Related papers: Distribution of phenotype sizes in sequence-to-str…
Summary: Genotype networks are a method used in systems biology to study the innovability of a given phenotype, determining whether the phenotype is robust to mutations, and how do the genotypes associated to it are distributed in the…
Geometric and structural constraints greatly restrict the selection of folds adapted by protein backbones, and yet, folded proteins show an astounding diversity in functionality. For structure to have any bearing on function, it is thus…
Phenotypically structured equations arise in population biology to describe the interaction of species with their environment that brings the nutrients. This interaction usually leads to selection of the fittest individuals. Models used in…
For much of biology, the manner in which genotype maps to phenotype remains a fundamental mystery. The few maps that are known tend to show modular pleiotropy: sets of phenotypes are determined by distinct sets of genes. One key map that…
Feature models are widely used to capture the configuration space of software systems. Although automated reasoning has been studied for detecting problematic features and supporting configuration tasks, significantly less attention has…
Networks of elastic fibers are ubiquitous in biological systems and often provide mechanical stability to cells and tissues. Fiber reinforced materials are also common in technology. An important characteristic of such materials is their…
Nuclear segmentation is an important step for profiling aberrant regions of histology sections. However, segmentation is a complex problem as a result of variations in nuclear geometry (e.g., size, shape), nuclear type (e.g., epithelial,…
Populations are heterogeneous, deviating in numerous ways. Phenotypic diversity refers to the range of traits or characteristics across a population, where for cells this could be the levels of signalling, movement and growth activity, etc.…
We study how correlations in the random fitness assignment may affect the structure of fitness landscapes. We consider three classes of fitness models. The first is a continuous phenotype space in which individuals are characterized by a…
Motivation: RNA design aims to find RNA sequences that fold into a given target secondary structure, a problem also known as RNA inverse folding. However, not all target structures are designable. Recent advances in RNA designability have…
A fundamental aspect of biological information processing is the ubiquity of sequence-function relationships -- functions that map the sequence of DNA, RNA, or protein to a biochemically relevant activity. Most sequence-function…
The association of a given human phenotype to a genetic variant remains a critical challenge for biology. We present a novel system called PhenoLinker capable of associating a score to a phenotype-gene relationship by using heterogeneous…
Chemotaxis-driven invasions have been proposed across a broad spectrum of biological processes, from cancer to ecology. The influential system of equations introduced by Keller and Segel has proven a popular choice in the modelling of such…
For the vast majority of naturally occurring, small, single domain proteins folding is often described as a two-state process that lacks detectable intermediates. This observation has often been rationalized on the basis of a nucleation…
Proteins are macromolecules that mediate a significant fraction of the cellular processes that underlie life. An important task in bioengineering is designing proteins with specific 3D structures and chemical properties which enable…
Phenomenological models are highly effective tools for forecasting disease dynamics using real world data, particularly in scenarios where detailed knowledge of disease mechanisms is limited. However, their reliability depends on the model…
Using an off-lattice model, we fully enumerate folded conformations of polypeptide chains of up to N = 19 monomers. Structures are found to differ markedly in designability, defined as the number of sequences with that structure as a unique…
A nucleotide sequence 35 base pairs long can take 1,180,591,620,717,411,303,424 possible values. An example of systems biology datasets, protein binding microarrays, contain activity data from about 40000 such sequences. The discrepancy…
Determination of sizes and flexibilities of RNA molecules is important in understanding the nature of packing in folded structures and in elucidating interactions between RNA and DNA or proteins. Using the coordinates of the structures of…
Sequencing by synthesis is used in many next-generation DNA sequencing technologies. Some of the technologies, especially those exploring the principle of single-molecule sequencing, allow incomplete nucleotide incorporation in each cycle.…