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A wealth of new research has highlighted the critical roles of small RNAs (sRNAs) in diverse processes such as quorum sensing and cellular responses to stress. The pathways controlling these processes often have a central motif comprising…
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…
MicroRNAs (miRNAs) are endogenous 22-nucleotide RNAs, which suppress gene expression by selectively binding to the 3-noncoding region of specific message RNAs through base-pairing. Given the diversity and abundance of miRNA targets, miRNAs…
As deep neural network (NN) methods have matured, there has been increasing interest in deploying NN solutions to "edge computing" platforms such as mobile phones or embedded controllers. These platforms are often resource-constrained,…
This paper aims to discuss and analyze the potentialities of Recurrent Neural Networks (RNN) in control design applications. The main families of RNN are considered, namely Neural Nonlinear AutoRegressive eXogenous, (NNARX), Echo State…
This paper proposes a Recurrent Neural Network (RNN) controller for lane-keeping systems, effectively handling model uncertainties and disturbances. First, quadratic constraints cover the nonlinearities brought by the RNN controller, and…
Dynamical systems in biology are complex, and one often does not have comprehensive knowledge about the interactions involved. Chemical reaction network (CRN) inference aims to identify, from observing species concentrations over time, the…
Gene regulatory networks typically have low in-degrees, whereby any given gene is regulated by few of the genes in the network. What mechanisms might be responsible for these low in-degrees? Starting with an accepted framework of the…
Pre-mRNA splicing relies on the poorly understood dynamic interplay between >150 protein components of the spliceosome. The steps at which splicing can be regulated remain largely unknown. We systematically analyzed the effect of knocking…
The ribosomal density along the coding region of the mRNA molecule affect various fundamental intracellular phenomena including: protein production rates, organismal fitness, ribosomal drop off, and co-translational protein folding. Thus,…
Neurons communicate with downstream systems via sparse and incredibly brief electrical pulses, or spikes. Using these events, they control various targets such as neuromuscular units, neurosecretory systems, and other neurons in connected…
Inferring functional relationships within complex networks from static snapshots of a subset of variables is a ubiquitous problem in science. For example, a key challenge of systems biology is to translate cellular heterogeneity data…
Complex dynamical systems are often modeled as networks, with nodes representing dynamical units which interact through the network's links. Gene regulatory networks, responsible for the production of proteins inside a cell, are an example…
Identifying the nodes that have the potential to influence the state of a network is a relevant question for many complex systems. In many applications it is often essential to test the ability of an individual node to control a specific…
The question of controllability of natural and man-made network systems has recently received considerable attention. In the context of the human brain, the study of controllability may not only shed light into the organization and function…
We advance our approach of analyzing the dynamics of interacting complex systems with the nonlinear dynamics of interacting nonlinear elements. We replace the widely used lattice-like connection topology of cellular neural networks (CNN) by…
Robust control theory has been successfully applied to numerous real-world problems using a small set of devices called {\it controllers}. However, the real systems represented by networks contain unreliable components and modern robust…
Distributed software-defined networks (SDN), consisting of multiple inter-connected network domains, each managed by one SDN controller, is an emerging networking architecture that offers balanced centralized control and distributed…
Networks of the brain are composed of a very large number of neurons connected through a random graph and interacting after random delays that both depend on the anatomical distance between cells. In order to comprehend the role of these…