Related papers: Punctuated evolution of influenza virus neuraminid…
Motivated by observations in sequence data of herpesviruses, we introduce a multi-locus model for the joint evolution of different genotypes in a virus population that is distributed across a population of hosts. In the model, virus…
Recently, an elegant approach in phylogenetics was introduced by Billera-Holmes-Vogtmann that allows a systematic comparison of different evolutionary histories using the metric geometry of tree spaces. In many problem settings one…
In temperate climates, infection rates of enveloped viruses peak during the winter. While these seasonal trends are established in influenza and human coronaviruses, the mechanisms driving the variation remain poorly understood and thus…
Reputed intractable, the question of the origin of viruses has long been neglected. In the modern literature 'Virus evolution' has come to refer to study more akin to population genetics, such as the world-wide scrutiny on new polymorphisms…
We investigate three aspects of aerosol-mediated air-borne viral infection mechanisms on different length and time scales. First, we address the evolution of the size distribution of a non-interacting ensemble of droplets that are subject…
Protein-protein interactions (PPIs) between a virus and its host govern infection, replication, and pathogenesis. While high-throughput mapping has identified thousands of virus-host associations, much of the virus-host interactome remains…
Viruses like influenza have long coevolved with host immune systems, gradually shaping the evolutionary trajectory of these pathogens. Host immune systems develop immunity against circulating strains, which in turn avoid extinction by…
Protein function depends on both protein structure and amino acid (aa) sequence. Here we show that modular features of both structure and function can be quantified from the aa sequences alone for the small (40,42 aa) plaque-forming amyloid…
Background: The pandemic of influenza A (H1N1) is a serious on-going global public crisis. Understanding its spreading dynamics is of fundamental importance for both public health and scientific researches. Recent studies have focused…
The influenza pandemic of 1918-1919 killed at least 50 million people. The reasons why this pandemic was so deadly remain largely unknown. However, It has been shown that the 1918 viral hemagglutinin allows to reproduce the hallmarks of the…
The influenza/H1N1 virus has caused hazard in the public health of many countries. Hence, existing influenza drugs could not cope with H1N1 infection due to the high mutation rate of the virus. In this respect, new method to block the virus…
RNA viruses are a widely used tool to study evolution experimentally. Many standard protocols of virus propagation and competition are done at nominally low multiplicity of infection (m.o.i.), but lead during one passage to two or more…
The innate immune system in insects consists of a conserved core signaling network and rapidly diversifying effector and recognition components, often containing a high proportion of taxonomically-restricted genes. In the absence of…
Recent studies reveal even the smallest genomes such as viruses evolve through complex and stochastic processes, and the assumption of independent alleles is not valid in most applications. Advances in sequencing technologies produce…
Intermittent density fluctuations of nucleotide molecules (adenine, guanine, cytosine and thymine) along DNA sequences are studied in the framework of a hierarchical structure (HS) model originally proposed for the study of fully developed…
Multivalent virus binding inhibitors are a promising new class of antivirals, preventing virus infection of cells by inhibiting the first step in the viral infection cycle - binding of viruses to the cell surface. The design of multivalent…
In this article, we focus on the analysis of the potential factors driving the spread of influenza, and possible policies to mitigate the adverse effects of the disease. To be precise, we first invoke discrete Fourier transform (DFT) to…
Language models have advanced sequence analysis, yet DNA foundation models often lag behind task-specific methods for unclear reasons. We present AntigenLM, a generative DNA language model pretrained on influenza genomes with intact,…
Mechanisms of immunity, and of the host-pathogen interactions in general are among the most fundamental problems of medicine, ecology, and evolution studies. Here, we present a microscopic, protein-level, sequence-based model of immune…
The unfolding of pandemic influenza A(H1N1) for Fall 2009 in the Northern Hemisphere is still uncertain. Plans for vaccination campaigns and vaccine trials are underway, with the first batches expected to be available early October. Several…