Publications

    2014

  1. 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).
  2. C. Campbell, R. Albert,
    Stabilization of perturbed Boolean network attractors through compensatory interactions,
    BMC Systems Biology 8:53 (2014).
  3. R. Albert, B. DasGupta, N. Mobasheri,
    Topological implications of negative curvature for biological and social networks,
    Phys. Rev. E 89, 032811 (2014).
  4. 2013

  5. R. Wang and R. Albert
    Effects of community structure on the dynamics of random threshold network
    Phys. Rev. E 87, 012810 (2013)
  6. S. Lass, P. J. Hudson, J. Thakar, J. Saric, E. Harvill, R. Albert, S.E. Perkins
    Generating super-shedders: co-infection increases bacterial load and egg production of a gastrointestinal helminth.
    J R Soc Interface 10, 20120588 (2013)
  7. R. Wang, Z. Sun and R. Albert,
    Minimal functional routes in directed graphs with dependent edges
    ,
    International Transactions in Operational Research 20, 391-409 (2013)
    .
  8. A. Saadatpour, R. Albert,
    Boolean modeling of biological regulatory networks: A methodology tutorial,
    Methods 62, 3-12 (2013)
    .
  9. S. Yang, R. Albert, T.A. Carlo,
    Transience and constancy of interactions in a plant-frugivore network,
    Ecosphere (in press, 2013).
  10. 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 (in press, 2013).
  11. A. Saadatpour, R. Albert, T. Reluga,
    A reduction method for Boolean network models proven to conserve attractors,
    SIAM Journal on Applied Dynamical Systems 12, 1997-2011 (2013).
  12. 2012

  13. C. Campbell, S. Yang, K. Shea, R. Albert
    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

  14. R. S. Wang, A. Saadatpour, R. Albert
    Boolean modeling in systems biology: an overview of methodology and applications
    Physical Biology 9 055001 (2012)
  15. J. Thakar, A.K. Pathak, L. Murphy, R. Albert, I.M. Cattadori
    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).

    2011

  16. Assieh Saadatpour, Rui-Sheng Wang, Aijun Liao, Xin Liu, Thomas P. Loughran, Istvan Albert Reka Albert
    Dynamical and Structural Analysis of a T Cell Survival Network Identifies Novel Candidate Therapeutic Targets for Large Granular Lymphocyte Leukemia biobio
    PLoS Computational Biology 7:e1002267 (2011)

  17. Nodes

    Colin Campbell, Juilee Thakar, and Réka Albert
    Network analysis reveals cross-links of the immune pathways activated by bacteria and allergen phys bio
    Phys. Rev. E 84, 031929 (2011)

  18. Reka Albert, Bhaskar DasGupta, Anthony Gitter, Gamze Gursoy, Pradyut Paul and Eduardo Sontag
    Computationally efficient measure of topological redundancy of biological and social networks phys bio
    Phys. Rev. E 84, 036117 (2011)

  19. 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) bio

  20. Rui-Sheng Wang and Réka Albert
    Elementary signaling modes predict the essentiality of signal transduction network components biobio
    BMC Systems Biology 5:44 (2011)

  21. 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) biobio

  22. Colin Campbell, Suann Yang, Réka Albert and Katriona Shea
    A network model for plant–pollinator community assembly biobio
    PNAS 108, 197-202 (2011)

    2010

  23. regulation 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 action, bio
    Molecular Systems Biology 6:372 (2010)
  24. Juilee Thakar, Mary Poss, Réka Albert, Gráinne H Long and Ranran Zhang
    Dynamic models of immune responses: what is the ideal level of detail? biobio
    Theoretical Biology and Medical Modelling 7:35 (2010)

  25. Assieh Saadatpour, Istvan Albert and Reka Albert
    Attractor analysis of asynchronous Boolean models of signal transduction networks bio bio
    Journal of Theoretical Biology 266 641-656 (2010)

  26. Juilee Thakar and Reka Albert
    Boolean models of within-host immune interactions bio
    Current Opinion in Microbiology 13, 377-381 (2010)

  27. C. Christensen, I. Albert, B. Grenfell, R. Albert
    Disease dynamics in a dynamic social network bio bio
    Physica A 389 2663-2674 (2010)

  28. Ranran Zhang, Thomas P. Loughran, Reka Albert
    Network model of survival signaling in T-cell large granular lymphocyte leukemia, biobio
    Cancer Systems Biology, E. Wang (ed.), Chapman & Hall/CRC Mathematical and Computational Biology Series, CRC Press, (2010)

  29. L.Y. Cui, S. Kumara and R. Albert,
    Complex Networks: An Engineering View,gen
    IEEE Circuits and Systems, vol 10, nr. 3, special issue on Complex Network Applications in Circuits and Systems, p. 10-26 (2010).

