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MicroRNAs (miRNAs) and transcription factors control eukaryotic cell proliferation, differentiation, and metabolism through their specific gene regulatory networks. However, differently from transcription factors, our understanding of the processes regulat ...
Numerous methods have been developed for inference of gene regulatory networks from expression data, however, their strengths and weaknesses remain poorly understood. Accurate and systematic evaluation of these methods is hampered by the difficulty of cons ...
Engineering of large-scale metabolic pathways to maximize production of a certain substance or to minimize creation of undesired chemicals require explicit information about the underlying enzyme kinetics. Unfortunately, such information is frequently not ...
Reinforcement Learning (RL) is an approach for training agent's behavior through trial-and-error interactions with a dynamic environment. An important problem of RL is that in large domains an enormous number of decisions are to be made. Hence, instead of ...
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The development of Statistical Total Correlation Spectroscopy (STOCSY), a representation of the autocorrelation matrix of a spectral data set as a 2D pseudospectrum, has allowed more reliable assignment of one- and two-dimensional NMR spectra acquired from ...
Within systems biology there is an increasing interest in the stochastic behaviour of biochemical reaction networks. An appropriate stochastic description is provided by the chemical master equation, which represents a continuous-time Markov chain (CTMC). ...
In this paper, we present an approach capable of extracting insights on ecosystem organization from merely occurrence (presence/absence) data. We extrapolate to the collective behavior by encapsulating some simplifying assumptions within a given set of con ...
Micro-electrode array (MEA) technology has been exploited as a powerful tool for providing distributed information on learning, memory and information processing in cultured neuronal tissue, enabling an experimental perspective from the single cell level u ...
Network models have been used to study the underlying processes and principles of biological systems for decades, providing many insights into the complexity of life. Biological systems require a constant flow of free energy to drive these processes that o ...
Recent years have seen advances in building large internet-scale index structures, generally known as structured overlays. Early structured overlays realized distributed hash tables (DHTs) which are ill suited for anything but exact queries. The need to su ...