相关论文: On the Number of Control Nodes of Threshold and XO…

This paper studies the minimum control node set problem for Boolean networks (BNs) with degree constraints. The main contribution is to derive the nontrivial lower and upper bounds on the size of the minimum control node set through…

This paper focuses on proposing a general control framework for large-scale Boolean networks (\texttt{BNs}). Only by the network structure, the concept of structural controllability for \texttt{BNs} is formalized. A necessary and sufficient…

A Boolean network (BN) is called observable if any initial state can be uniquely determined from the output sequence. In the existing literature on observability of BNs, there is almost no research on the relationship between the number of…

Regulatory networks (RNs) are a well-accepted modelling formalism in computational systems biology. The control of RNs is currently receiving a lot of attention because it provides a computational basis for cell reprogramming -- an…

Biological processes, including cell differentiation, organism development, and disease progression, can be interpreted as attractors (fixed points or limit cycles) of an underlying networked dynamical system. In this paper, we study the…

Boolean networks (BNs) are discrete-time systems where nodes are inter-connected (here we call such connection rule among nodes as network structure), and the dynamics of each gene node is determined by logical functions. In this paper, we…

We investigate to what extent the degree sequence of a directed network constrains the number of driver nodes. We develop a pair of algorithms that take a directed degree sequence as input and aim to output a network with the maximum or…

Boolean control networks (BCNs) are discrete-time dynamical systems with Boolean state-variables and inputs that are interconnected via Boolean functions. BCNs are recently attracting considerable interest as computational models for…

Boolean threshold networks have recently been proposed as useful tools to model the dynamics of genetic regulatory networks, and have been successfully applied to describe the cell cycles of \textit{S. cerevisiae} and \textit{S. pombe}.…

Effective control of biological systems can often be achieved through the control of a surprisingly small number of distinct variables. We bring clarity to such results using the formalism of Boolean dynamical networks, analyzing the…

Given a conjunctive Boolean network (CBN) with $n$ state-variables, we consider the problem of finding a minimal set of state-variables to directly affect with an input so that the resulting conjunctive Boolean control network (CBCN) is…

Using a graph-theoretic approach, we derive a new sufficient condition for observability of a Boolean control network (BCN). Based on this condition, we describe two algorithms: the first selects a set of nodes so that observing this set…

Control problem in a biological system is the problem of finding an interventional policy for changing the state of the biological system from an undesirable state, e.g. disease, into a desirable healthy state. Boolean networks are utilized…

Boolean networks are dynamical models of disease development in which the activation levels of genes are represented by binary variables. Given a Boolean network, controls represent mutations or medical treatments that fix the activation…

Binarization of gene expression data is a \textbf{critical prerequisite} for the synthesis of Boolean gene regulatory network (GRN) models from omics datasets. Because Boolean networks encode gene activity as binary variables, the accuracy…

The aim of this paper is to characterize an important class of marked digraphs, called structurally observable graphs (SOGs), and to solve two minimum realization problems. To begin with, by exploring structural observability of large-scale…

This paper is concerned with the problem of stochastic control of gene regulatory networks (GRNs) observed indirectly through noisy measurements and with uncertainty in the intervention inputs. The partial observability of the gene states…

Gene regulatory networks (GRNs) are increasingly used for explaining biological processes with complex transcriptional regulation. A GRN links the expression levels of a set of genes via regulatory controls that gene products exert on one…

Gene regulatory networks can be successfully modeled as Boolean networks. A much discussed hypothesis says that such model networks reproduce empirical findings the best if they are tuned to operate at criticality, i.e. at the borderline…

The problem of controllability of the dynamical state of a network is central in network theory and has wide applications ranging from network medicine to financial markets. The driver nodes of the network are the nodes that can bring the…