Reka Albert

Summary

Affiliation: Pennsylvania State University
Country: USA

Publications

  1. pmc Dynamical and structural analysis of a T cell survival network identifies novel candidate therapeutic targets for large granular lymphocyte leukemia
    Assieh Saadatpour
    Department of Mathematics, The Pennsylvania State University, University Park, United States of America
    PLoS Comput Biol 7:e1002267. 2011
  2. ncbi request reprint Computationally efficient measure of topological redundancy of biological and social networks
    Reka Albert
    Department of Physics, Pennsylvania State University, University Park, Pennsylvania 16802, USA
    Phys Rev E Stat Nonlin Soft Matter Phys 84:036117. 2011
  3. pmc Network inference, analysis, and modeling in systems biology
    Reka Albert
    Department of Physics, Pensylvania State University, University Park, PA 16802, USA
    Plant Cell 19:3327-38. 2007
  4. pmc Dynamic receptor team formation can explain the high signal transduction gain in Escherichia coli
    Reka Albert
    School of Mathematics, University of Minnesota, Minneapolis, Minnesota, USA
    Biophys J 86:2650-9. 2004
  5. ncbi request reprint Scale-free networks in cell biology
    Reka Albert
    Department of Physics and Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
    J Cell Sci 118:4947-57. 2005
  6. pmc Common and unique elements of the ABA-regulated transcriptome of Arabidopsis guard cells
    Rui Sheng Wang
    Department of Physics, Pennsylvania State University, University Park, PA 16802, USA
    BMC Genomics 12:216. 2011
  7. pmc Predicting essential components of signal transduction networks: a dynamic model of guard cell abscisic acid signaling
    Song Li
    Biology Department, Pennsylvania State University, University Park, Pennsylvania, USA
    PLoS Biol 4:e312. 2006
  8. pmc Boolean modeling of transcriptome data reveals novel modes of heterotrimeric G-protein action
    Sona Pandey
    Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
    Mol Syst Biol 6:372. 2010
  9. doi request reprint Boolean modeling of biological regulatory networks: a methodology tutorial
    Assieh Saadatpour
    Department of Mathematics, The Pennsylvania State University, University Park, PA 16802, USA
    Methods 62:3-12. 2013
  10. doi request reprint Boolean modeling in systems biology: an overview of methodology and applications
    Rui Sheng Wang
    Department of Physics, The Pennsylvania State University, University Park, PA 16802, USA
    Phys Biol 9:055001. 2012

