Abstract
<title>Abstract</title> <p>Boolean networks are widely used to model biological systems, yet a unified framework for understanding and controlling their dynamics has been lacking. Here we introduce a unified framework integrating three complementary control mechanisms: temporal control through update order, structural control through logical update functions and a hybrid strategy combining both. We show that update order alone can generate context-dependent (synchrony-sensitive) attractors without altering network structure, whereas structural control enables the rational design of fixed-point attractors, cyclic attractors and state trajectories through targeted modification of logical functions. The framework further reveals intrinsic dynamical properties of Boolean networks, including the conservation of global attractors across update schemes and the Lyapunov stability of network dynamics. Applications to T-cell and hematopoietic stem cell differentiation, together with benchmark analyses, demonstrate expanded control capabilities and competitive computational performance, providing a general framework for the rational engineering of biological network dynamics.</p>