Related papers: Epigenetic landscapes explain partially reprogramm…
Cells are known to sense and respond to their mechanical microenvironment in profound ways. Various evidence has implicated the adhesome, a body of adhesion associated proteins, in several cell fate decisions, including differentiation and…
Epigenetics is a driving force of important and ubiquitous phenomena in nature such as cell differentiation or even metamorphosis. Oppositely to its widespread role, understanding the biophysical principles that allow epigenetics to control…
Evolution is a dynamic process. The two classical forces of evolution are mutation and selection. Assuming small mutation rates, evolution can be predicted based solely on the fitness differences between phenotypes. Predicting an…
Metadynamics, a member of the `flat histogram' class of advanced sampling algorithms, has been widely used in molecular simulations to drive the exploration of states separated by high free energy barriers and promote comprehensive sampling…
The concept of a fitness landscape is a powerful metaphor that offers insight into various aspects of evolutionary processes and guidance for the study of evolution. Until recently, empirical evidence on the ruggedness of these landscapes…
In mathematical phylogenetics, evolutionary relationships are often represented by trees and networks. The latter are typically used whenever the relationships cannot be adequately described by a tree, which happens when so-called…
Ensemble methods such as random forests have transformed the landscape of supervised learning, offering highly accurate prediction through the aggregation of multiple weak learners. However, despite their effectiveness, these methods often…
Phylogenetic networks represent evolutionary history of species and can record natural reticulate evolutionary processes such as horizontal gene transfer and gene recombination. This makes phylogenetic networks a more comprehensive…
Understanding the origins of complexity is a fundamental challenge with implications for biological and technological systems. Network theory emerges as a powerful tool to model complex systems. Networks are an intuitive framework to…
Phylogenetic trees are widely used to display estimates of how groups of species evolved. Each phylogenetic tree can be seen as a collection of clusters, subgroups of the species that evolved from a common ancestor. When phylogenetic trees…
Rooted phylogenetic networks provide an explicit representation of the evolutionary history of a set $X$ of sampled species. In contrast to phylogenetic trees which show only speciation events, networks can also accommodate reticulate…
Predicting river flow in places without streamflow records is challenging because basins respond differently to climate, terrain, vegetation, and soils. Traditional basin attributes describe some of these differences, but they cannot fully…
We present a statistical method for complex energy landscape exploration which provides information on the metastable states--or valleys--actually explored by an unperturbed aging process following a quench. Energy fluctuations of record…
The concept of potential energy landscapes is applied in many areas of science. We experimentally realize a random potential energy landscape (rPEL) to which colloids are exposed. This is achieved exploiting the interaction of matter with…
As Evolutionary Dynamics moves from the realm of theory into application, algorithms are needed to move beyond simple models. Yet few such methods exist in the literature. Ecological and physiological factors are known to be central to…
Sequence modelling approaches for epigenetic profile prediction have recently expanded in terms of sequence length, model size, and profile diversity. However, current models cannot infer on many experimentally feasible tissue and assay…
We introduce and study a model which admits a complex landscape without containing quenched disorder. Continuing our previous investigation we introduce a disordered model which allows us to reconstruct all the main features of the original…
Many cellular processes involve information processing and decision making. We can probe these processes at increasing molecular detail. The analysis of heterogeneous data remains a challenge that requires new ways of thinking about cells…
As the amount and complexity of genetic information increases it is necessary that we explore some efficient ways of handling these data. This study takes the "divide and conquer" approach for analyzing high dimensional genomic data. Our…
A model of multicellular systems with several types of cells is developed from the phase field model. The model is presented as a set of partial differential equations of the field variables, each of which expresses the shape of one cell.…