Boolean modeling in systems biology: an overview of methodology and applications

RS Wang, A Saadatpour, R Albert - Physical biology, 2012 - iopscience.iop.org
Mathematical modeling of biological processes provides deep insights into complex cellular
systems. While quantitative and continuous models such as differential equations have been …

Boolean modeling: a logic‐based dynamic approach for understanding signaling and regulatory networks and for making useful predictions

R Albert, J Thakar - Wiley Interdisciplinary Reviews: Systems …, 2014 - Wiley Online Library
The biomolecules inside or near cells form a complex interacting system. Cellular
phenotypes and behaviors arise from the totality of interactions among the components of …

A state-flipped approach to complete synchronization of Boolean networks

L Du, Z Zhang, C Xia - Applied Mathematics and Computation, 2023 - Elsevier
State flipping is an effective control method that has just recently been proposed. In this
paper, the state-flipped mechanism is introduced to implement the complete synchronization …

A systems biology perspective on plant–microbe interactions: biochemical and structural targets of pathogen effectors

L Pritchard, P Birch - Plant Science, 2011 - Elsevier
Plants have biochemical defences against stresses from predators, parasites and
pathogens. In this review we discuss the interaction of plant defences with microbial …

State–time spectrum of signal transduction logic models

A MacNamara, C Terfve, D Henriques… - Physical …, 2012 - iopscience.iop.org
Despite the current wealth of high-throughput data, our understanding of signal transduction
is still incomplete. Mathematical modeling can be a tool to gain an insight into such …

Network model of immune responses reveals key effectors to single and co-infection dynamics by a respiratory bacterium and a gastrointestinal helminth

J Thakar, AK Pathak, L Murphy, R Albert… - PLoS computational …, 2012 - journals.plos.org
Co-infections alter the host immune response but how the systemic and local processes at
the site of infection interact is still unclear. The majority of studies on co-infections …

Logic modeling in quantitative systems pharmacology

P Traynard, L Tobalina, F Eduati… - CPT …, 2017 - Wiley Online Library
Here we present logic modeling as an approach to understand deregulation of signal
transduction in disease and to characterize a drug's mode of action. We discuss how to build …

[图书][B] PlantOmics: the omics of plant science

D Barh, MS Khan, E Davies - 2015 - Springer
The book consists of 29 chapters written by 90 experts from 15 countries that represent three-
fourths of the globe. In the introductory chapter (Chap. 1), Dr. Agrawal and colleagues have …

Computational and experimental analysis reveals a requirement for eosinophil-derived IL-13 for the development of allergic airway responses in C57BL/6 mice

ER Walsh, J Thakar, K Stokes, F Huang… - The Journal of …, 2011 - journals.aai.org
Eosinophils are found in the lungs of humans with allergic asthma, as well as in the lungs of
animals in models of this disease. Increasing evidence suggests that these cells are integral …

A node-pinning and state-flipped approach to partial synchronization of Boolean Networks

L Du, Z Zhang, C Xia - Nonlinear Analysis: Hybrid Systems, 2024 - Elsevier
In this paper, the partial synchronization of general Boolean Networks is studied from the
perspective of nodes and states by using the semi-tensor product of matrices. First, by …