Related papers: Virus-Encoded Ribonucleotide Reductases
There has been a recent explosion of computer vision models which perform many tasks and are composed of an image encoder (usually a ViT) and an autoregressive decoder (usually a Transformer). However, most of this work simply presents one…
In order to prevent detection and evade signature-based scanning methods, which are normally exploited by antivirus software, metamorphic viruses use several various obfuscation approaches. They transform their code in new instances as look…
Ribonucleic acid (RNA) plays fundamental roles in biological systems, from carrying genetic information to performing enzymatic function. Understanding and designing RNA can enable novel therapeutic application and biotechnological…
Modelising the translation errors by suitable mathematical operators in the crystal basis model of the genetic code and requiring that codons prone to be misread encode the same amino-acid, the main features of the organisation in…
We develop a stochastic model for the programmed frameshift of ribosomes synthesizing a protein while moving along a mRNA template. Normally the reading frame of a ribosome decodes successive triplets of nucleotides on the mRNA in a…
As I compress on the canvas of a few pages here major results of my research on the retinoblastoma tumor suppressor protein (RB) spreading over the past 15 years, an exciting picture emerges on this unique host molecule which surpasses in…
We present the discriminative recurrent sparse auto-encoder model, comprising a recurrent encoder of rectified linear units, unrolled for a fixed number of iterations, and connected to two linear decoders that reconstruct the input and…
Networks coming from protein-protein interactions, transcriptional regulation, signaling, or metabolism may appear to have "unusual" properties. To quantify this, it is appropriate to randomize the network and test the hypothesis that the…
Evolution of genetic code is studied as the change in the choice of enzymes that are used to synthesize amino acids from the genetic information of nucleic acids. We propose the following theory: the differentiation of physiological states…
Many {\it ribosomes} simultaneously move on the same messenger RNA (mRNA), each synthesizing separately a copy of the same protein. In contrast to the earlier models, here {\it we develop a ``unified'' theoretical model} that not only…
This paper presents the Ensemble Nucleotide Byte-level Encoder-Decoder (ENBED) foundation model, analyzing DNA sequences at byte-level precision with an encoder-decoder Transformer architecture. ENBED uses a sub-quadratic implementation of…
In this paper we show that living cells can multiplex biochemical signals, i.e. transmit multiple signals through the same signaling pathway simultaneously, and yet respond to them very specifically. We demonstrate how two binary input…
Enzyme is the major workhorse to carry out the diverse cellular functions. It catalyzes the biological reactions with a high specificity, with its topology playing a crucial role. For ecologically safe production of numerous bioproducts…
Restricted Boltzmann Machines are simple yet powerful neural networks. They can be used for learning structure in data, and are used as a building block of more complex neural architectures. At the same time, their simplicity makes them…
In recent years, substantial advancements have been achieved in understanding the diversity of the human virome and its intricate roles in human health and diseases. Despite this progress, the field of human virome research remains nascent,…
Generative processes in biology and other fields often produce data that can be regarded as resulting from a composition of basic features. Here we present an unsupervised method based on autoencoders for inferring these basic features of…
Tremendous effort has been given to the development of diagnostic tests, preventive vaccines, and therapeutic medicines for coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Much of…
Understanding the pathways by which viral capsid proteins assemble around their genomes could identify key intermediates as potential drug targets. In this work we use computer simulations to characterize assembly over a wide range of…
Living cells provide a fluctuating, out-of-equilibrium environment in which genes must coordinate cellular function. DNA looping, which is a common means of regulating transcription, is very much a stochastic process; the loops arise from…
Chromatin remodeling machineries are abundant and diverse in eukaryotic cells. They have been involved in a variety of situations such as histone exchange and DNA repair, but their importance in gene expression remains unclear. Although the…