- S. N. Steinway, J. G. T. Zanudo, P. J. Michel, D. J. Feith, T. P. Loughran, R. Albert
Combinatorial Interventions Inhibit TGFb-Driven Epithelial-Mesenchymal Transition and Support Hybrid Cellular Phenotypes
Systems Biology and Applications 1, 15014 (2015).
- C. Campbell, J. Ruths, D. Ruths. K. Shea, R. Albert,
Topological constraints on network control profiles
Scientific Reports 5, 18693 (2015).
- S. M. Rajtmajer, A. Roy, R. Albert, P. C.M. Molenaar, F. G. Hillary,
A voxelwise approach to determine consensus regions-of-interest for the study of brain network plasticity
Frontiers of Neuroanatomy 9:97, part of the research topic Mathematical description of brain plasticity (2015)
S. N. Steinway, M. Biggs, T. P. Loughran, J. Papin, R. Albert,
Inference of Network Dynamics and Metabolic Interactions in the Gut Microbiome,
PLOS Computational Biology (2015).
- J. G. T. Zanudo, R. Albert,
Cell Fate Reprogramming by Control of Intracellular Network Dynamics,
PLOS Computational Biology 11, e1004193 (2015).
- C. Campbell, K. Shea, S. Yang, R. Albert,
Motif profile dynamics and transient species in a Boolean model of mutualistic ecological communities,
J. Complex Networks (2015).
Plant-pollinator community network response to species invasion depends on both invader and community characteristics,
Oikos 124, 406-413 (2015).
C. Campbell, R. Albert,
Stabilization of perturbed Boolean network attractors through compensatory interactions,
BMC Systems Biology 8:53 (2014).
- A. M. Jones, Y. Xuan, M. Xu, R. S. Wang, C. H. Ho, S. Lalonde, C. H. You, M. I. Sardi, S. A. Parsa, E. Smith-Valle, T. Su, K. A. Frazer, G. Pilot, R. Pratelli, G. Grossmann, B. R. Acharya, H.-C. Hu, C. Engineer, F. Villiers, C. Ju, K. Takeda, Z. Su, Q. Dong, S. M. Assmann, J. Chen, J. M. Kwak, J. I. Schroeder, R. Albert, S. Y. Rhee, and W. B. Frommer,
Border Control—A Membrane-Linked Interactome of Arabidopsis,
Science 344, 711-716 (2014).
Multi-level modeling of light-induced stomatal opening offers new insight into its regulation by drought,
PLOS Computational Biology 10, e1003930 (2014).
Network modeling of TGFβ signaling in hepatocellular carcinoma epithelial-to-mesenchymal transition reveals joint Sonic hedgehog and Wnt pathway activation,
Cancer Research 74, 5963 (2014).
Restoration of plant-pollinator interaction networks via species translocation,
Theoretical Ecology 7, 209-220 (2014).
- R. Albert, B. DasGupta, N. Mobasheri
Topological implications of negative curvature for biological and social networks,
Phys. Rev. E 89, 032811 (2014)
- R. Albert, J. Thakar,
Boolean modeling: a logic-based dynamic approach for understanding signaling and regulatory networks and for making useful predictions,
WIREs Systems Biology and Medicine 6, 353-369 (2014).
- X. Jin, R.S. Wang, M. Zhu, B. W. Jeon, R. Albert, S. Chen, and S. M. Assmann,
Abscisic Acid–Responsive Guard Cell Metabolomes of Arabidopsis Wild-Type and gpa1 G-Protein Mutants,
The Plant Cell 25, 4789-4811 (2013).
- S. Yang, R. Albert, T.A. Carlo,
Transience and constancy of interactions in a plant-frugivore network,
Ecosphere 4, 147 (2013).
- T. LaBar, C. Campbell, S. Yang, R. Albert, and K. Shea,
Global versus local extinction in a network model of plant–pollinator communities,
Theoretical Ecology 6, 495-503 (2013).
