List of Publications
Publications
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Leveraging network structure in nonlinear controlnpj Systems Biology and Applications, 2022
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PLOS Computational Biology, 2022
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Frontiers in Genetics, 2022
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Bioinformatics, 2022
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Chaos: An Interdisciplinary Journal of Nonlinear Science, 2022
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Physical Review E, 2021
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Proceedings of the National Academy of Sciences, 2021
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Journal of Personalized Medicine, 2021
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Cancer research, 2021
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Science Advances, 2021
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PLoS Computational Biology, 2021
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Frontiers in Physiology, 2020
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A feedback loop of conditionally stable circuits drives the cell cycle from checkpoint to checkpointScientific Reports, 2019
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PLoS Comp. Biology, 2019
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Physical Biology, 2019
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Chaos, 2019
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J. Theor. Biol, 2018
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PLoS Comput Biol, 2018
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Phys Rev E, 2018
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Current opinion in Systems Biology, 2018
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Frontiers in Physiology, 2018
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BMC Systems Biology, 2017
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PLoS Biology, 2017
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bioRxiv, 2017
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Scientific Reports, 2017
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Physical Review E, 2017
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Network Science, 2017
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BMC Systems Biology, 2017
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Proceedings of the National Academy of Sciences , 2017
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Journal of Complex Networks, 2016
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A comparative study of qualitative and quantitative dynamic models of biological regulatory networksEPJ Nonlinear Biomedical Physics, 2016
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PLoS Comput Biol, 2015
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Oikos, 2015
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Algebraic and discrete mathematical methods for modern biology, 2015
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Frontiers in neuroanatomy, 2015
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Scientific reports, 2015
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NPJ Systems Biology and Applications, 2015
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Theoretical ecology, 2014
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Physical Review E, 2014
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BMC systems biology, 2014
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Science, 2014
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Wiley Interdisciplinary Reviews: Systems Biology and Medicine, 2014
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Cancer research, 2014
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Science, 2014
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PLoS Comput Biol, 2014
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Methods, 2013
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Journal of The Royal Society Interface, 2013
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SIAM Journal on Applied Dynamical Systems, 2013
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Physical Review E, 2013
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International Transactions in Operational Research, 2013
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Theoretical ecology, 2013
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Chaos: An Interdisciplinary Journal of Nonlinear Science, 2013
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Chaos: An Interdisciplinary Journal of Nonlinear Science, 2013
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Ecosphere, 2013
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The Plant Cell, 2013
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Handbook of Optimization in Complex Networks, 2012
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Plos Comput biol, 2012
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Phys. Today, 2012
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Physical Review E, 2012
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Physical biology, 2012
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Computational Modeling of Signaling Networks, 2012
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BMC Systems biology, 2011
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Proceedings of the National Academy of Sciences, 2011
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The Journal of Immunology, 2011
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BMC genomics, 2011
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Physical Review E, 2011
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Physical Review E, 2011
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PLoS Comput Biol, 2011
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Frontiers in Systems Physiology, 2011
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Molecular systems biology, 2010
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Complex networks: An engineering viewIEEE Circuits and Systems Magazine, 2010
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Disease dynamics in a dynamic social networkPhysica A: Statistical Mechanics and its Applications, 2010
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Boolean models of within-host immune interactionsCurrent opinion in microbiology, 2010
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Attractor analysis of asynchronous Boolean models of signal transduction networksJournal of theoretical biology, 2010
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Inference of signal transduction networks from double causal evidenceComputational Biology, 2010
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Boolean Networks in Inference and Dynamic Modeling of Biological Systems at the Molecular and Physiological LevelHandbook On Biological Networks, 2010
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Discrete dynamic modeling of cellular signaling networksMethods in enzymology, 2009
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Constraint-based network model of pathogen immune system interactionsJournal of the Royal Society Interface, 2009
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An Overview of Systems BiologyAnnual Plant Reviews, Plant Systems Biology, 2009
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Boolean Networks in Inference and Dynamic Modeling of Biological Systems at the Molecular and Physiological LevelHandbook on Biological Networks, World Scientific, Singapore, 2009
