List of Publications
Publications

Leveraging network structure in nonlinear controlnpj Systems Biology and Applications, 2022

PLOS Computational Biology, 2022

Frontiers in Genetics, 2022

Bioinformatics, 2022

Chaos: An Interdisciplinary Journal of Nonlinear Science, 2022

Physical Review E, 2021

Proceedings of the National Academy of Sciences, 2021

Journal of Personalized Medicine, 2021

Cancer research, 2021

Science Advances, 2021

PLoS Computational Biology, 2021

Frontiers in Physiology, 2020

A feedback loop of conditionally stable circuits drives the cell cycle from checkpoint to checkpointScientific Reports, 2019

PLoS Comp. Biology, 2019

Physical Biology, 2019

Chaos, 2019

J. Theor. Biol, 2018

PLoS Comput Biol, 2018

Phys Rev E, 2018

Current opinion in Systems Biology, 2018

Frontiers in Physiology, 2018

BMC Systems Biology, 2017

PLoS Biology, 2017

bioRxiv, 2017

Scientific Reports, 2017

Physical Review E, 2017

Network Science, 2017

BMC Systems Biology, 2017

Proceedings of the National Academy of Sciences , 2017

Journal of Complex Networks, 2016

A comparative study of qualitative and quantitative dynamic models of biological regulatory networksEPJ Nonlinear Biomedical Physics, 2016

PLoS Comput Biol, 2015

Oikos, 2015

Algebraic and discrete mathematical methods for modern biology, 2015

Frontiers in neuroanatomy, 2015

Scientific reports, 2015

NPJ Systems Biology and Applications, 2015

Theoretical ecology, 2014

Physical Review E, 2014

BMC systems biology, 2014

Science, 2014

Wiley Interdisciplinary Reviews: Systems Biology and Medicine, 2014

Cancer research, 2014

Science, 2014

PLoS Comput Biol, 2014

Methods, 2013

Journal of The Royal Society Interface, 2013

SIAM Journal on Applied Dynamical Systems, 2013

Physical Review E, 2013

International Transactions in Operational Research, 2013

Theoretical ecology, 2013

Chaos: An Interdisciplinary Journal of Nonlinear Science, 2013

Chaos: An Interdisciplinary Journal of Nonlinear Science, 2013

Ecosphere, 2013

The Plant Cell, 2013

Handbook of Optimization in Complex Networks, 2012

Plos Comput biol, 2012

Phys. Today, 2012

Physical Review E, 2012

Physical biology, 2012

Computational Modeling of Signaling Networks, 2012

BMC Systems biology, 2011

Proceedings of the National Academy of Sciences, 2011

The Journal of Immunology, 2011

BMC genomics, 2011

Physical Review E, 2011

Physical Review E, 2011

PLoS Comput Biol, 2011

Frontiers in Systems Physiology, 2011

Molecular systems biology, 2010

Complex networks: An engineering viewIEEE Circuits and Systems Magazine, 2010

Disease dynamics in a dynamic social networkPhysica A: Statistical Mechanics and its Applications, 2010

Boolean models of withinhost immune interactionsCurrent opinion in microbiology, 2010

Attractor analysis of asynchronous Boolean models of signal transduction networksJournal of theoretical biology, 2010

Inference of signal transduction networks from double causal evidenceComputational Biology, 2010

Boolean Networks in Inference and Dynamic Modeling of Biological Systems at the Molecular and Physiological LevelHandbook On Biological Networks, 2010

Discrete dynamic modeling of cellular signaling networksMethods in enzymology, 2009

Constraintbased network model of pathogen immune system interactionsJournal of the Royal Society Interface, 2009

An Overview of Systems BiologyAnnual Plant Reviews, Plant Systems Biology, 2009

Boolean Networks in Inference and Dynamic Modeling of Biological Systems at the Molecular and Physiological LevelHandbook on Biological Networks, World Scientific, Singapore, 2009

Network model of survival signaling in large granular lymphocyte leukemiaProceedings of the National Academy of Sciences, 2008

Inferring (biological) signal transduction networks via transitive reductions of directed graphsAlgorithmica, 2008

NETSYNTHESIS: a software for synthesis, inference and simplification of signal transduction networksBioinformatics, 2008

