Related papers: Combinatorial RNA Design: Designability and Struct…
Messenger RNA (mRNA) vaccines are being used for COVID-19, but still suffer from the critical issue of mRNA instability and degradation, which is a major obstacle in the storage, distribution, and efficacy of the vaccine. Previous work…
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…
RNA co-transcriptionality is the process where RNA sequences are spliced while being transcribed from DNA templates. This process holds potential as a key tool for molecular programming. Co-transcriptional folding has been shown to be…
In this work, we investigate a challenging problem, which has been considered to be an important criterion in designing codewords for DNA computing purposes, namely secondary structure avoidance in single-stranded DNA molecules. In short,…
In this paper, we investigate a new variant of neural architecture search (NAS) paradigm -- searching with random labels (RLNAS). The task sounds counter-intuitive for most existing NAS algorithms since random label provides few information…
In this paper, we study the combinatorial set of RNA secondary structures of length $n$ with $m$ base-pairs. For a compact representation, we encode an RNA secondary structure by the corresponding Motzkin word. For this combinatorial set,…
We construct a minimalist model of RNA secondary-structure formation and use it to study the mapping from sequence to structure. There are strong, qualitative differences between two-letter and four or six-letter alphabets. With only two…
Many computerized methods for RNA-RNA interaction structure prediction have been developed. Recently, $O(N^6)$ time and $O(N^4)$ space dynamic programming algorithms have become available that compute the partition function of RNA-RNA…
Combinatorial algorithms such as those that arise in graph analysis, modeling of discrete systems, bioinformatics, and chemistry, are often hard to parallelize. The Combinatorial BLAS library implements key computational primitives for…
Wideband communication receivers often deal with the problems of detecting weak signals from distant sources received together with strong nearby interferers. When the techniques of random modulation are used in communication system…
RNA-Seq technology offers new high-throughput ways for transcript identification and quantification based on short reads, and has recently attracted great interest. The problem is usually modeled by a weighted splicing graph whose nodes…
The presence of low dimensional chaos in the protein secondary structures, using the binary coded $\alpha$-helices and $\beta$-sheet motifs, has been investigated. In order to analyse symbolic DNA/RNA sequences the assignment, based on the…
We introduce and investigate binary $(k,k)$-designs -- combinatorial structures which are related to binary orthogonal arrays. We derive general linear programming bound and propose as a consequence a universal bound on the minimum possible…
Context: Detecting arrays are mathematical structures aimed at fault identification in combinatorial interaction testing. However, they cannot be directly applied to systems that have constraints among test parameters. Such constraints are…
No existing algorithm can start with arbitrary RNA sequences and return the precise, three-dimensional structures that ensures their biological function. This chapter outlines current algorithms for automated RNA structure prediction…
We introduce the strongly NP-complete pagination problem, an extension of BIN PACKING where packing together two items may make them occupy less volume than the sum of their individual sizes. To achieve this property, an item is defined as…
We consider the problem of neural association for a network of non-binary neurons. Here, the task is to first memorize a set of patterns using a network of neurons whose states assume values from a finite number of integer levels. Later,…
We investigate the service-rate region (SRR) of distributed storage systems that employ linear codes. We focus on systems where each server stores one code symbol, and a user recovers a data symbol by accessing any of its recovery groups,…
Many combinatorial optimisation problems hide algebraic structures that, once exposed, shrink the search space and improve the chance of finding the global optimal solution. We present a general framework that (i) identifies algebraic…
The structure of an RNA molecule plays a significant role in its biological function. Predicting structure given a one dimensional sequence of RNA nucleotide bases is a difficult and important problem. Many computer programs (known as in…