Related papers: Forest structure in epigenetic landscapes
Successful biological development via spatial regulation of cell differentiation relies on action of multiple signaling molecules that are known as morphogens. It is now well established that signaling molecules create non-uniform…
Cells often exhibit different and stable phenotypes from the same DNA sequence. Robustness and plasticity of such cellular states are controlled by diverse transcriptional and epigenetic mechanisms, among them the modification of…
In molecular phylogeny, relationships among organisms are reconstructed using DNA or protein sequences and are displayed as trees. A linear increase in the number of sequences results in an exponential increase of possible trees. Thus,…
A geophylogeny is a phylogenetic tree (or dendrogram) where each leaf (e.g. biological taxon) has an associated geographic location (site). To clearly visualize a geophylogeny, the tree is typically represented as a crossing-free drawing…
The hierarchical organisation of cell identity is a fundamental feature of animal development with rich and well-characterized experimental phenomenology, yet the mechanisms driving its emergence remain unknown. The regulation of cell…
Inferring the structure of gene regulatory networks (GRN) from gene expression data has many applications, from the elucidation of complex biological processes to the identification of potential drug targets. It is however a notoriously…
Neuronal morphology is essential for studying brain functioning and understanding neurodegenerative disorders. As acquiring real-world morphology data is expensive, computational approaches for morphology generation have been studied.…
Natural slender structures, such as plant leaves, petals, and tendrils, often exhibit complex three-dimensional (3D) morphologies-including twisting, helical coiling, and saddle-bending-driven by differential growth. The resulting internal…
Cities emerged independently across different world regions and historical periods, raising fundamental questions: How did the first urban settlements develop? What social and spatial conditions enabled their emergence? Are these processes…
A fundamental question in neuroscience is how structure and function of neural systems are related. We study this interplay by combining a familiar auto-associative neural network with an evolving mechanism for the birth and death of…
This study presents the approach to analyzing the evolution of an arbitrary complex system whose behavior is characterized by a set of different time-dependent factors. The key requirement for these factors is only that they must contain an…
Rhizomes play fundamental roles in plant evolution, persistence, and environmental adaptation by enabling clonal propagation, resource storage, and stress resilience. Despite their ecological and agronomic importance across diverse plant…
Multicellular organisms exhibit a high degree of structural organization with specific cell types always occurring in characteristic locations. The conventional framework for describing the emergence of such consistent spatial patterns is…
Regulatory networks consist of interacting molecules with a high degree of mutual chemical specificity. How can these molecules evolve when their function depends on maintenance of interactions with cognate partners and simultaneous…
Although accumulation of molecular damage is suggested to be an important molecular mechanism of aging, a quantitative link between the dynamics of damage accumulation and mortality of species has so far remained elusive. To address this…
Orthologous genes, which arise through speciation, play a key role in comparative genomics and functional inference. In particular, graph-based methods allow for the inference of orthology estimates without prior knowledge of the underlying…
Arabidopsis thaliana is an important model organism for understanding the genetics and molecular biology of plants. Its highly selfing nature, together with other important features, such as small size, short generation time, small genome…
Phylogenetic tree shapes capture fundamental signatures of evolution. We consider ``ranked'' tree shapes, which are equipped with a total order on the internal nodes compatible with the tree graph. Recent work has established an elegant…
Understanding the dynamics of genome rearrangements is a major issue of phylogenetics. Phylogenetics is the study of species evolution. A major goal of the field is to establish evolutionary relationships within groups of species, in order…
This paper proposes an original theory of aging of multicellular organisms. The cells of multicellular organisms, in contrast to unicellular organisms, are burdened with a two- part genome: housekeeping and specialized (multicellular),…