Related papers: RNA as a Permutation
We introduce a novel approach for inferring natural preconditions from code. Our technique produces preconditions of high quality in terms of both correctness (modulo a test generator) and naturalness. Prior works generate preconditions…
We introduce a novel fully convolutional neural network (FCN) architecture for predicting the secondary structure of ribonucleic acid (RNA) molecules. Interpreting RNA structures as weighted graphs, we employ deep learning to estimate the…
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…
The field of RNA secondary structure prediction has made significant progress with the adoption of deep learning techniques. In this work, we present the RNAformer, a lean deep learning model using axial attention and recycling in the…
We describe a dynamic programming algorithm for predicting optimal RNA secondary structure, including pseudoknots. The algorithm has a worst case complexity of ${\cal O}(N^6)$ in time and ${\cal O}(N^4)$ in storage. The description of the…
We have presented some arguments to substantiate the usefulness of neural replicator analysis (NRA) for constructing variants of the natural binomial classification of virus genomes based only on knowledge of their complete genomic…
In this paper we derive the generating function of RNA structures with pseudoknots. We enumerate all $k$-noncrossing RNA pseudoknot structures categorized by their maximal sets of mutually intersecting arcs. In addition we enumerate…
Analysis of the sequence-structure relationship in RNA molecules are essential to evolutionary studies but also to concrete applications such as error-correction methodologies in sequencing technologies. The prohibitive sizes of the…
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…
In this paper, we consider the problem of designing DNA sequences (codewords) for DNA storage systems and DNA computing that are unlikely to fold back onto themselves to form undesirable secondary structures. The paper addresses both the…
In this paper we model several simple biochemical operations on RNA molecules that modify their secondary structure by means of a suitable variation of Gro\ss e-Rhode's Algebra Transformation Systems.
Using machine learning, especially deep learning, to facilitate biological research is a fascinating research direction. However, in addition to the standard classification or regression problems, in bioinformatics, we often need to predict…
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…
RNA virus populations will undergo processes of mutation and selection resulting in a mixed population of viral particles. High throughput sequencing of a viral population subsequently contains a mixed signal of the underlying clones. We…
The Ribonucleic Acid (RNA) inverse folding problem, designing nucleotide sequences that fold into specific tertiary structures, is a fundamental computational biology problem with important applications in synthetic biology and…
RNA function is tied to secondary structure, operating through dynamic and heterogeneous structural ensembles. While current analysis tools typically output single static structures or averaged contact maps, chemical probing methods like…
Background: RNA exhibits a variety of structural configurations. Here we consider a structure to be tantamount to the noncrossing Watson-Crick and \pairGU-base pairings (secondary structure) and additional cross-serial base pairs. These…
Molecular structures of RNA molecules reconstructed from X-ray crystallography frequently contain errors. Motivated by this problem we examine clustering on a torus since RNA shapes can be described by dihedral angles. A previously…
This is a companion draft to paper 'Software Clustering: Unifying Syntactic and Semantic Features', in proceedings of the 19th Working Conference on Reverse Engineering (WCRE 2012). It discusses the clustering process in detail, which…
Prediction of protein secondary structure from the amino acid sequence is a classical bioinformatics problem. Common methods use feed forward neural networks or SVMs combined with a sliding window, as these models does not naturally handle…