相关论文: Neutral evolution of model proteins: diffusion in …
The site frequency spectrum (SFS) is a widely used summary statistic of genomic data. Motivated by recent evidence for the role of neutral evolution in cancer, we investigate the SFS of neutral mutations in an exponentially growing…
In the course of evolution, proteins undergo important changes in their amino acid sequences, while their three-dimensional folded structure and their biological function remain remarkably conserved. Thanks to modern sequencing techniques,…
We review the task of aligning simple models for language dynamics with relevant empirical data, motivated by the fact that this is rarely attempted in practice despite an abundance of abstract models. We propose that one way to meet this…
We study the coupled dynamics of primary and secondary structure formation (i.e. slow genetic sequence selection and fast folding) in the context of a solvable microscopic model that includes both short-range steric forces and and…
Biological diversity has evolved despite the essentially infinite complexity of protein sequence space. We present a hierarchical approach to the efficient searching of this space and quantify the evolutionary potential of our approach with…
One of the first successes of neutral ecology was to predict realistically-broad distributions of rare and abundant species. However, it has remained an outstanding theoretical challenge to describe how this distribution of abundances…
We study in detail a recently proposed simple discrete model for evolution on smooth landscapes. An asymptotic solution of this model for long times is constructed. We find that the dynamics of the population are governed by correlation…
Protein folding and evolution are intimately linked phenomena. Here, we revisit the concept of exons as potential protein folding modules across 38 abundant and conserved protein families. Taking advantage of genomic exon-intron…
Inverse protein folding is challenging due to its inherent one-to-many mapping characteristic, where numerous possible amino acid sequences can fold into a single, identical protein backbone. This task involves not only identifying viable…
The diffusion equation is extended by including spatial-temporal memory in such a manner that the conservation of the concentration is maintained. The additional memory term gives rise to the formation of non-trivial stationary solutions.…
Protein sequences are believed to have been selected to provide the stability of, and reliable renaturation to, an encoded unique spatial fold. In recently proposed theoretical schemes, this selection is modeled as ``minimal frustration,''…
Information networks are ubiquitous and are ideal for modeling relational data. Networks being sparse and irregular, network embedding algorithms have caught the attention of many researchers, who came up with numerous embeddings algorithms…
Consider a mathematical model of evolutionary adaptation of fitness landscape and mutation matrix as a reaction to population changes. As a basis, we use an open quasispecies model, which is modified to include explicit death flow. We…
We propose a model that explains the hierarchical organization of proteins in fold families. The model, which is based on the evolutionary selection of proteins by their native state stability, reproduces patterns of amino acids conserved…
Biological networks have evolved to be highly functional within uncertain environments while remaining extremely adaptable. One of the main contributors to the robustness and evolvability of biological networks is believed to be their…
When modeling network data using a latent position model, it is typical to assume that the nodes' positions are independently and identically distributed. However, this assumption implies the average node degree grows linearly with the…
We study genetic networks that produce many species of non-coding RNA molecules that are present at a moderate density, as typically exists in the cell. The associations of the many species of these RNA are modeled physically, taking into…
Determining the different conformational states of a protein and the transition paths between them is key to fully understanding the relationship between biomolecular structure and function. This can be accomplished by sampling protein…
Understanding the principles of protein folding is a cornerstone of computational biology, with implications for drug design, bioengineering, and the understanding of fundamental biological processes. Lattice protein folding models offer a…
The protein folding problem must ultimately be solved on all length scales from the atomic up through a hierarchy of complicated structures. By analyzing the stability of the folding process using physics and mathematics, this paper shows…