Towards control of cellular decision-making networks in the epithelial-to-mesenchymal transition
We present the epithelial-to-mesenchymal transition (EMT) from two perspectives:
experimental/technological and theoretical. We review the state of the current understanding …
experimental/technological and theoretical. We review the state of the current understanding …
Leveraging network structure in nonlinear control
Over the last twenty years, dynamic modeling of biomolecular networks has exploded in
popularity. Many of the classical tools for understanding dynamical systems are unwieldy in …
popularity. Many of the classical tools for understanding dynamical systems are unwieldy in …
Parity and time reversal elucidate both decision-making in empirical models and attractor scaling in critical Boolean networks
We present new applications of parity inversion and time reversal to the emergence of
complex behavior from simple dynamical rules in stochastic discrete models. Our parity …
complex behavior from simple dynamical rules in stochastic discrete models. Our parity …
Minimal frustration underlies the usefulness of incomplete regulatory network models in biology
Regulatory networks as large and complex as those implicated in cell-fate choice are
expected to exhibit intricate, very high-dimensional dynamics. Cell-fate choice, however, is a …
expected to exhibit intricate, very high-dimensional dynamics. Cell-fate choice, however, is a …
A computational model of the endothelial to mesenchymal transition
Endothelial cells (ECs) form the lining of lymph and blood vessels. Changes in tissue
requirements or wounds may cause ECs to behave as tip or stalk cells. Alternatively, they …
requirements or wounds may cause ECs to behave as tip or stalk cells. Alternatively, they …
Pillars of biology: Boolean modeling of gene-regulatory networks
J Thakar - Journal of Theoretical Biology, 2024 - Elsevier
Boolean modeling is a mathematical modeling framework used for defining and studying
gene-regulatory networks (GRNs). It serves as a means to develop mechanistic models …
gene-regulatory networks (GRNs). It serves as a means to develop mechanistic models …
A guard cell abscisic acid (ABA) network model that captures the stomatal resting state
Stomatal pores play a central role in the control of carbon assimilation and plant water
status. The guard cell pair that borders each pore integrates information from environmental …
status. The guard cell pair that borders each pore integrates information from environmental …
Boolean Networks as Predictive Models of Emergent Biological Behaviors
Interacting biological systems at all organizational levels display emergent behavior.
Modeling these systems is made challenging by the number and variety of biological …
Modeling these systems is made challenging by the number and variety of biological …
[图书][B] Boolean Networks as Predictive Models of Emergent Biological Behaviors
Interacting biological systems at all organizational levels display emergent behavior.
Modeling these systems is made challenging by the number and variety of biological …
Modeling these systems is made challenging by the number and variety of biological …
Mapping the attractor landscape of Boolean networks
Boolean networks are popular dynamical models of cellular processes in systems biology.
Their attractors model phenotypes that arise from the interplay of key regulatory subcircuits …
Their attractors model phenotypes that arise from the interplay of key regulatory subcircuits …