Related papers: Virus-Encoded Ribonucleotide Reductases
A novel permutation decoding method for Reed-Muller codes is presented. The complexity and the error correction performance of the suggested permutation decoding approach are similar to that of the recursive lists decoder. It is…
We use a simple construction called `recursive subproducts' (that is known to yield good codes of lengths $n^m$, $n \geq 3$) to identify a family of codes sandwiched between first-order and second-order Reed-Muller (RM) codes. These codes…
The aim of the study is to analyze viruses using parameters obtained from distributions of nucleotide sequences in the viral RNA. Seeking for the input data homogeneity, we analyze single-stranded RNA viruses only. Two approaches are used…
The packaging of genetic material within a protein shell, called the capsid, marks a pivotal step in the life cycle of numerous single-stranded RNA viruses. Understanding how hundreds, or even thousands, of proteins assemble around the…
Computational screening of naturally occurring proteins has the potential to identify efficient catalysts among the hundreds of millions of sequences that remain uncharacterized. Current experimental methods remain time, cost and labor…
Giant viruses contain large genomes, encode many proteins atypical for viruses, replicate in large viral factories, and tend to infect protists. The giant virus replication factories can in turn be infected by so called virophages, which…
Cancer is one of the leading causes of human death. Many efforts have made to understand its mechanism and have further identified many proteins and DNA sequence variations as suspected targets for therapy. However, drugs targeting these…
The molecular network in an organism consists of transcription/translation regulation, protein-protein interactions/modifications and a metabolic network, together forming a system that allows the cell to respond sensibly to the multiple…
Receptor-mediated endocytosis is an ubiquitous process through which cells internalize biological or synthetic nanoscale objects, including viruses, unicellular parasites, and nanomedical vectors for drug or gene delivery. In passive…
Ribonucleic acid (RNA) is involved in many regulatory and catalytic processes in the cell. The function of any RNA molecule is intimately related with its structure. In-line probing experiments provide valuable structural datasets for a…
Probabilistic inference provides a language for describing how organisms may learn from and adapt to their environment. The computations needed to implement probabilistic inference often require specific representations, akin to having the…
Enabling effective brain-computer interfaces requires understanding how the human brain encodes stimuli across modalities such as visual, language (or text), etc. Brain encoding aims at constructing fMRI brain activity given a stimulus.…
Decoding sequences that stem from multiple transmissions of a codeword over an insertion, deletion, and substitution channel is a critical component of efficient deoxyribonucleic acid (DNA) data storage systems. In this paper, we consider a…
The epigenome, i.e. the whole of chromatin modifications, is transferred from mother to daughter cells during cell differentiation. When de novo chromatin modifications (establishment or erasure of, respectively, new or pre-existing DNA…
This paper analyzes the role of neutral viruses in the phenomenon of local immunodeficiency. We show that, even in the absence of altruistic viruses, neutral viruses can support the existence of persistent viruses, and thus local…
A permutation-invariant code on m qubits is a subspace of the symmetric subspace of the m qubits. We derive permutation-invariant codes that can encode an increasing amount of quantum information while suppressing leading order spontaneous…
The ribosome is one of the largest and most complex macromolecular machines in living cells. It polymerizes a protein in a step-by-step manner as directed by the corresponding nucleotide sequence on the template messenger RNA (mRNA) and…
The yearly global production of data is growing exponentially, outpacing the capacity of existing storage media, such as tape and disk, and surpassing our ability to store it. DNA storage - the representation of arbitrary information as…
The emerging field of immunometabolism has underscored the central role of metabolic pathways in orchestrating immune cell function. Far from being passive background processes, metabolic activities actively regulate key immune responses.…
The mechanical properties of DNA play a critical role in many biological functions. For example, DNA packing in viruses involves confining the viral genome in a volume (the viral capsid) with dimensions that are comparable to the DNA…