Related papers: A Molecular Model for Communication through a Secr…
How proteins fold remains a central unsolved problem in biology. While the idea of a folding code embedded in the amino acid sequence was introduced more than 6 decades ago, this code remains undefined. While we now have powerful predictive…
We must recognize that natural language is a way of information encoding, and it encodes not only the information but also the procedures for how information is processed. To understand natural language, the same as we conceive and design…
Recent technological advancements in data acquisition tools allowed life scientists to acquire multimodal data from different biological application domains. Broadly categorized in three types (i.e., sequences, images, and signals), these…
DNA as a data storage medium has several advantages, including far greater data density compared to electronic media. We propose that schemes for data storage in the DNA of living organisms may benefit from studying the reconstruction…
This groundbreaking research extracted DNA from petroleum using nanoparticle affinity bead technology, yielding 3,159,020 petroleum DNA (pDNA) sequences, primarily environmental DNA. While most original in situ DNA (oriDNA) was lost,…
DNA exhibits remarkable potential as a data storage solution due to its impressive storage density and long-term stability, stemming from its inherent biomolecular structure. However, developing this novel medium comes with its own set of…
We study the amount of reliable information that can be stored in a DNA-based storage system with noisy sequencing, where each codeword is composed of short DNA molecules. We analyze a concatenated coding scheme, where the outer code is…
Over the past years, the ever-growing trend on data storage demand, more specifically for "cold" data (i.e. rarely accessed), has motivated research for alternative systems of data storage. Because of its biochemical characteristics,…
The paper explores a novel methodology in source code obfuscation through the application of text-based recurrent neural network (RNN) encoder-decoder models in ciphertext generation and key generation. Sequence-to-sequence models are…
Programming languages are engineered languages that allow to instruct a machine and share algorithmic information; they have a great influence on the society since they underlie almost every information technology artefact, and they are at…
Scientists across disciplines write code for critical activities like data collection and generation, statistical modeling, and visualization. As large language models that can generate code have become widely available, scientists may…
Composite DNA is a recent method to increase the base alphabet size in DNA-based data storage.This paper models synthesizing and sequencing of composite DNA and introduces coding techniques to correct substitutions, losses of entire…
We show that our recently published Arithmetic Model of the genetic code based on Godel Encoding is robust against symmetry transformations, specially Rumer s one U > G, A > C, and constitutes a link between the degeneracy structure and the…
Many proofs in discrete mathematics and theoretical computer science are based on the probabilistic method. To prove the existence of a good object, we pick a random object and show that it is bad with low probability. This method is…
The possible role of quantum effects in transfer of genetic information is studied. It's argued that the nucleotides selection during DNA replication is performed by means of proton tunneling between nucleotide and DNA-polimerase bound by…
Molecular communication, as implied by its name, uses molecules as information carriers for communication between objects. It has an advantage over traditional electromagnetic-wave-based communication in that molecule-based systems could be…
This paper is dealing with DNA cyclic codes which play an important role in DNA computing and have attracted a particular attention in the literature. Firstly, we introduce a new family of DNA cyclic codes over the ring…
Spread codes and cyclic orbit codes are special families of constant dimension subspace codes. These codes have been well-studied for their error correction capability, transmission rate and decoding methods, but the question of how to…
A hypothesis of the evolution of the genetic code is proposed, the leading mechanism of which is the nucleotide spontaneous damage leading to AT-enrichment of the genome. The hypothesis accounts for stability of the genetic code towards…
With different genomes available, unsupervised learning algorithms are essential in learning genome-wide biological insights. Especially, the functional characterization of different genomes is essential for us to understand lives. In this…