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This paper surveys foundation models for AI-enabled biological design, focusing on recent developments in applying large-scale, self-supervised models to tasks such as protein engineering, small molecule design, and genomic sequence design.…
We propose a mathematical model of DNA self-assembly using 2D tiles to form 3D nanostructures. This is the first work to combine studies in self-assembly and nanotechnology in 3D, just as Rothemund and Winfree did in the 2D case. Our model…
Deep neural networks (DNN) have achieved unprecedented performance in computer-vision tasks almost ubiquitously in business, technology, and science. While substantial efforts are made to engineer highly accurate architectures and provide…
There is a concerted effort to build domain-general artificial intelligence in the form of universal neural network models with sufficient computational flexibility to solve a wide variety of cognitive tasks but without requiring…
The potential of synthetic biology techniques for designing complex cellular circuits able to solve complicated computations opens a whole domain of exploration, beyond experiments and theory. Such cellular circuits could be used to carry…
The genome sequence contains the blueprint for governing cellular processes. While the availability of genomes has vastly increased over the last decades, experimental annotation of the various functional, non-coding and regulatory elements…
Creating autonomous, self-supporting, self-replicating, sustainable systems is a great challenge. To some extent, understanding life means not only being able to create it from scratch, but also improving, supporting, saving it, or even…
In this report a framework for the collection of clinical images and data for use when training and validating artificial intelligence (AI) tools is described. The report contains not only information about the collection of the images and…
This paper presents our computational methodology using Genetic Algorithms (GA) for exploring the nature of RNA editing. These models are constructed using several genetic editing characteristics that are gleaned from the RNA editing system…
In [1], the authors proposed a new model of DNA storage system that integrates all three steps of retrieval and introduced the concept of DNA-correcting codes, which guarantees that the output of the storage system can be decoded to the…
DNA-based storage is an emerging technology that enables digital information to be archived in DNA molecules. This method enjoys major advantages over magnetic and optical storage solutions such as exceptional information density, enhanced…
DNA pattern matching is essential for many widely used bioinformatics applications. Disease diagnosis is one of these applications, since analyzing changes in DNA sequences can increase our understanding of possible genetic diseases. The…
The deep Convolutional Neural Network (CNN) is the state-of-the-art solution for large-scale visual recognition. Following basic principles such as increasing the depth and constructing highway connections, researchers have manually…
The Human Genome Project has led to an exponential increase in data related to the sequence, structure, and function of biomolecules. Bioinformatics is an interdisciplinary research field that primarily uses computational methods to analyze…
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…
Fabrication of DNA nanostructures primarily follows two fundamental rules. First, DNA oligonucleotides mutually combine by Watson-Crick base pairing rules between complementary base sequences. Second, the geometrical compatibility of the…
The escalating cost, extended timelines, and low success rates in pharmaceutical research demand a fundamental rethinking of biotechnology R&D infrastructure. This chapter introduces the concept of the AI-Integrated Biotechnology Hub, a…
The Artificial Neural network is a functional imitation of simplified model of the biological neurons and their goal is to construct useful computers for real world problems. The ANN applications have increased dramatically in the last few…
Radiology reports remain the primary mechanism by which imaging findings are communicated to clinical teams. However, much of the structured information behind these reports, including measurements, image evidence, prior comparisons, lesion…
Governance efforts for artificial intelligence (AI) are taking on increasingly more concrete forms, drawing on a variety of approaches and instruments from hard regulation to standardisation efforts, aimed at mitigating challenges from…