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A central question in computational neuroscience is whether the learning rule used to train a neural network determines how well its internal representations align with those of the human visual cortex. We present a systematic comparison of…
Implicit neural representation (INR) methods for video compression have recently achieved visual quality and compression ratios that are competitive with traditional pipelines. However, due to the need for per-sample network training, the…
Stem cells can precisely and robustly undergo cellular differentiation and lineage commitment, referred to as stemness. However, how the gene network underlying stemness regulation reliably specifies cell fates is not well understood. To…
Discoveries of endogenous human stem cell-associated retroviruses (SCARs) revealed consistent activation of specific endogenous retroviral elements in human preimplantation embryos and documented the essential role of the sustained…
Non-coding RNAs are crucial regulators of gene expression in prokaryotes and eukaryotes, but it remains poorly understood how they affect the dynamics of transcriptional networks. We analyzed the temporal characteristics of the…
We introduce a minimal multiscale framework that links within-host virus dynamics to population-level SIRS epidemiology through explicit, bidirectional coupling. At the microscopic layer, a two variant quasispecies (master and mutant…
Single-stranded RNA viruses efficiently encapsulate their genome into a protein shell called the capsid. Electrostatic interactions between the positive charges in the capsid protein's N-terminal tail and the negatively charged genome have…
A realistic physical model for the so called rate promoting vibration (RPV) at enzyme action is constructed. The origin of the RPV is assumed to be an oscillating electric field produced by long-lived localized vibrational modes in protein…
Mendelian randomization (MR) is a popular instrumental variable (IV) approach, in which one or several genetic markers serve as IVs that can sometimes be leveraged to recover valid inferences about a given exposure-outcome causal…
Although several synonymous codons can encode the same aminoacid, this symmetry is generally broken in natural genetic systems. In this article, we show that the symmetry breaking can result from selective pressures due to the violation of…
The clear transparency of Deep Neural Networks (DNNs) is hampered by complex internal structures and nonlinear transformations along deep hierarchies. In this paper, we propose a new attribution method, Relative Sectional Propagation (RSP),…
The eukaryotic protein synthesis process entails intricate stages governed by diverse mechanisms to tightly regulate translation. Translational regulation during stress is pivotal for maintaining cellular homeostasis, ensuring the accurate…
We investigate the evolution of Boolean networks subject to a selective pressure which favors robustness against noise, as a model of evolved genetic regulatory systems. By mapping the evolutionary process into a statistical ensemble and…
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infectivity is a major concern in coronavirus disease 2019 (COVID-19) prevention and economic reopening. However, rigorous determination of SARS-COV-2 infectivity is essentially…
The novel coronavirus (2019-nCoV) has been declared to be a new international health emergence and no specific drug has been yet identified. Several methods are currently being evaluated such as protease and glycosylated spike (S) protein…
Finding out statistically significant words in DNA and protein sequences forms the basis for many genetic studies. By applying the maximal entropy principle, we give one systematic way to study the nonrandom occurrence of words in DNA or…
In this letter we study the full semi-conservative treatment of a model for the co-evolution of a virus and an adaptive immune system. Regions of viability are calculated for both conservatively and semi-conservatively replicating viruses…
We have presented some arguments to substantiate the usefulness of neural replicator analysis (NRA) for constructing variants of the natural binomial classification of virus genomes based only on knowledge of their complete genomic…
Newcastle Disease Virus (NDV), classified as Avian orthoavulavirus 1 (avian paramyxovirus type 1), is a promising oncolytic agent that selectively targets and destroys cancer cells while sparing normal tissues. Its oncoselectivity exploits…
A single gene can encode for different protein versions through a process called alternative splicing. Since proteins play major roles in cellular functions, aberrant splicing profiles can result in a variety of diseases, including cancers.…