Detail Information

Publications40

  1. pmc Dynamical and structural analysis of a T cell survival network identifies novel candidate therapeutic targets for large granular lymphocyte leukemia
    Assieh Saadatpour
    Department of Mathematics, The Pennsylvania State University, University Park, United States of America
    PLoS Comput Biol 7:e1002267. 2011
    ..Overall, this study provides a bird's-eye-view of the avenues available for identification of therapeutic targets for similar diseases through perturbation of the underlying signal transduction network...
  2. ncbi request reprint Computationally efficient measure of topological redundancy of biological and social networks
    Reka Albert
    Department of Physics, Pennsylvania State University, University Park, Pennsylvania 16802, USA
    Phys Rev E Stat Nonlin Soft Matter Phys 84:036117. 2011
    ..elegans metabolic network is largely due to its inclusion of currency metabolites, and (4) the redundancy of signaling networks is highly (negatively) correlated with the monotonicity of their dynamics...
  3. pmc Network inference, analysis, and modeling in systems biology
    Reka Albert
    Department of Physics, Pensylvania State University, University Park, PA 16802, USA
    Plant Cell 19:3327-38. 2007
  4. pmc Dynamic receptor team formation can explain the high signal transduction gain in Escherichia coli
    Reka Albert
    School of Mathematics, University of Minnesota, Minneapolis, Minnesota, USA
    Biophys J 86:2650-9. 2004
    ..Only recently has a source of gain in the signal transduction network been identified experimentally, and here we present a mathematical model based on dynamic assembly of receptor teams that can explain this observation...
  5. ncbi request reprint Scale-free networks in cell biology
    Reka Albert
    Department of Physics and Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
    J Cell Sci 118:4947-57. 2005
    ..Moreover, the observed topologies of cellular networks give us clues about their evolution and how their organization influences their function and dynamic responses...
  6. pmc Common and unique elements of the ABA-regulated transcriptome of Arabidopsis guard cells
    Rui Sheng Wang
    Department of Physics, Pennsylvania State University, University Park, PA 16802, USA
    BMC Genomics 12:216. 2011
    ....
  7. pmc Predicting essential components of signal transduction networks: a dynamic model of guard cell abscisic acid signaling
    Song Li
    Biology Department, Pennsylvania State University, University Park, Pennsylvania, USA
    PLoS Biol 4:e312. 2006
    ..Our method can be readily applied to other biological signaling networks to identify key regulatory components in systems where quantitative information is limited...
  8. pmc Boolean modeling of transcriptome data reveals novel modes of heterotrimeric G-protein action
    Sona Pandey
    Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
    Mol Syst Biol 6:372. 2010
    ..Our method holds significant promise for analyzing analogous 'switch-like' signal transduction events in any organism...
  9. doi request reprint Boolean modeling of biological regulatory networks: a methodology tutorial
    Assieh Saadatpour
    Department of Mathematics, The Pennsylvania State University, University Park, PA 16802, USA
    Methods 62:3-12. 2013
    ..For each step, the pitfalls one may encounter and possible ways to circumvent them are also discussed. We illustrate these steps on a toy network as well as in the context of the Drosophila melanogaster segment polarity gene network. ..
  10. doi request reprint Boolean modeling in systems biology: an overview of methodology and applications
    Rui Sheng Wang
    Department of Physics, The Pennsylvania State University, University Park, PA 16802, USA
    Phys Biol 9:055001. 2012
    ..This overview aims to acquaint life science researchers with the basic steps of Boolean modeling and its applications in several areas of systems biology...
  11. ncbi request reprint A novel method for signal transduction network inference from indirect experimental evidence
    Reka Albert
    Department of Physics, Pennsylvania State University, University Park, Pennsylvania, USA
    J Comput Biol 14:927-49. 2007
    ..2006) and show that our algorithm for the transitive reduction substep performs well on graphs with a structure similar to those observed in transcriptional regulatory and signal transduction networks...
  12. pmc Constraint-based network model of pathogen-immune system interactions
    Juilee Thakar
    Department of Physics, 104 Davey Laboratory, Pennsylvania State University, University Park, PA 16802, USA
    J R Soc Interface 6:599-612. 2009
    ..Some of these predictions are supported by the literature, and many can serve as targets of future experiments...
  13. pmc Why Do CD8+ T Cells become Indifferent to Tumors: A Dynamic Modeling Approach
    Colin Campbell
    Department of Physics, The Pennsylvania State University University Park, PA, USA
    Front Physiol 2:32. 2011
    ..Moreover, the model highlights differences in apoptosis rates that contribute to compromised CD8+ T cell responses and tumor progression, knowledge of which is essential for development of cancer immunotherapy...
  14. ncbi request reprint Topology of plant-pollinator networks that are vulnerable to collapse from species extinction
    Colin Campbell
    Department of Physics, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
    Phys Rev E Stat Nonlin Soft Matter Phys 86:021924. 2012
    ..Our results suggest that network measures may be applied to real ecosystems to yield insight into both their stability and the identity of potentially critical species...