Biological switches and clocksJournal of The Royal Society Interface, 2008

Studying the effect of cell division on expression patterns of the segment polarity genesJournal of The Royal Society Interface, 2008

Toward understanding the structure and function of cellular interaction networksHandbook of LargeScale Random Networks, 2008

Boolean network simulations for life scientistsSource Code for Biology and Medicine, 2008

Differential gene expression in Arabidopsis wild_��type and mutant anthers: insights into anther cell differentiation and regulatory networksThe Plant Journal, 2007

Network inference, analysis, and modeling in systems biologyThe Plant Cell, 2007

Modeling systemslevel regulation of host immune responsesPLoS Comput Biol, 2007

A novel method for signal transduction network inference from indirect experimental evidenceJournal of Computational Biology, 2007

Systemslevel insights into cellular regulation: inferring, analysing, and modelling intracellular networksIET systems biology, 2007

Using graph concepts to understand the organization of complex systemsInternational Journal of Bifurcation and Chaos, 2007

Variation in host susceptibility and infectiousness generated by coinfection: the myxoma Trichostrongylus retortaeformis case in wild rabbitsJournal of the Royal Society Interface, 2007

Search in spatial scalefree networksNew Journal of Physics, 2007

Shaping specificity in signaling networksNature genetics, 2007

Largescale inference and graphtheoretical analysis of generegulatory networks in B. SubtilisPhysica A: Statistical Mechanics and its Applications, 2007

Effects of Noise on Ecological Invasion Processes: BacteriophageMediated Competition in BacteriaJournal of Statistical Physics, 2007

Near linear time algorithm to detect community structures in largescale networksPhysical review. E, Statistical, nonlinear, and soft matter physics, 2007

Predicting essential components of signal transduction networks: a dynamic model of guard cell abscisic acid signalingPLoS Biol, 2006

Methods of robustness analysis for Boolean models of gene control networksIEE Proc. Syst. Biol, 2006

Elucidation of directionality for coexpressed genes: predicting intraoperon termination sitesBioinformatics, 2006

Bacteriophagemediated competition in Bordetella bacteriaProceedings of the Royal Society of London B: Biological Sciences, 2006

Structure and timescale analysis in genetic regulatory networksProceedings of the 45th IEEE Conference on Decision and Control, 2006

Scalefree networks in cell biologyJournal of cell science, 2005

Robustness and fragility of Boolean models for genetic regulatory networksJournal of theoretical biology, 2005

Modeling cascading failures in the North American power gridThe European Physical Journal BCondensed Matter and Complex Systems, 2005

Search in weighted complex networksPhysical Review E, 2005

Structural vulnerability of the North American power gridPhysical review E, 2004

Conserved network motifs allow protein protein interaction predictionBioinformatics, 2004

Dynamic Receptor Team Formation Can Explain the High Signal Transduction Gain in Escherichia coliBiophysical journal, 2004

The topology and signature of the regulatory interactions predict the expression pattern of the segment polarity genes in Drosophila melanogasterJournal of Theoretical Biology, 2003

Statistical mechanics of complex networksRev. Mod. Phys., 2002

Stickslip fluctuations in granular dragPhysical Review E, 2001

correction: Error and attack tolerance of complex networksNature, 2001

Error and attack tolerance of complex networksNature, 2000

Jamming and fluctuations in granular dragPhysical review letters, 2000

Topology of Evolving Networks: Local Events and UniversalityPhysical Review Letters, 2000

Scaling Laws for the Period of Boolean NetworksPhysical Review Letters, 2000

The largescale organization of metabolic networksNature, 2000

Diameter of the worldwide webNature, 1999

Meanfield theory for scalefree random networksPhysica A: Statistical Mechanics and its Applications, 1999

Emergence of scaling in random networksScience, 1999

Slow drag in a granular mediumPhysical review letters, 1999

The physics of sand castles: maximum angle of stability in wet and dry granular mediaPhysica A: Statistical Mechanics and its Applications, 1999

Liquidinduced transitions in granular mediaPhysical Review E, 1999

Driven interfaces in disordered media: determination of universality classes from experimental dataPhysical review letters, 1998

What keeps sandcastles standing?Nature, 1997

Maximum angle of stability in wet and dry spherical granular mediaPhysical Review E, 1997