Related papers: Virus-Encoded Ribonucleotide Reductases
Mutations are typically classified by their effects on the nucleotide sequence and by their size. Here, we argue that if our main aim is to understand the effect of mutations on evolutionary outcomes (such as adaptation or speciation), we…
Vision encoders are increasingly used in modern applications, from vision-only models to multimodal systems such as vision-language models. Despite their remarkable success, it remains unclear how these architectures represent features…
{\it Caenorhabditis elegans} nematode worms are the only animals with the known detailed neural connectivity diagram, well characterized genomics, and relatively simple quantifiable behavioral output. With this in mind, many researchers…
In this perspective we address the question: why are proteins seemingly so hard to crystallize? We suggest that this is because of evolutionary negative design, i.e. proteins have evolved not to crystallize, because crystallization, as with…
This article introduces a novel binary representation of the canonical genetic code based on both the structural similarities of the nucleotides, as well as the physicochemical properties of the encoded amino acids. Each of the four mRNA…
Quantum effects are mainly used for the determination of molecular shapes in molecular biology, but quantum information theory may be a more useful tool to understand the physics of life. Organic molecules and quantum circuits/protocols can…
While confirming the long held view that viruses do not closely imitate the use of their host's codon catalogue, Esposito and coworkers nevertheless consider it surprising that, despite having the ability to infect the same host, many…
Prior work has analyzed the robustness of visual encoders to image transformations and corruptions, particularly in cases where such alterations are not seen during training. When this occurs, they introduce a form of distribution shift at…
Hepatitis B virus (HBV) is considered as etiological agent of the lethal liver disease hepatitis B. Globally, hepatitis B is recognized as one of the prevailing infectious diseases with a significant impact on human health. In spite of…
The ongoing effort to detect and characterize physical entanglement in biopolymers has so far established that knots are present in many globular proteins and also abound in viral DNA packaged inside bacteriophages. RNA molecules, on the…
This paper addresses the decomposition of biochemical networks into functional modules that preserve their dynamic properties upon interconnection with other modules, which permits the inference of network behavior from the properties of…
Viral infection requires the binding of receptors on the target cell membrane to glycoproteins, or ``spikes,'' on the viral membrane. The initial entry is usually classified as fusogenic or endocytotic. However, binding of viral spikes to…
Multiscale mathematical models of hepatitis C infection have been instrumental in our understanding of direct acting antivirals. These models include the mechanisms driving intracellular viral production and explicitly model the…
Viruses and their hosts are involved in an 'arms race' where they continually evolve mechanisms to overcome each other. It has long been proposed that intrinsic disorder provides a substrate for the evolution of viral hijack functions and…
During a fight between viruses and anti-viruses it is not always predictable that the anti-virus is going to win. There are many malicious viruses which target to attack and paralyze the anti-viruses. It is necessary for an anti-virus to…
This methods paper presents computational protocols for the identification of non-coding RNA genes or RNA motifs within genomic sequences. An application to bacterial small RNA is proposed.
Biological nanomachines are nanometer-size macromolecular complexes that catalyze chemical reactions in the presence of substrate molecules. The catalytic functions carried out by such nanomachines in the cytoplasm, and biological membranes…
The structural flexibility of nucleic acids plays a key role in many fundamental life processes, such as gene replication and expression, DNA-protein recognition, and gene regulation. To obtain a thorough understanding of nucleic acid…
In this paper, we address the problem of real-time detection of viruses docking to nanowires, especially when multiple viruses dock to the same nano-wire. The task becomes more complicated when there is an array of nanowires coated with…
Proteins are essential components of living systems, capable of performing a huge variety of tasks at the molecular level, such as recognition, signalling, copy, transport, ... The protein sequences realizing a given function may largely…