  15. doi request reprint Inference of signal transduction networks from double causal evidence
    Reka Albert
    Department of Physics, Penn State University, University Park, PA, USA
    Methods Mol Biol 673:239-51. 2010
    ..The novelty of our algorithmic methodology based on nontrivial combinatorial optimization techniques makes it appealing to computational biologists as well...
  16. pmc Elementary signaling modes predict the essentiality of signal transduction network components
    Rui Sheng Wang
    Department of Physics, Pennsylvania State University, University Park, PA 16802, USA
    BMC Syst Biol 5:44. 2011
    ..Structural and qualitative analysis is emerging as a feasible and useful alternative for interpreting signal transduction...
  17. pmc Bacteriophage-mediated competition in Bordetella bacteria
    Jaewook Joo
    Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, 16802, USA
    Proc Biol Sci 273:1843-8. 2006
    ..This work combines experimental and mathematical approaches to the study of phage-driven competition, and provides an experimentally tested framework for evaluation of the effects of pathogens/parasites on interspecific competition...
  18. doi request reprint Discrete dynamic modeling of cellular signaling networks
    Reka Albert
    Department of Physics, Pennsylvania State University, University Park, Pennsylvania, USA
    Methods Enzymol 467:281-306. 2009
    ..Several variants of Boolean dynamic models including threshold Boolean networks and piecewise linear systems are also covered, followed by two examples of successful application of discrete dynamic modeling in cell biology...
  19. pmc Boolean network simulations for life scientists
    Istvan Albert
    Huck Institutes for the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
    Source Code Biol Med 3:16. 2008
    ..Our software is distributed via a liberal Open Source license and is freely accessible from http://booleannet.googlecode.com...
  20. doi request reprint An effective network reduction approach to find the dynamical repertoire of discrete dynamic networks
    Jorge G T Zañudo
    Department of Physics, The Pennsylvania State University, University Park, Pennsylvania 16802 6300, USA
    Chaos 23:025111. 2013
    ..Our results show that our method goes beyond reducing the network and in most cases can actually predict the dynamical repertoire of the nodes (fixed states or oscillations) in the attractors of the system. ..
  21. pmc Network model of immune responses reveals key effectors to single and co-infection dynamics by a respiratory bacterium and a gastrointestinal helminth
    Juilee Thakar
    Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, Pennsylvania, United States of America
    PLoS Comput Biol 8:e1002345. 2012
    ....
  22. doi request reprint Attractor analysis of asynchronous Boolean models of signal transduction networks
    Assieh Saadatpour
    Department of Mathematics, The Pennsylvania State University, University Park, PA 16802, USA
    J Theor Biol 266:641-56. 2010
    ..Overall, our work provides a roadmap on how Boolean network modeling can be used as a predictive tool to uncover the dynamic patterns of a biological system under various internal and environmental perturbations...
  23. doi request reprint Discrete dynamic modeling of signal transduction networks
    Assieh Saadatpour
    Department of Mathematics, The Pennsylvania State University, University Park, PA, USA
    Methods Mol Biol 880:255-72. 2012
    ..This is followed by practical examples of a Boolean dynamic framework applied to the modeling of the abscisic acid signal transduction network in plants as well as the T-cell survival signaling network in humans...
  24. ncbi request reprint Effects of community structure on the dynamics of random threshold networks
    Rui Sheng Wang
    Department of Physics, Pennsylvania State University, University Park, Pennsylvania 16802, USA
    Phys Rev E Stat Nonlin Soft Matter Phys 87:012810. 2013
    ..This study shows that community structure has a strong effect on the dynamics of RTNs...
  25. pmc Generating super-shedders: co-infection increases bacterial load and egg production of a gastrointestinal helminth
    Sandra Lass
    Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA 16802, USA
    J R Soc Interface 10:20120588. 2013
    ..Thus, we present bioluminescent imaging as a novel, non-invasive tool offering great potential to be taken forward into other applications of infectious disease ecology...
  26. ncbi request reprint Network analysis reveals cross-links of the immune pathways activated by bacteria and allergen
    Colin Campbell
    Department of Physics, Pennsylvania State University, University Park, Pennsylvania 16803, USA
    Phys Rev E Stat Nonlin Soft Matter Phys 84:031929. 2011
    ..We identify key immune components in this cross-talk; particularly revealing the importance of natural killer cells as a key regulatory target in the cross-talk...
  27. pmc Rapid and asymmetric divergence of duplicate genes in the human gene coexpression network
    Wen Yu Chung
    Department of Biology, Penn State University, University Park, PA 16802, USA
    BMC Bioinformatics 7:46. 2006
    ..One aspect of gene function, that is the expression profile in gene coexpression network, has been largely unexplored for duplicate genes...
  28. ncbi request reprint Differential gene expression in Arabidopsis wild-type and mutant anthers: insights into anther cell differentiation and regulatory networks
    Asela J Wijeratne