Effects of community structure on the dynamics of random threshold network
Phys. Rev. E 87, 012810 (2013)
Generating super-shedders: co-infection increases bacterial load and egg production of a gastrointestinal helminth.
Soc Interface 10, 20120588 (2013)
Minimal functional routes in directed graphs with dependent edges,
International Transactions in Operational Research 20, 391-409 (2013).
Boolean modeling of biological regulatory networks: A methodology tutorial,
Methods 62, 3-12 (2013).
Topology of plant-pollinator networks that are vulnerable to
collapse from species extinction
Phys. Rev. E 86, 021924 (2012).
Highlighted in Physics Focus http://physics.aps.org/articles/v5/98
Boolean modeling in systems biology: an overview of methodology and applications
Physical Biology 9 055001 (2012)
Network Model of Immune Responses
Reveals Key Effectors to Single and
Co-infection Dynamics by a Respiratory Bacterium and a Gastrointestinal Helminth
PLoS Computational Biology 8:e1002345 (2012).
Dynamical and Structural Analysis of a T Cell Survival Network Identifies Novel Candidate Therapeutic Targets for Large Granular Lymphocyte Leukemia
PLoS Computational Biology 7:e1002267 (2011)
Network analysis reveals cross-links of the immune pathways activated by
bacteria and allergen
Phys. Rev. E 84, 031929 (2011)
Computationally efficient measure of topological redundancy of
biological and social networks
Phys. Rev. E 84, 036117 (2011)
Walsh, E. R., J. Thakar, F. Huang, K. Stokes, R. Albert and A. August
Computational and experimental analysis reveals a requirement for IL-13
production by eosinophils for the development of allergic airway responses.
J. Immunol. 186:2936-2949. (2011)
Elementary signaling modes predict the essentiality of signal
transduction network components
BMC Systems Biology 5:44 (2011)
Colin Campbell, Ranran Zhang, Jeremy S. Haley, Xin Liu, Thomas Loughran,Todd D. Schell, Réka Albert and Juilee Thakar
Why do CD8+ T cells become indifferent
to tumors: a dynamic modeling approach
Frontiers in Physiology 2:32 (2011)
A network model for plant–pollinator community assembly
PNAS 108, 197-202 (2011)
S. Pandey, R. Wang, L. Wilson, S. Li, Z. Zhao, T. Gookin, S.M. Assmann, R. Albert,
Boolean modeling of transcriptome data reveals novel modes of heterotrimeric G-protein
Molecular Systems Biology 6:372 (2010)
Dynamic models of immune responses: what is the ideal level of detail?
Theoretical Biology and Medical Modelling 7:35 (2010)
Attractor analysis of asynchronous Boolean models of signal
Journal of Theoretical Biology 266 641-656 (2010)
models of within-host immune interactions
Current Opinion in Microbiology 13, 377-381 (2010)
Disease dynamics in a dynamic social network
389 2663-2674 (2010)
Network model of survival signaling in T-cell large granular lymphocyte leukemia,
Cancer Systems Biology, E. Wang (ed.), Chapman & Hall/CRC Mathematical and Computational Biology Series, CRC Press, (2010)
Complex Networks: An Engineering View,
IEEE Circuits and Systems, vol 10, nr. 3, special issue on Complex Network Applications in Circuits and Systems, p. 10-26 (2010).
Inference of signal transduction networks from double causal evidence
in Methods in Molecular Biology: Topics in Computational Biology, D. Fenyo (ed.), Humana Press (2010)
Constraint-Based Network Model of Pathogen-Immune System
Journal of the Royal Society Interface 6, 599-612 (2009)
Overview of Systems Biology
Annual Plant Reviews 35: Plant Systems Biology,
G. Coruzzi and R. Gutierrez (eds.), 41-66, Oxford: Blackwell Publishing (2009).
Discrete dynamic modeling with asynchronous update or, how to
model complex systems in the absence of quantitative information
Methods in Molecular Biology 553:
Plant Systems Biology, ed. D. Belostotsky, 207-225,Totowa NJ: Humana Press (2009).
