Related papers: Complete Human Mitochondrial Genome Construction U…
DNA-coated colloids can crystallize into a multitude of lattices, ranging from face-centered cubic to diamond and thereby contribute to our understanding of crystallization and open avenues to producing structures with useful photonic…
Developing high-performance GPU kernels is critical for AI and scientific computing, but remains challenging due to its reliance on expert crafting and poor portability. While LLMs offer promise for automation, both general-purpose and…
More than 1000 complete or near-complete mitochondrial DNA (mtDNA) sequences have been deposited in GenBank for eight common domestic animals (i.e. cattle, dog, goat, horse, pig, sheep, yak and chicken) and their close wild ancestors or…
While large language models (LLMs) have been used for automated grading, they have not yet achieved the same level of performance as humans, especially when it comes to grading complex questions. Existing research on this topic focuses on a…
Proteins are essential components of all living organisms and play a critical role in cellular survival. They have a broad range of applications, from clinical treatments to material engineering. This versatility has spurred the development…
Labeling of DNA molecules is a fundamental technique for DNA visualization and analysis. This process was mathematically modeled in [1], where the received sequence indicates the positions of the used labels. In this work, we develop error…
Deep neural network-based architectures give promising results in various domains including pattern recognition. Finding the optimal combination of the hyper-parameters of such a large-sized architecture is tedious and requires a large…
P-systems are abstract computational models inspired by the phospholipid bilayer membranes generated by biological cells. Illustrated here is a mechanism by which recursive liposome structures (multivesicular liposomes) may be…
Antibodies are versatile proteins that can bind to pathogens and provide effective protection for human body. Recently, deep learning-based computational antibody design has attracted popular attention since it automatically mines the…
DNA, with remarkable properties of high density, durability, and replicability, is one of the most appealing storage media. Emerging DNA storage technologies use composite DNA letters, where information is represented by probability…
A method to construct and count all the linear codes (of arbitrary length) in $\mathbb{F}_{4}$ that are invariant under reverse permutation and that contain the repetition code is presented. These codes are suitable for constructing DNA…
The interactions between DNA, RNA, and proteins are fundamental to biological processes, as illustrated by the central dogma of molecular biology. Although modern biological pre-trained models have achieved great success in analyzing these…
The determination of a patient's DNA sequence can, in principle, reveal an increased risk to fall ill with particular diseases [1,2] and help to design "personalized medicine" [3]. Moreover, statistical studies and comparison of genomes [4]…
In this paper, we review the literature on statistical long-range correlation in DNA sequences. We examine the current evidence for these correlations, and conclude that a mixture of many length scales (including some relatively long ones)…
Neural network potentials (NNPs) enable large-scale molecular dynamics (MD) simulations of systems containing >10,000 atoms with the accuracy comparable to ab initio methods and play a crucial role in material studies. Although NNPs are…
This paper shows how Long Short-term Memory recurrent neural networks can be used to generate complex sequences with long-range structure, simply by predicting one data point at a time. The approach is demonstrated for text (where the data…
We consider the task of detecting regulatory elements in the human genome directly from raw DNA. Past work has focused on small snippets of DNA, making it difficult to model long-distance dependencies that arise from DNA's 3-dimensional…
The rapidly changing landscape of sequencing technologies brings new opportunities to genomics research. Longer sequence reads and higher sequence throughput coupled with ever-improving base accuracy and decreasing per-base cost is now…
Proteins are macromolecules that mediate a significant fraction of the cellular processes that underlie life. An important task in bioengineering is designing proteins with specific 3D structures and chemical properties which enable…
Requiring stability of genetic code against translation errors, modelised by suitable mathematical operators in the crystal basis model of the genetic code, the main features of the organisation in multiplets of the mitochondrial and of the…