相关论文: Category theoretic analysis of hierarchical protei…
Complex hierarchical structures composed of simple nanoscale building blocks form the basis of most biological materials. Here we demonstrate how analogies between seemingly different fields enable the understanding of general principles by…
In this paper we introduce the olog, or ontology log, a category-theoretic model for knowledge representation (KR). Grounded in formal mathematics, ologs can be rigorously formulated and cross-compared in ways that other KR models (such as…
Structural hierarchy, in which materials possess distinct features on multiple length scales, is ubiquitous in nature; diverse biological materials, such as bone, cellulose, and muscle, have as many as ten hierarchical levels. Structural…
Networks have become a key approach to understanding systems of interacting objects, unifying the study of diverse phenomena including biological organisms and human society. One crucial step when studying the structure and dynamics of…
Network representations of systems from various scientific and societal domains are neither completely random nor fully regular, but instead appear to contain recurring structural building blocks. These features tend to be shared by…
We introduce the relational ontology log, or relational olog, a knowledge representation system based on the category of sets and relations. It is inspired by Spivak and Kent's olog, a recent categorical framework for knowledge…
Understanding how genes interact and relate to each other is a fundamental question in biology. However, current practices for describing these relationships, such as drawing diagrams or graphs in a somewhat arbitrary manner, limit our…
A major issue in biology is the understanding of the interactions between proteins. These interactions can be described by a network, where the proteins are modeled by nodes and the interactions by edges. The origin of these protein…
Molecular interactions have widely been modelled as networks. The local wiring patterns around molecules in molecular networks are linked with their biological functions. However, networks model only pairwise interactions between molecules…
Proteins are an important class of biomolecules that serve as essential building blocks of the cells. Their three-dimensional structures are responsible for their functions. In this thesis we have investigated the protein structures using a…
Recent computational advances in the accurate prediction of protein three-dimensional (3D) structures from amino acid sequences now present a unique opportunity to decipher the interrelationships between proteins. This task entails--but is…
Context-dependent nature of biological phenomena are well documented in every branch of biology. While there have been few previous attempts to (implicitly) model various facets of biological context-dependence, a formal and general…
Proteins are biomolecules of life. They fold into a great variety of three-dimensional (3D) shapes. Underlying these folding patterns are many recurrent structural fragments or building blocks (analogous to `LEGO bricks'). This paper…
The arrangements of particles and forces in granular materials have a complex organization on multiple spatial scales that ranges from local structures to mesoscale and system-wide ones. This multiscale organization can affect how a…
Proteins are inherently multiscale physical systems whose functional properties emerge from coordinated structural organization across multiple spatial resolutions, ranging from atomic interactions to global fold topology. However, existing…
Networks have in recent years emerged as an invaluable tool for describing and quantifying complex systems in many branches of science. Recent studies suggest that networks often exhibit hierarchical organization, where vertices divide into…
Background: If biology is modular then clusters, or communities, of proteins derived using only protein interaction network structure should define protein modules with similar biological roles. We investigate the link between biological…
Protein structures can be studied as complex networks of interacting amino acids. We study proteins of different structural classes from the network perspective. Our results indicate that proteins, regardless of their structural class, show…
Analogical reasoning depends fundamentally on the ability to learn and generalize about relations between objects. We develop an approach to relational learning which, given a set of pairs of objects…
Since proteins carry out biological processes by interacting with other proteins, analyzing the structure of protein-protein interaction (PPI) networks could explain complex biological mechanisms, evolution, and disease. Similarly, studying…