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We examined protein residue networks (PRNs) from a local search perspective to understand why PRNs are highly clustered when having short paths is important for protein functionality. We found that by adopting a local search perspective,…
We explore the interplay between the protein-protein interactions network and the expression of the interacting proteins. It is shown that interacting proteins are expressed in significantly more similar cellular concentrations. This is…
Understanding protein sequences is vital and urgent for biology, healthcare, and medicine. Labeling approaches are expensive yet time-consuming, while the amount of unlabeled data is increasing quite faster than that of the labeled data due…
The adsorption or adhesion of large particles (proteins, colloids, cells, >...) at the liquid-solid interface plays an important role in many diverse applications. Despite the apparent complexity of the process, two features are…
Computational protein-protein interaction (PPI) prediction techniques can contribute greatly in reducing time, cost and false-positive interactions compared to experimental approaches. Sequence is one of the key and primary information of…
Conformation of a protein (CorA) is examined in a matrix with mobile solute constituents as a function of solute-residue interaction strength (f) by a coarse-grained model with a Monte Carlo simulation. Solute particles are found to reach…
Biological networks provide insight into the complex organization of biological processes in a cell at the system level. They are an effective tool for understanding the comprehensive map of functional interactions, finding the functional…
The properties of certain networks are determined by hidden variables that are not explicitly measured. The conditional probability (propagator) that a vertex with a given value of the hidden variable is connected to k of other vertices…
RNA, whose functionality is largely determined by its structure, plays an important role in many biological activities. The prediction of pairwise structural proximity between each nucleotide of an RNA sequence can characterize the…
Sequential activation of neurons is a common feature of network activity during a variety of behaviors, including working memory and decision making. Previous network models for sequences and memory emphasized specialized architectures in…
Machine-learning models that learn from data to predict how protein sequence encodes function are emerging as a useful protein engineering tool. However, when using these models to suggest new protein designs, one must deal with the vast…
Methods to find correlation among variables are of interest to many disciplines, including statistics, machine learning, (big) data mining and neurosciences. Parameters that measure correlation between two variables are of limited utility…
A central challenge in the study of protein evolution is the identification of historic amino acid sequence changes responsible for creating novel functions observed in present-day proteins. To address this problem, we developed a new…
A Profile Mixture Model is a model of protein evolution, describing sequence data in which sites are assumed to follow many related substitution processes on a single evolutionary tree. The processes depend in part on different amino acid…
Here we review the development of protein scaling theory, starting from backgrounds in mathematics and statistical mechanics, and leading to biomedical applications. Evolution has organized each protein family in different ways, but scaling…
Proteins are fundamental biological entities that play a key role in life activities. The amino acid sequences of proteins can be folded into stable 3D structures in the real physicochemical world, forming a special kind of…
Protein interaction networks (PIN) are popular means to visualize the proteome. However, PIN datasets are known to be noisy, incomplete and biased by the experimental protocols used to detect protein interactions. This paper aims at…
Networks describe a variety of interacting complex systems in social science, biology and information technology. Usually the nodes of real networks are identified not only by their connections but also by some other characteristics.…
Given genetic variations and various phenotypical traits, such as Magnetic Resonance Imaging (MRI) features, we consider two important and related tasks in biomedical research: i)to select genetic and phenotypical markers for disease…
Circular permutation connects the N and C termini of a protein and concurrently cleaves elsewhere in the chain, providing an important mechanism for generating novel protein fold and functions. However, their in genomes is unknown because…