Toward Understanding the Structure and Function of Cellular Interaction Networks,
Handbook of Large-Scale Random Networks, B. Bollobas and R. Kozma (eds.), Springer, 2009.
Discrete dynamic modeling of cellular signaling networks,
Methods in Enzymology 476: Computer Methods B, M. L. Johnson and L. Brand (eds.), p. 281- 306, Academic Press, 2009
Boolean networks in inference and dynamic modeling of biological systems at the molecular and physiological level,
in Handbook of Biological Networks, S. Boccaletti,V.Latora, Y. Moreno (eds.), World Scientific Publishing, to appear
Ranran Zhang, Mithun Vinod Shah, Jun Yang, Susan B. Nyland, Xin Liu, Jong K. Yun, Réka Albert, and Thomas P. Loughran, Jr.
Network Model of Survival Signaling in LGL Leukemia
PNAS vol. 105 no. 42 16308-16313 (2008)
See also the press release: Silencing a protein could kill T-cells, reverse leukemia
Boolean network simulations for life scientist
Source Code for Biology and Medicine 3, 16 (2008) | see related
Studying the effect of cell division on expression patterns of the segment
Journal of the Royal Society Interface 6, 5 (2008)
NET-SYNTHESIS: A software for synthesis, inference and simplification of signal transduction
Bioinformatics 2008 24(2):293-295
Inferring (biological) signal transduction networks via transitive
reductions of directed graphs
Algorithmica, Volume 51, Number 2, pp. 129-159, June 2008
Network Inference, Analysis, and Modeling in Systems
The Plant Cell 19: 3327-3338 (2007)
A novel method for signal transduction network inference from indirect
Journal of Computational Biology 14, 927-949 (2007)
Systems-Level Regulation of Host Immune Responses
PLoS Computational Biology 6, e109 (2007)
Shaping specificity in signaling networks
Nature Genetics (News and Views) 39, 286 - 287 (2007)
Systems-level insights into cellular regulation: inferring, analyzing and modeling
IET Systems Biology 1, 61-77 (2007)
Variation in Host Susceptibility and Infectiousness Generated by Co-infection: The
Myxoma-Trichostrongylus Retortaeformis Case in Wild Rabbits,
Journal of the Royal Society Interface 4, 831-840 (2007)
Inference and graph-theoretical analysis of Bacillus Subtilis gene regulatory
Physica A 373, 796-810 (2007)
time algorithm to detect community structures in large-scale networks
Phys. Rev. E 76, 036106 (2007)
gene expression in Arabidopsis wild-type and mutant anthers: insights into anther cell differentiation and regulatory networks
The Plant Journal 52, 14-29 (2007)
Search in spatial scale free networks
New Journal of Physics 9, 190 (2007)
Using graph concepts to understand the organization of complex systems
invited tutorial in the special issue "Complex Networks' Structure and Dynamics'' of the International Journal of Bifurcation and Chaos 17, Issue 7, July 2007,
edited by S. Boccaletti and V. Latora.
Complexity and Large-scale Networks,
Chapter 11 in Operations Research and Management Science Handbook edited by A. R. Ravindran, CRC press,
Effects of noise on bacteriophage-mediated competition
Journal of Statistical Physics 128, 229-256 (2007).
