Boolean modeling in systems biology: an overview of methodology and applications
Mathematical modeling of biological processes provides deep insights into complex cellular
systems. While quantitative and continuous models such as differential equations have been …
systems. While quantitative and continuous models such as differential equations have been …
Mathematical and computational modeling in complex biological systems
The biological process and molecular functions involved in the cancer progression remain
difficult to understand for biologists and clinical doctors. Recent developments in high …
difficult to understand for biologists and clinical doctors. Recent developments in high …
Integrated unsupervised–supervised modeling and prediction of protein–peptide affinities at structural level
P Zhou, L Wen, J Lin, L Mei, Q Liu… - Briefings in …, 2022 - academic.oup.com
Cell signal networks are orchestrated directly or indirectly by various peptide-mediated
protein–protein interactions, which are normally weak and transient and thus ideal for …
protein–protein interactions, which are normally weak and transient and thus ideal for …
[HTML][HTML] Dynamical and structural analysis of a T cell survival network identifies novel candidate therapeutic targets for large granular lymphocyte leukemia
A Saadatpour, RS Wang, A Liao, X Liu… - PLoS computational …, 2011 - journals.plos.org
The blood cancer T cell large granular lymphocyte (T-LGL) leukemia is a chronic disease
characterized by a clonal proliferation of cytotoxic T cells. As no curative therapy is yet …
characterized by a clonal proliferation of cytotoxic T cells. As no curative therapy is yet …
[HTML][HTML] Modeling formalisms in systems biology
Abstract Systems Biology has taken advantage of computational tools and high-throughput
experimental data to model several biological processes. These include signaling, gene …
experimental data to model several biological processes. These include signaling, gene …
Aggregation algorithm towards large-scale Boolean network analysis
Y Zhao, J Kim, M Filippone - IEEE Transactions on Automatic …, 2013 - ieeexplore.ieee.org
The analysis of large-scale Boolean network dynamics is of great importance in
understanding complex phenomena where systems are characterized by a large number of …
understanding complex phenomena where systems are characterized by a large number of …
An effective network reduction approach to find the dynamical repertoire of discrete dynamic networks
JGT Zañudo, R Albert - Chaos: An Interdisciplinary Journal of …, 2013 - pubs.aip.org
Discrete dynamic models are a powerful tool for the understanding and modeling of large
biological networks. Although a lot of progress has been made in developing analysis tools …
biological networks. Although a lot of progress has been made in developing analysis tools …
A network model for plant–pollinator community assembly
Community assembly models, usually constructed for food webs, are an important
component of our understanding of how ecological communities are formed. However …
component of our understanding of how ecological communities are formed. However …
Control of large-scale Boolean networks via network aggregation
Y Zhao, BK Ghosh, D Cheng - IEEE transactions on neural …, 2015 - ieeexplore.ieee.org
A major challenge to solve problems in control of Boolean networks is that the computational
cost increases exponentially when the number of nodes in the network increases. We …
cost increases exponentially when the number of nodes in the network increases. We …
Dynamical systems approach to endothelial heterogeneity
ER Regan, WC Aird - Circulation research, 2012 - Am Heart Assoc
Endothelial cells display remarkable phenotypic heterogeneity. An important goal is to
elucidate the scope and mechanisms of endothelial heterogeneity and to use this …
elucidate the scope and mechanisms of endothelial heterogeneity and to use this …