Related papers: Viral Dark Matter: Illuminating Protein Function, …
Motivation: Viruses represent the most abundant biological entities on the planet and play vital roles in diverse ecosystems. Cataloging viruses across various environments is essential for understanding their properties and functions.…
Pangenome variation graphs (PVGs) allow for the representation of genetic diversity in a more nuanced way than traditional reference-based approaches. Here we focus on how PVGs are a powerful tool for studying genetic variation in viruses,…
Dark matter constitutes $26\%$ of the total energy in our universe, but its nature remains elusive. Among the assortment of viable dark matter candidates, particles and fields with masses lighter than $40 \mathrm{eV}$, called ultralight…
The explosion in known microbial diversity in the last two decades has made it abundantly clear that microbes in the environment do not exist in isolation; they are members of communities. Accordingly, omics approaches such as metagenomics…
Identifying viral pathogens and characterizing their transmission is essential to developing effective public health measures in response to a pandemic. Phylogenetics, though currently the most popular tool used to characterize the likely…
Background: Representing biological networks as graphs is a powerful approach to reveal underlying patterns, signatures, and critical components from high-throughput biomolecular data. However, graphs do not natively capture the multi-way…
Proteins are the fundamental macromolecules that play diverse and crucial roles in all living matter and have tremendous implications in healthcare, manufacturing, and biotechnology. Their functions are largely determined by the sequences…
Living systems are made of active materials with microscopic components that work together to perform macroscopic biological tasks. The breakdown of these collective functionalities leads to diseases, which, conversely, could be treated by…
Activity and autonomous motion are fundamental aspects of many living and engineering systems. Here, the scale of biological agents covers a wide range, from nanomotors, cytoskeleton, and cells, to insects, fish, birds, and people. Inspired…
Significant fraction (98.5% in humans) of most animal genomes is non- coding dark matter. Its largely unknown function (1-5) is related to programming (rather than to spontaneous mutations) of accurate adaptation to rapidly changing…
Viruses utilize various means to circumvent the immune detection in the biological systems. Several mathematical models have been investigated for the description of viral dynamics in the biological system of human and various other…
Viral infections are causing significant morbidity and mortality worldwide. Understanding the interaction patterns between a particular virus and human proteins plays a crucial role in unveiling the underlying mechanism of viral infection…
Motivation: As viruses that mainly infect bacteria, phages are key players across a wide range of ecosystems. Analyzing phage proteins is indispensable for understanding phages' functions and roles in microbiomes. High-throughput sequencing…
Proteins are responsible for the most diverse set of functions in biology. The ability to extract information from protein sequences and to predict the effects of mutations is extremely valuable in many domains of biology and medicine.…
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…
A fundamental question for evolutionary biology is why rates of evolution vary dramatically between proteins. Perhaps surprisingly, it is controversial how much a protein's functional importance affects its rate of evolution. In most…
Viruses are submicroscopic agents that can infect all kinds of lifeforms and use their hosts' living cells to replicate themselves. Despite having some of the simplest genetic structures among all living beings, viruses are highly…
One of the major challenges of modern physics is to decipher the nature of dark matter. Astrophysical observations provide ample evidence for the existence of an invisible and dominant mass component in the observable universe, from the…
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…
The microbiome constitutes a complex microbial ecology of interacting components that regulates important pathways in the host. Measurements of microbial abundances are key to learning the intricate network of interactions amongst microbes.…