Related papers: The energy-spectrum of bicompatible sequences
The relationship between sequences and secondary structures or shapes in RNA exhibits robust statistical properties summarized by three notions: (1) the notion of a typical shape (that among all sequences of fixed length certain shapes are…
Ribonucleic acid (RNA) binds to molecules to achieve specific biological functions. While generative models are advancing biomolecule design, existing methods for designing RNA that target specific ligands face limitations in capturing…
RNA secondary structure is an important computational model to understand how genetic variation maps into phenotypic (structural) variation. Evolutionary innovation in RNA structures is facilitated by neutral networks, large connected sets…
Natural protein sequences contain a record of their history. A common constraint in a given protein family is the ability to fold to specific structures, and it has been shown possible to infer the main native ensemble by analyzing…
The kinetic folding of RNA sequences into secondary structures is modeled as a complex adaptive system, the components of which are possible RNA structural rearrangements (SRs) and their associated bases and base pairs. RNA bases and base…
Motivation: DNA data is transcribed into single-stranded RNA, which folds into specific molecular structures. In this paper we pose the question to what extent sequence- and structure-information correlate. We view this correlation as…
RNA co-transcriptional folding has long been suspected to play an active role in helping proper native folding of ribozymes and structured regulatory motifs in mRNA untranslated regions. Yet, the underlying mechanisms and coding…
Accurate RNA structure modeling remains difficult because RNA backbones are highly flexible, non-canonical interactions are prevalent, and experimentally determined 3D structures are comparatively scarce. We introduce \emph{RiboSphere}, a…
We view the folding of RNA-sequences as a map that assigns a pattern of base pairings to each sequence, known as secondary structure. These preimages can be constructed as random graphs (i.e. the neutral networks associated to the structure…
An essential quantity to ensure evolvability of populations is the navigability of the genotype space. Navigability relies on the existence of sufficiently large genotype networks, that is ensembles of sequences with the same phenotype that…
Recently, a framework considering RNA sequences and their RNA secondary structures as pairs, led to some information-theoretic perspectives on how the semantics encoded in RNA sequences can be inferred. In this context, the pairing arises…
Genetic sequences are known to possess non-trivial composition together with symmetries in the frequencies of their components. Recently, it has been shown that symmetry and structure are hierarchically intertwined in DNA, suggesting a…
Background: A metabolic genotype comprises all chemical reactions an organism can catalyze via enzymes encoded in its genome. A genotype is viable in a given environment if it is capable of producing all biomass components the organism…
Rhythmic activities that alternate between coherent and incoherent phases are ubiquitous in chemical, ecological, climate, or neural systems. Despite their importance, general mechanisms for their emergence are little understood. In order…
We discuss the transition paths in a coupled bistable system consisting of interacting multiple identical bistable motifs. We propose a simple model of coupled bistable gene circuits as an example, and show that its transition paths are…
In evolution, the effects of a single deleterious mutation can sometimes be compensated for by a second mutation which recovers the original phenotype. Such epistatic interactions have implications for the structure of genome space -…
Biological systems must be robust for stable function against perturbations, but robustness alone is not sufficient. The ability to switch between appropriate states (phenotypes) in response to different conditions is essential for…
Riboswitches, RNA elements found in the untranslated region, regulate gene expression by binding to target metaboloites with exquisite specificity. Binding of metabolites to the conserved aptamer domain allosterically alters the…
The number of protein structures is far less than the number of sequences. By imposing simple generic features of proteins (low energy and compaction) on all possible sequences we show that the structure space is sparse compared to the…
Unstoppable feedback loops and tipping points in socio-ecological systems are the main threats to sustainability. These behaviors have been extensively studied, notably to predict, and arguably deviate, dead-end trajectories. Behind the…