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The relaxation dynamics of many disordered systems, such as structural glasses, proteins, granular materials or spin glasses, is not completely frozen even at very low temperatures. This residual motion leads to a change of the properties…
Cells grown in culture act as a model system for analyzing the effects of anticancer compounds, which may affect cell behavior in a cell cycle position-dependent manner. Cell synchronization techniques have been generally employed to…
The study of signatures of aging in terms of genomic biomarkers can be uniquely helpful in understanding the mechanisms of aging and developing models to accurately predict the age. Prior studies have employed gene expression and DNA…
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…
Any organism is embedded in an environment that changes over time. The timescale for and statistics of environmental change, the precision with which the organism can detect its environment, and the costs and benefits of particular protein…
Cell migration is essential for regulating many biological processes in physiological or pathological conditions, including embryonic development and cancer invasion. In vitro and in silico studies suggest that collective cell migration is…
Statistical properties of environments experienced by biological signaling systems in the real world change, which necessitate adaptive responses to achieve high fidelity information transmission. One form of such adaptive response is gain…
Motility is an essential factor for an organism's survival and diversification. With the advent of novel single-cell technologies, analytical frameworks and theoretical methods, we can begin to probe the complex lives of microscopic motile…
Emerging data analysis involves the ingestion and exploration of new data sets, application of complex functions, and frequent query revisions based on observing prior query answers. We call this new type of analysis evolutionary analytics…
Quantitative Fitness Analysis (QFA) is a high-throughput experimental and computational methodology for measuring the growth of microbial populations. QFA screens can be used to compare the health of cell populations with and without a…
Background: Brain maturation and aging involve significant microstructural changes, resulting in functional and cognitive alterations. Quantitative MRI (qMRI) can measure this evolution, distinguishing the physiological effects of normal…
The antibody repertoire of each individual is continuously updated by the evolutionary process of B cell receptor mutation and selection. It has recently become possible to gain detailed information concerning this process through…
Reconstruction of gene regulatory networks is the process of identifying gene dependency from gene expression profile through some computation techniques. In our human body, though all cells pose similar genetic material but the activation…
How self-organized networks develop, mature and degenerate is a key question for sociotechnical, cyberphysical and biological systems with potential applications from tackling violent extremism through to neurological diseases. So far, it…
Most microorganisms regulate their cell size. We review here some of the mathematical formulations of the problem of cell size regulation. We focus on coarse-grained stochastic models and the statistics they generate. We review the…
The behaviour of gene regulatory networks (GRNs) is typically analysed using simulation-based statistical testing-like methods. In this paper, we demonstrate that we can replace this approach by a formal verification-like method that gives…
We investigate the scaling properties of the Penna model, which has become a popular tool for the study of population dynamics and evolutionary problems in recent years. We find that the model generates a normalised age distribution for…
Biological circuits such as neural or gene regulation networks use internal states to map sensory input to an adaptive repertoire of behavior. Characterizing this mapping is a major challenge for systems biology, and though experiments that…
Recently we have used a cellular automata model which describes the dynamics of a multi-connected network to reproduce the refractory behavior and aging effects obtained in immunization experiments performed with mice when subjected to…
We present a novel machine learning approach to understanding conformation dynamics of biomolecules. The approach combines kernel-based techniques that are popular in the machine learning community with transfer operator theory for…