Related papers: An algebraic view of bacterial genome evolution
In the present paper we study some algebraic properties of evolution algebras. Moreover, we reduce the study of evolution algebras of permutations to two special types of evolution algebras, idempotents and absolute nilpotent elements of…
Genome rearrangement distances are an established method in genome comparison. Works in this area may include various rearrangement operations representing large-scale mutations, gene orientation information, the number of nucleotides in…
A problem concerning the shift of roots of a system of homogeneous algebraic equations is investigated. Its conservation and decomposition of a multiple root into simple roots are discussed.
Understanding the rules underlying organismal development is a major unsolved problem in biology. Each cell in a developing organism responds to signals in its local environment by dividing, excreting, consuming, or reorganizing, yet how…
We investigate subshifts with a general algebraic structure and cellular automata on them, with an emphasis on (order-theoretic) lattices. Our main results concern the characterization of Boolean algebraic subshifts, conditions for…
The development of multicellular organisms relies on the precise coordination of molecular events across multiple spatial and temporal scales. Understanding how information flows from molecular interactions to cellular processes and tissue…
We discuss the role coarse-grained models play in the investigation of the structure and thermodynamics of bilayer membranes, and we place them in the context of alternative approaches. Because they reduce the degrees of freedom and employ…
A general theory of the Frolicher-Nijenhuis and Schouten-Nijenhuis brackets in the category of modules over a commutative algebra is described. Some related structures and (co)homology invariants are discussed, as well as applications to…
The rapid development of high-throughput sequencing technologies has led to an explosive increase in biological sequence data, making sequence clustering a fundamental task in large-scale bioinformatics analyses. Unlike traditional…
Antibiotic resistance is a growing public health problem. To gain a fundamental understanding of resistance evolution, a combination of systematic experimental and theoretical approaches is required. Evolution experiments combined with…
In this paper, we define the cohomology of a modified Rota-Baxter Leibniz algebra with coefficients in a suitable representation. As applications of our cohomology, we study formal one-parameter deformations and abelian extensions of…
A topological approach to the study of genetic recombination, based on persistent homology, was introduced by Chan, Carlsson, and Rabad\'an in 2013. This associates a sequence of signatures called barcodes to genomic data sampled from an…
Researchers in the field of biocomputing have, for many years, successfully "harvested and exploited" the natural world for inspiration in developing systems that are robust, adaptable and capable of generating novel and even "creative"…
We study open-ended evolution by focusing on computational and information-processing dynamics underlying major evolutionary transitions. In doing so, we consider biological organisms as hierarchical dynamical systems that generate…
A common trait of complex systems is that they can be represented by means of a network of interacting parts. It is, in fact, the network organisation (more than the parts) what largely conditions most higher-level properties, which are not…
In the biclustering problem, we seek to simultaneously group observations and features. While biclustering has applications in a wide array of domains, ranging from text mining to collaborative filtering, the problem of identifying…
A long-term research proposal on the algebraic structure, the representations and the possible applications of paraparticle algebras is structured in three modules: The first part stems from an attempt to classify the inequivalent gradings…
Globular proteins are expected to assume folds with fixed secondary structures, alpha-helices and beta-sheets. Fold-switching proteins challenge this expectation by remodeling their secondary and/or tertiary structures in response to…
Radical shifts in the genetic composition of large cell populations are rare events with quite low probabilities, which direct numerical simulations generally fail to evaluate accurately. In this paper, we develop a theoretical large…
We survey the notion and history of error-correcting codes and the algorithms needed to make them effective in information transmission. We then give some basic as well as more modern constructions of, and algorithms for, error-correcting…