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Understanding to what extent stem cell potential is a cell-intrinsic property, or an emergent behavior coming from global tissue dynamics and geometry, is a key outstanding question of systems and stem cell biology. Here, we propose a…
Collective biological systems display power laws for macroscopic quantities and are fertile probing grounds for statistical physics. Besides power laws, natural insect swarms present strong scale-free correlations, suggesting closeness to…
The vast majority of biological sequences encode unknown functions and bear little resemblance to experimentally characterized proteins, limiting both our understanding of biology and our ability to harness functional potential for the…
Protein structure prediction often hinges on multiple sequence alignments (MSAs), which underperform on low-homology and orphan proteins. We introduce PLAME, a lightweight MSA design framework that leverages evolutionary embeddings from…
Nonlinear coupling between inter- and intra-element dynamics appears as a collective behaviour of elements. The elements in this paper denote symptoms such as a bacterium having an internal network of genes and proteins, a reactive droplet,…
Cooperation is a major factor in the evolution of human societies. The structure of human social networks, which affects the dynamics of cooperation and other interpersonal phenomena, have common structural signatures. One of these…
Autism spectrum disorder (ASD) is one of the most significant neurological disorders that disrupt a person's social communication skills. The progression and development of neuroimaging technologies has made structural network construction…
Recently described stochastic models of protein evolution have demonstrated that the inclusion of structural information in addition to amino acid sequences leads to a more reliable estimation of evolutionary parameters. We present a…
Recent breakthroughs in computer vision and natural language processing have spurred interest in challenging multi-modal tasks such as visual question-answering and visual dialogue. For such tasks, one successful approach is to condition…
We introduce a data-driven epistatic model of protein evolution, capable of generating evolutionary trajectories spanning very different time scales reaching from individual mutations to diverged homologs. Our in silico evolution…
Despite their vast morphological diversity, many invertebrates have similar larval forms characterized by ciliary bands, innervated arrays of beating cilia that facilitate swimming and feeding. Hydrodynamics suggests that these bands should…
Scaffolding is an important subproblem in "de novo" genome assembly in which mate pair data are used to construct a linear sequence of contigs separated by gaps. Here we present SLIQ, a set of simple linear inequalities derived from the…
It is well-known that intrinsically disordered proteins (IDP) are highly dynamic, which is related to their functionality in various biological processes. However, the characterization of the intricate structures of IDP has been a…
The automatic design of robots has existed for 30 years but has been constricted by serial non-differentiable design evaluations, premature convergence to simple bodies or clumsy behaviors, and a lack of sim2real transfer to physical…
We investigate a randomly evolving process of subgraphs in an underlying host graph using the spectral theory of semigroups related to the Tsetlin library and hyperplane arrangements. Starting with some initial subgraph, at each iteration,…
The presence of functional diversity within a group has been demonstrated to lead to greater robustness, higher performance and increased problem-solving ability in a broad range of studies that includes insect groups, human groups and…
There are diverse mechanisms driving the evolution of social networks. A key open question dealing with understanding their evolution is: How various preferential linking mechanisms produce networks with different features? In this paper we…
Though biological and artificial complex systems having inhibitory connections exhibit high degree of clustering in their interaction pattern, the evolutionary origin of clustering in such systems remains a challenging problem. Using…
Swimming cells and microorganisms must often move though complex fluids that contain an immersed microstructure such as polymer molecules, or filaments. In many important biological processes, such as mammalian reproduction and bacterial…
Self-assembly of proteins into amyloid aggregates is an important biological phenomenon associated with human diseases such as Alzheimer's disease. Amyloid fibrils also have potential applications in nano-engineering of biomaterials. The…