Related papers: Towards Automated Design of Riboswitches
Designing RNA molecules has garnered recent interest in medicine, synthetic biology, biotechnology and bioinformatics since many functional RNA molecules were shown to be involved in regulatory processes for transcription, epigenetics and…
Artificial RNA molecules with novel functionality have many applications in synthetic biology, pharmacy and white biotechnology. The de novo design of such devices using computational methods and prediction tools is a resource-efficient…
While RNA technologies hold immense therapeutic potential in a range of applications from vaccination to gene editing, the broad implementation of these technologies is hindered by the challenge of delivering these agents effectively. Lipid…
RNA design aims to identify RNA sequences that fold into a target secondary structure. This task is challenging in terms of computational efficiency. Most existing methods focus on either minimum free energy (MFE)-based or ensemble-based…
In this paper the TileShuffle method is evaluated as a search method for candidate lncRNAs at 8q24.2. The method is run on three microarrays. Microarrays which all contained the same sample and repeated copies of tiled probes. This allows…
Accurate RNA structure modeling remains difficult because RNA backbones are highly flexible, non-canonical interactions are prevalent, and experimentally determined 3D structures are comparatively scarce. We introduce \emph{RiboSphere}, a…
Ribonucleic acid (RNA) binds to molecules to achieve specific biological functions. While generative models are advancing biomolecule design, existing methods for designing RNA that target specific ligands face limitations in capturing…
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…
Designing RNA sequences that reliably adopt specified three-dimensional structures while maintaining thermodynamic stability remains challenging for synthetic biology and therapeutics. Current inverse folding approaches optimize for…
The emergence of the Next Generation Sequencing increases drastically the volume of transcriptomic data. Although many standalone algorithms and workflows for novel microRNA (miRNA) prediction have been proposed, few are designed for…
RNA design, the task of finding a sequence that folds into a target secondary structure, has broad biological and biomedical impact but remains computationally challenging due to the exponentially large sequence space and exponentially many…
Screening is a time-consuming and labour-intensive yet required task for medical systematic reviews, as tens of thousands of studies often need to be screened. Prioritising relevant studies to be screened allows downstream systematic review…
High-throughput screening, in which multiwell plates are used to test large numbers of compounds against specific targets, is widely used across many areas of the biological sciences and most prominently in drug discovery. We propose a…
The problem of RNA secondary structure design (also called inverse folding) is the following: given a target secondary structure, one aims to create a sequence that folds into, or is compatible with, a given structure. In several practical…
The effectiveness of the machine learning methods for real-world tasks depends on the proper structure of the modeling pipeline. The proposed approach is aimed to automate the design of composite machine learning pipelines, which is…
Nanotechnology and synthetic biology currently constitute one of the most innovative, interdisciplinary fields of research, poised to radically transform society in the 21st century. This paper concerns the synthetic design of ribonucleic…
Practical use of neural networks often involves requirements on latency, energy and memory among others. A popular approach to find networks under such requirements is through constrained Neural Architecture Search (NAS). However, previous…
Design of de novo biological sequences with desired properties, like protein and DNA sequences, often involves an active loop with several rounds of molecule ideation and expensive wet-lab evaluations. These experiments can consist of…
The task of RNA design given a target structure aims to find a sequence that can fold into that structure. It is a computationally hard problem where some version(s) have been proven to be NP-hard. As a result, heuristic methods such as…
Motivation: RNA design aims to find RNA sequences that fold into a given target secondary structure, a problem also known as RNA inverse folding. However, not all target structures are designable. Recent advances in RNA designability have…