Related papers: Cell fate reprogramming by control of intracellula…
This paper deals with gene networks whose dynamics is assumed to be generated by a continuous-time, linear, time invariant, finite dimensional system (LTI) at steady state. In particular, we deal with the problem of network reconstruction…
This paper proposes a control strategy for a Reverse Fuel Cell used to manage a Renewable Energy Community. A two-stage scenario-based Model Predictive Control algorithm is designed to define the best economic strategy to be followed during…
Recent evidence suggests that nongenetic (epigenetic) mechanisms play an important role at all stages of cancer evolution. In many cancers, these mechanisms have been observed to induce dynamic switching between two or more cell states,…
Cancers remain the lead cause of disease-related, pediatric death in North America. The emerging field of complex systems has redefined cancer networks as a computational system with intractable algorithmic complexity. Herein, a tumor and…
Gene regulatory networks (GRNs) orchestrate cellular decision making and survival strategies. Inferring the structure of these networks from high-dimensional transcriptomics data is a central challenge in systems biology. Traditional…
Like distributed systems, biological multicellular processes are subject to dynamic changes and a biological system will not pass the survival-of-the-fittest test unless it exhibits certain features that enable fast recovery from these…
All stem cell fate transitions, including the metabolic reprogramming of stem cells and the somatic reprogramming of fibroblasts into pluripotent stem cells, can be understood from a unified theoretical model of cell fates. Each cell fate…
Effective therapy of complex diseases requires control of highly non-linear complex networks that remain incompletely characterized. In particular, drug intervention can be seen as control of signaling in cellular networks. Identification…
Following antigen stimulation, the net outcomes of a T cell response are shaped by integrated signals from both positive co-stimulatory and negative regulatory molecules. Recently, the blockade of negative regulatory molecules (i.e. immune…
The understanding of molecular cell biology requires insight into the structure and dynamics of networks that are made up of thousands of interacting molecules of DNA, RNA, proteins, metabolites, and other components. One of the central…
This paper addresses the problem of controlling the temporal dynamics of complex nonlinear network-coupled dynamical systems, specifically in terms of neurodynamics. Based on the Lyapunov direct method, we derive a control strategy with…
We review a recent trend in computational systems biology which aims at using pattern recognition algorithms to infer the structure of large-scale biological networks from heterogeneous genomic data. We present several strategies that have…
In this thesis we present the novel semi-supervised network-based algorithm P-Net, which is able to rank and classify patients with respect to a specific phenotype or clinical outcome under study. The peculiar and innovative characteristic…
To meet ongoing cognitive demands, the human brain must seamlessly transition from one brain state to another, in the process drawing on different cognitive systems. How does the brain's network of anatomical connections help facilitate…
The study of network structure has uncovered signatures of the organization of complex systems. However, there is also a need to understand how to control them; for example, identifying strategies to revert a diseased cell to a healthy…
Predictive modeling of the evolutionary dynamics of cancer is a challenge issue in computational cancer biology. In this paper, we propose a general mathematical model framework for the evolutionary dynamics of cancer with plasticity and…
We propose a novel method of reconstructing the topology and interaction functions for a general oscillator network. An ensemble of initial phases and the corresponding instantaneous frequencies is constructed by repeating random…
Cellular responses to death-promoting stimuli typically proceed through a differentiated multistage process, involving a lag phase, extensive death, and potential adaptation. Deregulation of this chain of events is at the root of many…
A cell can be seen as an adaptive autonomous agent or as a society of adaptive autonomous agents, where each can exhibit a particular behaviour depending on its cognitive capabilities. We present an intracellular signalling model obtained…
Many modern networks are \emph{reconfigurable}, in the sense that the topology of the network can be changed by the nodes in the network. For example, peer-to-peer, wireless and ad-hoc networks are reconfigurable. More generally, many…