Related papers: On Binary de Bruijn Sequences from LFSRs with Arbi…
Two arrays form a periodic complementary pair if the sum of their periodic autocorrelations is a delta function. Finding such pairs, however, is challenging for large arrays whose entries are constrained to a small alphabet. One such…
We introduce the notion of unavoidable (complete) sets of word patterns, which is a refinement for that of words, and study certain numerical characteristics for unavoidable sets of patterns. In some cases we employ the graph of pattern…
A method for engineering the behavior of populations of rhythmic elements is presented. The framework, which is based on phase models, allows a nonlinear time-delayed global feedback signal to be constructed which produces an interaction…
In this article we mainly study linear codes over $\mathbb{F}_{2^n}$ and their binary subfield codes. We construct linear codes over $\mathbb{F}_{2^n}$ whose defining sets are the certain subsets of $\mathbb{F}_{2^n}^m$ obtained from…
This paper presents a twist to the generation of binary random sequences by starting with decimal sequences. Rather than representing the prime reciprocal sequence directly in base 2, we first right the prime reciprocal in base 10 and then…
The main challenge in de novo assembly of NGS data is certainly to deal with repeats that are longer than the reads. This is particularly true for RNA- seq data, since coverage information cannot be used to flag repeated sequences, of which…
Due to their simple construction, LFSRs are commonly used as building blocks in various random number generators. Nonlinear feedforward logic is incorporated in LFSRs to increase the linear complexity of the generated sequence. In this…
We describe combinatorial approaches to the question of whether families of real matrices admit pairs of nonreal eigenvalues passing through the imaginary axis. When the matrices arise as Jacobian matrices in the study of dynamical systems,…
We define a de Bruijn process with parameters n and L as a certain continuous-time Markov chain on the de Bruijn graph with words of length L over an n-letter alphabet as vertices. We determine explicitly its steady state distribution and…
In the realm of modern digital communication, cryptography, and signal processing, binary sequences with a low correlation properties play a pivotal role. In the literature, considerable efforts have been dedicated to constructing good…
We study an interesting family of cooperating coroutines, which is able to generate all patterns of bits that satisfy certain fairly general ordering constraints, changing only one bit at a time. (More precisely, the directed graph of…
The de Bruijn graph $G_K$ of a set of strings $S$ is a key data structure in genome assembly that represents overlaps between all the $K$-length substrings of $S$. Construction and navigation of the graph is a space and time bottleneck in…
This paper is focused in designing an efficient on-line algorithm to reconstruct a DNA sequence and search the genes in it, we assume that the segment have no mutation or reading error, the algorithm is based on de Bruijn Graph for…
Sequences with low auto-correlation property have been applied in code-division multiple access communication systems, radar and cryptography. Using the inverse Gray mapping, a quaternary sequence of even length $N$ can be obtained from two…
For a set of integers $I$, we define a $q$-ary $I$-cycle to be a assignment of the symbols 1 through $q$ to the integers modulo $q^n$ so that every word appears on some translate of $I$. This definition generalizes that of de Bruijn cycles,…
We recast homogeneous linear recurrence sequences with fixed coefficients in terms of partial Bell polynomials, and use their properties to obtain various combinatorial identities and multifold convolution formulas. Our approach relies on a…
Complex systems are often driven by higher-order interactions among multiple units, naturally represented as hypergraphs. Understanding dependency structures within these hypergraphs is crucial for understanding and predicting the behavior…
Maximum-length sequences (m-sequences for short) over finite fields are generated by linear feedback shift registers with primitive characteristic polynomials. These sequences have nice mathematical structures and good randomness properties…
A finite sequence of numbers is perfect if it has zero periodic autocorrelation after a nontrivial cyclic shift. In this work, we study quaternionic perfect sequences having a one-to-one correspondence with the binary sequences arising in…
In human cells, estrogenic signals induce cyclical association and dissociation of specific proteins with the DNA in order to activate transcription of estrogen-responsive genes. These oscillations can be modeled by assuming a large number…