components of signal transduction networks: dynamic model of guard cell abscisic acid signaling
PLoS Biology 4 (10): e312, 2006 | read synopsis
Methods of robustness analysis for Boolean models of gene control networks
IEE Proceedings in Systems Biology 153, 154-167 (2006)
Bacteriophage-mediated competition in Bordetella bacteria
Proceedings of the
Royal Society B 273, 1843-1848 (2006)
Rapid and Asymmetric Divergence of Duplicate Genes in the Human Gene
BMC Bioinformatics 7 : 46 (2006)
of directionality for co-expressed genes: predicting intra-operon termination sites | supplementary material
Bioinformatics 22 (2):209-214 , (2006)
Structure and timescale analysis in genetic regulatory
Proc. IEEE Conf. Decision and Control, San Diego, Dec. 2006 , 2006. IEEE
General Network Theory
LACUS Forum 32: Networks (2006), edited by Shin Ja Hwang, William J. Sullivan, Arle R. Lommel, Houston TX,
Forum 32, 3–20 (2006)
Scale-free networks in cell biology
Journal of Cell Science 118 , 4947-4957 (2005)
Search in weighted complex networks
Phys. Rev. E 72 , 066128 (2005)
Modeling Cascading Failures in the North American Power Grid
Eur. Phys. J. B 46 , 101-107 (2005)
Robustness and fragility of Boolean models for genetic regulatory networks
Journal of Theoretical Biology, Volume 235 , pp 431-449 (2005)
Survivability of Multiagent-Based Supply Networks: A
IEEE Intelligent Systems, Volume 19 , issue 5, pp 24-31 (2004)
Conserved network motifs allow protein-protein interaction prediction
Bioinformatics , Vol. 20, No. 18, (2004)
Boolean modeling of genetic regulatory networks
In: Complex Networks editors: E. Ben-Naim, H. Frauenfelder and Z. Toroczkai),
(Springer Verlag 2004)
Dynamic receptor team formation can explain the high signal transduction gain
in E. coli
Biophysics Journal 86, 2650-59 (2004)
Structural Vulnerability of the North American Power Grid
Phys. Rev. E 69, 025103(R) (2004)
... but no kinetic details are needed
Siam News, Dec. (2003)
(This article appeared next to another paper and it was laid out such that the two titles could be read as one sentence: "Some assembly required ... but no kinetic details are needed". See this link for details)
The topology of the regulatory interactions predicts the expression pattern
of the Drosophila segment polarity genes
Journal of Theoretical Biology 223, 1-18 (2003)
Spatial Pattern Formation and Morphogenesis in Development: Recent Progress for Two Model Systems
in Morphogenesis and Pattern
Formation in Biological Systems: Experiments and Models , editors: T. Sekimura, S. Noji, N. Ueno and P.K. Maini (Springer Verlag,
Statistical mechanics of complex networks,
Rev. Mod. Phys. 74, 47-97 (2002)
selected by ISI as Fast Breaking Paper in Dec 2002
Stick-slip fluctuations in granular drag
Phys. Rev. E 64, 031307 (2001)
The Internet's Achilles' heel: Error and attack tolerance in
Nature 406, 378-382 (2000) (cover story)
Topology of complex networks: local events and universality
Phys. Rev. Lett. 85, 5234 (2000)
Topological properties of metabolic networks
Nature, 407, 651s-654 (2000)
Scale-free characteristics of random networks:
The topology of the World Wide Web
Physica A 281 69-77 (2000)
Dynamics of Complex Systems: Calculating the Period of Boolean
Phys. Rev. Lett. 84 5660-5663 (2000)
Jamming and Fluctuations in Granular Drag
Phys. Rev. Lett. 84 5122-5125 (2000)
Mean-field theory for scale-free random networks
Physica A 272 173-187 (1999)
Emergence of scaling in random networks
Science 286 509-512 (1999)
The Diameter of the World-Wide Web
Nature 401 130-131 (1999)
Liquid-Induced Transitions in Granular Media
Phys. Rev. E 60 5823-5827 (1999)
Physics of Sandcastles
Physica A 266 340-345 (1999)
Slow drag in a granular medium
Phys. Rev. Lett. 82 205-208 (1999)
What keeps sandcastles standing?
Nature 387 765 (1997) (cover story)
Driven interfaces in disordered media: determination of universality
classes from experimental data
Phys. Rev. Lett. 81 2926-2929 (1998)
Maximum angle of stability in wet and dry spherical granular
Phys. Rev. E 56 R6271-R6274 (1997).