The large-scale organization of metabolic networks
- H. Jeong, B. Tombor, R. Albert, Z. Oltvai, A. Barabasi
- BiologyNature
- 5 October 2000
This analysis of metabolic networks of 43 organisms representing all three domains of life shows that, despite significant variation in their individual constituents and pathways, these metabolic networks have the same topological scaling properties and show striking similarities to the inherent organization of complex non-biological systems.
Scale-free networks in cell biology
- R. Albert
- BiologyJournal of Cell Science
- 28 October 2005
The observed topologies of cellular networks give clues about their evolution and how their organization influences their function and dynamic responses, and the opportunity to describe quantitatively a network of hundreds or thousands of interacting components is offered.
Network model of survival signaling in large granular lymphocyte leukemia
- Ranran Zhang, M. Shah, T. Loughran
- BiologyProceedings of the National Academy of Sciences
- 21 October 2008
This study provides a model describing the signaling network involved in maintaining the long-term survival of competent CTL in humans and suggests that the persistence of IL-15 and PDGF is sufficient to reproduce all known deregulations in leukemic T-LGL.
Predicting Essential Components of Signal Transduction Networks: A Dynamic Model of Guard Cell Abscisic Acid Signaling
- Song Li, S. Assmann, R. Albert
- Environmental SciencePLoS Biology
- 12 September 2006
A dynamic model of ABA-induced stomatal closure is developed and it is revealed that the disruption of membrane depolarizability, anion efflux, actin cytoskeleton reorganization, cytosolic pH increase, the phosphatidic acid pathway, or K+ efflux through slowly activating K+ channels at the plasma membrane lead to the strongest reduction in ABA responsiveness.
Boolean network simulations for life scientists
- I. Albert, J. Thakar, Song Li, Ranran Zhang, R. Albert
- Computer ScienceSource Code for Biology and Medicine
- 14 November 2008
This paper provides a clear overview of the concepts used in Boolean simulations, a software library that can perform these simulations based on simple text inputs and gives three case studies to demonstrate the Boolean paradigms and their applicability.
Boolean modeling in systems biology: an overview of methodology and applications
- Rui-Sheng Wang, A. Saadatpour, R. Albert
- Biology, Computer SciencePhysical Biology
- 25 September 2012
This paper builds on research to provide a methodology overview of Boolean modeling in systems biology, including Boolean dynamic modeling of cellular networks, attractor analysis of Boolean dynamic models, as well as inferring biological regulatory mechanisms from high-throughput data using Boolean models.
Common and unique elements of the ABA-regulated transcriptome of Arabidopsis guard cells
- Rui-Sheng Wang, S. Pandey, S. Assmann
- Environmental Science, BiologyBMC Genomics
- 9 May 2011
Within the ABA-regulated gene set of guard cells, it is found that many of the genes known to encode ion transporters associated with stomatal opening are down-regulated by ABA, providing one mechanism for long-term maintenance ofStomatal closure during drought.
Robustness and fragility of Boolean models for genetic regulatory networks.
- M. Chaves, R. Albert, Eduardo Sontag
- BiologyJournal of Theoretical Biology
- 27 January 2005
Network modeling of TGFβ signaling in hepatocellular carcinoma epithelial-to-mesenchymal transition reveals joint sonic hedgehog and Wnt pathway activation.
- S. Steinway, J. G. T. Zañudo, R. Albert
- BiologyCancer Research
- 1 November 2014
This model will be useful in identifying potential therapeutic targets for the suppression of EMT, invasion, and metastasis in HCC and identifies by network analysis eight regulatory feedback motifs that stabilize the EMT process and shows that these motifs involve cross-talk among multiple major pathways.
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