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Genomic alterations lead to cancer complexity and form a major hurdle for a comprehensive understanding of the molecular mechanisms underlying oncogenesis. In this review, we describe the recent advances in studying cancer-associated genes…

Immune cells learn about their antigenic targets using tactile sense: during recognition, a highly organized yet dynamic motif, named immunological synapse, forms between immune cells and antigen-presenting cells (APCs). Via synapses,…

Cellular ingredient concentrations can be stabilized by adjusting generation and consumption rates through multiple pathways. To explore the portion of cellular metabolism equipped with multiple pathways, we categorize individual metabolic…

Repeat proteins are made with tandem copies of similar amino acid stretches that fold into elongated architectures. Due to their symmetry, these proteins constitute excellent model systems to investigate how evolution relates to structure,…

Cryptic genetic sequences have attenuated effects on phenotypes. In the classic view, relaxed selection allows cryptic genetic diversity to build up across individuals in a population, providing alleles that may later contribute to…

A principle of evolutionary adaptation is applied to the Lotka--Volterra models, in particular to the food webs. We present a relatively simple computational algorithm of optimization with respect to a given criterion. This algorithm boils…

Large sets of genotypes give rise to the same phenotype because phenotypic expression is highly redundant. Accordingly, a population can accept mutations without altering its phenotype, as long as thegenotype mutates into another one on the…

We devise an approach for targeted molecular design, a problem of interest in computational drug discovery: given a target protein site, we wish to generate a chemical with both high binding affinity to the target and satisfactory…

Cellular nuclei recognition serves as a fundamental and essential step in the workflow of digital pathology. However, with disparate source organs and staining procedures among histology image clusters, the scanned tiles inherently conform…

Most complex systems are intrinsically dynamic in nature. The evolution of a dynamic complex system is typically represented as a sequence of snapshots, where each snapshot describes the configuration of the system at a particular instant…

Residue-residue interactions that fold a protein into a unique three-dimensional structure and make it play a specific function impose structural and functional constraints on each residue site. Selective constraints on residue sites are…

How can a microorganism adapt to a variety of environmental conditions despite there exists a limited number of signal transduction machineries? We show that for any growing cells whose gene expression is under stochastic fluctuations,…

This paper concerns applications of genetic algorithms and genetic programming to tasks for which it is difficult to find a representation that does not map to a highly complex and discontinuous fitness landscape. In such cases the standard…

Single atomic sites often determine the functionality and performance of materials, such as catalysts, semi-conductors or enzymes. Computing and understanding the properties of such sites is therefore a crucial component of the rational…

We introduce a new model of evolution on a fitness landscape possessing a tunable degree of neutrality. The model allows us to study the general properties of molecular species undergoing neutral evolution. We find that a number of…

Adaptive networks are a novel class of dynamical networks whose topologies and states coevolve. Many real-world complex systems can be modeled as adaptive networks, including social networks, transportation networks, neural networks and…

A reaction network is a chemical system involving multiple reactions and chemical species. Stochastic models of such networks treat the system as a continuous time Markov chain on the number of molecules of each species with reactions as…

Resistive switches are a class of emerging nanoelectronics devices that exhibit a wide variety of switching characteristics closely resembling behaviors of biological synapses. Assembled into random networks, such resistive switches produce…

Evolutionary dynamics and patterns of molecular evolution are strongly influenced by selection on linked regions of the genome, but our quantitative understanding of these effects remains incomplete. Recent work has focused on predicting…

Many organisms exhibit branching morphologies that twist around each other and become entangled. Entanglement occurs when different objects interlock, creating complex and often irreversible configurations. This physical phenomenon is…