相关论文: RNA secondary structure design

This contribution focuses on the fascinating RNA molecule, its sequence-dependent folding driven by base-pairing interactions, the interplay between these interactions and natural evolution, and its multiple regulatory roles. The four of us…

Despite great interest in solving RNA secondary structures due to their impact on function, it remains an open problem to determine structure from sequence. Among experimental approaches, a promising candidate is the "chemical modification…

The research of developing a general methodology for the construction of good nonregular designs has been very active in the last decade. Recent research by Xu and Wong [Statist. Sinica 17 (2007) 1191--1213] suggested a new class of…

RNA plays a pivotal role in diverse biological processes, ranging from gene regulation to catalysis. Recent advances in RNA design, such as RfamGen, Ribodiffusion and RDesign, have demonstrated promising results, with successful designs of…

This paper considers the construction of minimum aberration (MA) blocked factorial designs. Based on coding theory, the concept of minimum moment aberration due to Xu [Statist. Sinica 13 (2003) 691--708] for unblocked designs is extended to…

We study RNA foldings and investigate their topology using a combination of knot theory and embedded rigid vertex graphs. Knot theory has been helpful in modeling biomolecules, but classical knots place emphasis on a biomolecule's…

Background: We study the sparsification of dynamic programming folding algorithms of RNA structures. Sparsification applies to the mfe-folding of RNA structures and can lead to a significant reduction of time complexity. Results: We analyze…

RNA forms elaborate secondary structures through intramolecular base pairing. These structures perform critical biological functions within each cell. Due to the availability of a polynomial algorithm to calculate the partition function…

Prior results for tRNA and 5S rRNA demonstrated that secondary structure prediction accuracy can be significantly improved by modifying the parameters in the multibranch loop entropic penalty function. However, for reasons not well…

Accurate prediction of RNA secondary structure underpins transcriptome annotation, mechanistic analysis of non-coding RNAs, and RNA therapeutic design. Recent gains from deep learning and RNA foundation models are difficult to interpret…

When the inverse of an algorithm is well-defined -- that is, when its output can be deterministically transformed into the input producing it -- we say that the algorithm is invertible. While one can describe an invertible algorithm using a…

Consider the network of all secondary structures of a given RNA sequence, where nodes are connected when the corresponding structures have base pair distance one. The expected degree of the network is the average number of neighbors, where…

DNA codes have garnered significant interest due to their utilization in digital media storage, cryptography, and DNA computing. In this paper, we first extend the results of constructing reversible group codes \cite{Cengellenmis} and…

Despite recent progress in our understanding of complex dynamic networks, it remains challenging to devisesufficiently accurate models to observe, control or predict the state of real systems in biology, economics or other fields. A largely…

Deep learning has become in recent years a cornerstone tool fueling key innovations in the industry, such as autonomous driving. To attain good performances, the neural network architecture used for a given application must be chosen with…

Self-folding is an emerging paradigm for the inverse design of three-dimensional structures. While most efforts have concentrated on the shape of the net, our approach introduces a new design dimension-bond specificity between the edges. We…

Tandem duplication in DNA 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 {\em et al.} (2016) proposed the study of codes that…

The classical branch-and-bound algorithm for the integer feasibility problem has exponential worst case complexity. We prove that it is surprisingly efficient on reformulated problems, in which the columns of the constraint matrix are…

The multi-modal nature of many vision problems calls for neural network architectures that can perform multiple tasks concurrently. Typically, such architectures have been handcrafted in the literature. However, given the size and…

Reversible algorithms are algorithms in which each step represents a partial injective function; they are useful for performance optimization in reversible systems. In this study, using Janus, a reversible imperative high-level programming…