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Network model of survival signaling in large granular lymphocyte leukemiaProceedings of the National Academy of Sciences, 2008
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Inferring (biological) signal transduction networks via transitive reductions of directed graphsAlgorithmica, 2008
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NET-SYNTHESIS: a software for synthesis, inference and simplification of signal transduction networksBioinformatics, 2008
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Biological switches and clocksJournal of The Royal Society Interface, 2008
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Studying the effect of cell division on expression patterns of the segment polarity genesJournal of The Royal Society Interface, 2008
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Toward understanding the structure and function of cellular interaction networksHandbook of Large-Scale Random Networks, 2008
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Boolean network simulations for life scientistsSource Code for Biology and Medicine, 2008
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Differential gene expression in Arabidopsis wild_��type and mutant anthers: insights into anther cell differentiation and regulatory networksThe Plant Journal, 2007
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Network inference, analysis, and modeling in systems biologyThe Plant Cell, 2007
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Modeling systems-level regulation of host immune responsesPLoS Comput Biol, 2007
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A novel method for signal transduction network inference from indirect experimental evidenceJournal of Computational Biology, 2007
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Systems-level insights into cellular regulation: inferring, analysing, and modelling intracellular networksIET systems biology, 2007
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Using graph concepts to understand the organization of complex systemsInternational Journal of Bifurcation and Chaos, 2007
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Variation in host susceptibility and infectiousness generated by co-infection: the myxoma Trichostrongylus retortaeformis case in wild rabbitsJournal of the Royal Society Interface, 2007
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Search in spatial scale-free networksNew Journal of Physics, 2007
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Shaping specificity in signaling networksNature genetics, 2007
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Large-scale inference and graph-theoretical analysis of gene-regulatory networks in B. SubtilisPhysica A: Statistical Mechanics and its Applications, 2007
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Effects of Noise on Ecological Invasion Processes: Bacteriophage-Mediated Competition in BacteriaJournal of Statistical Physics, 2007
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Near linear time algorithm to detect community structures in large-scale networksPhysical review. E, Statistical, nonlinear, and soft matter physics, 2007
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Predicting essential components of signal transduction networks: a dynamic model of guard cell abscisic acid signalingPLoS Biol, 2006
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Methods of robustness analysis for Boolean models of gene control networksIEE Proc. Syst. Biol, 2006
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Elucidation of directionality for co-expressed genes: predicting intra-operon termination sitesBioinformatics, 2006
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Bacteriophage-mediated competition in Bordetella bacteriaProceedings of the Royal Society of London B: Biological Sciences, 2006
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Structure and timescale analysis in genetic regulatory networksProceedings of the 45th IEEE Conference on Decision and Control, 2006
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Scale-free networks in cell biologyJournal of cell science, 2005
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Robustness and fragility of Boolean models for genetic regulatory networksJournal of theoretical biology, 2005
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Modeling cascading failures in the North American power gridThe European Physical Journal B-Condensed Matter and Complex Systems, 2005
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Search in weighted complex networksPhysical Review E, 2005
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Structural vulnerability of the North American power gridPhysical review E, 2004
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Conserved network motifs allow protein protein interaction predictionBioinformatics, 2004
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Dynamic Receptor Team Formation Can Explain the High Signal Transduction Gain in Escherichia coliBiophysical journal, 2004
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The topology and signature of the regulatory interactions predict the expression pattern of the segment polarity genes in Drosophila melanogasterJournal of Theoretical Biology, 2003
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Statistical mechanics of complex networksRev. Mod. Phys., 2002
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Stick-slip fluctuations in granular dragPhysical Review E, 2001
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correction: Error and attack tolerance of complex networksNature, 2001
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Error and attack tolerance of complex networksNature, 2000
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Jamming and fluctuations in granular dragPhysical review letters, 2000
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Topology of Evolving Networks: Local Events and UniversalityPhysical Review Letters, 2000
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Scaling Laws for the Period of Boolean NetworksPhysical Review Letters, 2000
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The large-scale organization of metabolic networksNature, 2000
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Diameter of the world-wide webNature, 1999
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Mean-field theory for scale-free random networksPhysica A: Statistical Mechanics and its Applications, 1999
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Emergence of scaling in random networksScience, 1999
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Slow drag in a granular mediumPhysical review letters, 1999
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The physics of sand castles: maximum angle of stability in wet and dry granular mediaPhysica A: Statistical Mechanics and its Applications, 1999
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Liquid-induced transitions in granular mediaPhysical Review E, 1999
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Driven interfaces in disordered media: determination of universality classes from experimental dataPhysical review letters, 1998
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What keeps sandcastles standing?Nature, 1997
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Maximum angle of stability in wet and dry spherical granular mediaPhysical Review E, 1997