    Intercollege Graduate Program in Plant Biology, Pennsylvania State University, University Park, PA 16802, USA
    Plant J 52:14-29. 2007
    ..This model includes hypotheses that can be tested experimentally to gain further understanding of the mechanisms controlling anther development...
  29. doi request reprint Discrete dynamic modeling with asynchronous update, or how to model complex systems in the absence of quantitative information
    Sarah M Assmann
    Biology Department, Penn State University, University Park, PA, USA
    Methods Mol Biol 553:207-25. 2009
    ..The method also serves as a starting point from which more quantitative models can be developed as additional information becomes available...
  30. ncbi request reprint The topology of the regulatory interactions predicts the expression pattern of the segment polarity genes in Drosophila melanogaster
    Reka Albert
    School of Mathematics, University of Minnesota, 127 Vincent Hall, Minneapolis, MN 55455, USA
    J Theor Biol 223:1-18. 2003
    ..The model gives important insights into the functioning of the segment polarity gene network, such as the crucial role of the wingless and sloppy paired genes, and the network's ability to correct errors in the pre-pattern...
  31. pmc Abscisic acid-responsive guard cell metabolomes of Arabidopsis wild-type and gpa1 G-protein mutants
    Xiaofen Jin
    Biology Department, Pensylvania State University, University Park, Pensylvania 16802
    Plant Cell 25:4789-811. 2013
    ..Consistent with this observation, the auxin antagonist α-(phenyl ethyl-2-one)-indole-3-acetic acid enhanced ABA-regulated stomatal movement and restored partial ABA sensitivity to gpa1...
  32. ncbi request reprint Conserved network motifs allow protein-protein interaction prediction
    Istvan Albert
    The Huck Institutes for the Life Sciences, Pennsylvania State University, PA 16802, USA
    Bioinformatics 20:3346-52. 2004
    ..Developing reliable computational methods assisting this decision process is a pressing need in bioinformatics...
  33. doi request reprint Introduction to focus issue: quantitative approaches to genetic networks
    Reka Albert
    Department of Physics, Penn State University, University Park, Pennsylvania 16802, USA
    Chaos 23:025001. 2013
    ..Mathematical analyses will be essential for understanding naturally occurring genetic networks in diverse organisms and for providing a foundation for the improved development of synthetic genetic networks. ..
  34. pmc Dynamic models of immune responses: what is the ideal level of detail?
    Juilee Thakar
    Center for Infectious Disease Dynamics and Department of Physics, Pennsylvania State University, University Park, PA 16802, USA
    Theor Biol Med Model 7:35. 2010
    ..Dynamic models constructed to study the interactions between pathogens and hosts' immune responses have revealed key regulatory processes in the infection...
  35. doi request reprint Computational and experimental analysis reveals a requirement for eosinophil-derived IL-13 for the development of allergic airway responses in C57BL/6 mice
    Elizabeth R Walsh
    Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, Center for Molecular Immunology and Infectious Disease, University Park, PA 16802, USA
    J Immunol 186:2936-49. 2011
    ..These experiments suggest that eosinophils and T cells have an interdependent relationship, centered on IL-13, which regulates T cell recruitment to the lung and development of allergic asthma...
  36. pmc A network model for plant-pollinator community assembly
    Colin Campbell
    Department of Physics, Pennsylvania State University, University Park, PA 16802, USA
    Proc Natl Acad Sci U S A 108:197-202. 2011
    ..The unique application of this Boolean network approach to the study of mutualistic community assembly offers a great opportunity to improve our understanding of these critical communities...
  37. pmc Modeling systems-level regulation of host immune responses
    Juilee Thakar
    Department of Physics, Pennsylvania State University, University Park, Pennsylvania, United States of America
    PLoS Comput Biol 3:e109. 2007
    ..This type of modeling provides new insights into the virulence, pathogenesis, and host adaptation of disease-causing microorganisms and allows systems-level analysis that is not always possible using traditional methods...
  38. ncbi request reprint Topological implications of negative curvature for biological and social networks
    Reka Albert
    Department of Physics, Pennsylvania State University, University Park, Pennsylvania 16802, USA
    Phys Rev E Stat Nonlin Soft Matter Phys 89:032811. 2014
    ..We describe two implications of these bounds to crosstalk in biological networks, and to the existence of central, influential neighborhoods in both biological and social networks. ..
  39. pmc Stabilization of perturbed Boolean network attractors through compensatory interactions
    Colin Campbell
    Department of Physics, The Pennsylvania State University, University Park, PA 16802, USA
    BMC Syst Biol 8:53. 2014
    ..Here, we propose a complementary approach wherein interactions are instead modified to alter key regulatory functions and prevent the network damage from triggering a deregulatory cascade...
  40. ncbi request reprint Boolean models of within-host immune interactions
    Juilee Thakar
    Department of Physics and Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA 16802, USA
    Curr Opin Microbiol 13:377-81. 2010
    ..The models make testable predictions regarding yet undetected interactions, process durations and strengths, and novel therapeutic targets, several of which have been experimentally validated...