Research Topics
Genomes and Genes | Reka AlbertSummaryAffiliation: Pennsylvania State University Country: USA Publications
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Publications
Computationally efficient measure of topological redundancy of biological and social networksReka 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...
Dynamic receptor team formation can explain the high signal transduction gain in Escherichia coliReka 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...- Scale-free networks in cell biologyReka 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... - Network inference, analysis, and modeling in systems biologyReka Albert
Department of Physics, Pensylvania State University, University Park, PA 16802, USA
Plant Cell 19:3327-38. 2007 - Common and unique elements of the ABA-regulated transcriptome of Arabidopsis guard cellsRui Sheng Wang
Department of Physics, Pennsylvania State University, University Park, PA 16802, USA
BMC Genomics 12:216. 2011.... - Boolean modeling of transcriptome data reveals novel modes of heterotrimeric G-protein actionSona 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... - Constraint-based network model of pathogen-immune system interactionsJuilee 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... - A novel method for signal transduction network inference from indirect experimental evidenceReka 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... 
Inference of signal transduction networks from double causal evidenceReka 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...- Elementary signaling modes predict the essentiality of signal transduction network componentsRui 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... - Bacteriophage-mediated competition in Bordetella bacteriaJaewook 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... - Topology of plant-pollinator networks that are vulnerable to collapse from species extinctionColin 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... - Network analysis reveals cross-links of the immune pathways activated by bacteria and allergenColin 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... - Rapid and asymmetric divergence of duplicate genes in the human gene coexpression networkWen 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... - Boolean network simulations for life scientistsIstvan 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... - Why Do CD8+ T Cells become Indifferent to Tumors: A Dynamic Modeling ApproachColin 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... - Boolean modeling in systems biology: an overview of methodology and applicationsRui 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... - Attractor analysis of asynchronous Boolean models of signal transduction networksAssieh 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... - The topology of the regulatory interactions predicts the expression pattern of the segment polarity genes in Drosophila melanogasterReka 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... - Differential gene expression in Arabidopsis wild-type and mutant anthers: insights into anther cell differentiation and regulatory networksAsela 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... - 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..Incorporation of the large number and variety of immune processes involved in pathogenesis requires tradeoffs in modeling... - Discrete dynamic modeling of cellular signaling networksReka 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... - Discrete dynamic modeling with asynchronous update, or how to model complex systems in the absence of quantitative informationSarah 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... - A network model for plant-pollinator community assemblyColin 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... - Computational and experimental analysis reveals a requirement for eosinophil-derived IL-13 for the development of allergic airway responses in C57BL/6 miceElizabeth 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... - Modeling systems-level regulation of host immune responsesJuilee 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... - Generating super-shedders: co-infection increases bacterial load and egg production of a gastrointestinal helminthSandra 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... - Conserved network motifs allow protein-protein interaction predictionIstvan 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... - Boolean models of within-host immune interactionsJuilee 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... - Predicting essential components of signal transduction networks: a dynamic model of guard cell abscisic acid signalingSong 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...