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RNA co-transcriptionality, where RNA is spliced or folded during transcription from DNA templates, offers promising potential for molecular programming. It enables programmable folding of nano-scale RNA structures and has recently been…
Machine learning algorithms are everywhere, ranging from simple data analysis and pattern recognition tools used across the sciences to complex systems that achieve super-human performance on various tasks. Ensuring that they are…
DNA microarrays are a relatively new technology that can simultaneously measure the expression level of thousands of genes. They have become an important tool for a wide variety of biological experiments. One of the most common goals of DNA…
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…
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…
Structural DNA nanotechnology has advanced to the extent that extremely complex structures can be designed. Much of this advancement has been due to the development of automated DNA design and simulation tools. Typically, the tools (e.g.…
We consider the problem of storing and retrieving information from synthetic DNA media. The mathematical basis of the problem is the construction and design of sequences that may be discriminated based on their collection of substrings…
Our goal is to build systems which write code automatically from the kinds of specifications humans can most easily provide, such as examples and natural language instruction. The key idea of this work is that a flexible combination of…
Branched junction molecule assembly of DNA nanostructures, pioneered by Seeman's laboratory in the 1980s, has become increasingly sophisticated, as have the assembly targets. A critical design step is finding minimal sets of branched…
DNN pruning reduces memory footprint and computational work of DNN-based solutions to improve performance and energy-efficiency. An effective pruning scheme should be able to systematically remove connections and/or neurons that are…
Nucleic acid sequence design via codon optimization is a fundamental task with applications across synthetic biology, mRNA therapeutics, and vaccine design. Given a target protein, it is a major open challenge to navigate the…
To increase the information capacity of DNA storage, composite DNA letters were introduced. We propose a novel channel model for composite DNA in which composite sequences are decomposed into ordered standard non-composite sequences. The…
Storing data in DNA is being explored as an efficient solution for archiving and in-object storage. Synthesis time and cost remain challenging, significantly limiting some applications at this stage. In this paper we investigate efficient…
Motivation: Gene selection has become a common task in most gene expression studies. The objective of such research is often to identify the smallest possible set of genes that can still achieve good predictive performance. The problem of…
In order to survive, reproduce and (in multicellular organisms) differentiate, cells must control the concentrations of the myriad different proteins that are encoded in the genome. The precision of this control is limited by the inevitable…
The design of genetic networks with specific functions is one of the major goals of synthetic biology. However, constructing biological devices that work "as required" remains challenging, while the cost of uncovering flawed designs…
Structured pruning is an effective approach for compressing large pre-trained neural networks without significantly affecting their performance. However, most current structured pruning methods do not provide any performance guarantees, and…
Embeddings are one of the fundamental building blocks for data analysis tasks. Embeddings are already essential tools for large language models and image analysis, and their use is being extended to many other research domains. The…
Gene Regulatory Networks are networks of interactions in biological organisms responsible for determining the production levels of proteins and peptides. Proteins are workers of a cell factory, and their production defines the goal of a…
RNA motifs typically consist of short, modular patterns that include base pairs formed within and between modules. Estimating the abundance of these patterns is of fundamental importance for assessing the statistical significance of matches…