it takes to transform one tree into another. There are no known polynomial-time algorithms for computing rotation distance. We give an efficient,…