  30. R. Albert, B. DasGupta, E. D. Sontag
    Inference of signal transduction networks from double causal evidence bio bio
    in Methods in Molecular Biology: Topics in Computational Biology, D. Fenyo (ed.), Humana Press (2010)

    2009

  31. Motif

    Juilee Thakar, Assieh Saadatpour-Moghaddam, Eric T. Harvill and Réka Albert,
    Constraint-Based Network Model of Pathogen-Immune System Interactions,biobio
    Journal of the Royal Society Interface 6, 599-612 (2009)

  32. Reka Albert and Sarah M. Assmann
    Overview of Systems Biology biogen
    Annual Plant Reviews 35: Plant Systems Biology, G. Coruzzi and R. Gutierrez (eds.),  41-66, Oxford: Blackwell Publishing (2009).

  33. Reka Albert and Sarah M. Assmann
    Discrete dynamic modeling with asynchronous update or, how to model complex systems in the absence of quantitative information bio
    Methods in Molecular Biology 553: Plant Systems Biology, ed. D. Belostotsky, 207-225,Totowa NJ: Humana Press (2009).

  34. Juilee Thakar, Claire Christensen and Reka Albert
    Toward Understanding the Structure and Function of Cellular Interaction Networks, bio
    Handbook of Large-Scale Random Networks, B. Bollobas and R. Kozma (eds.), Springer, 2009.

  35. Ruisheng Wang, Reka Albert
    Discrete dynamic modeling of cellular signaling networks, bio
    Methods in Enzymology 476: Computer Methods B, M. L. Johnson and L. Brand (eds.), p. 281- 306, Academic Press, 2009 biobio

  36. Juilee Thakar, Reka Albert
    Boolean networks in inference and dynamic modeling of biological systems at the molecular and physiological level, biobio
    in Handbook of Biological Networks, S. Boccaletti,V.Latora, Y. Moreno (eds.),  World Scientific Publishing, to appear

    2008

  37. 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 biobio
    PNAS  vol. 105  no. 42  16308-16313 (2008)
    See also the press release: Silencing a protein could kill T-cells, reverse leukemia

  38. BooleanIstván Albert, Juilee Thakar, Song Li, Ranran Zhang , Réka Albert
    Boolean network simulations for life scientist bio
    Source Code for Biology and Medicine 3, 16 (2008) | see related website

  39. Madalena Chaves and Réka Albert
    Studying the effect of cell division on expression patterns of the segment polarity genes biomat
    Journal of the Royal Society Interface 6, 5 (2008)

  40. Sema Kachalo, Ranran Zhang, Eduardo Sontag, Réka Albert and Bhaskar DasGupta
    NET-SYNTHESIS: A software for synthesis, inference and simplification of signal transduction networks bio
    Bioinformatics 2008 24(2):293-295

  41. R. Albert, B. DasGupta, R. Dondi and E. D. Sontag
    Inferring (biological) signal transduction networks via transitive reductions of directed graphsmatcomp
    Algorithmica, Volume 51, Number 2, pp. 129-159, June 2008

    2007

  42. Réka Albert
    Network Inference, Analysis, and Modeling in Systems Biology biogeneral
    The Plant Cell 19: 3327-3338 (2007)

  43. Réka Albert, Bhaskar DasGupta, Ricardo Dondi, Sema Kachalo, Eduardo Sontag, Alexander Zelikovsky, Kelly Westbrooks
    A novel method for signal transduction network inference from indirect experimental evidencematcomp
    Journal of Computational Biology 14, 927-949 (2007)

  44. J. Thakar, M. Pilione, G. Kirimanjeswara, E. Harvill and R. Albert
    Modeling Systems-Level Regulation of Host Immune Responses bio
    PLoS Computational Biology 6, e109 (2007)

  45. BioImageRéka Albert and Zoltán N Oltvai
    Shaping specificity in signaling networks biogeneral
    Nature Genetics (News and Views) 39, 286 - 287 (2007)

  46. Claire Christensen, Juilee Thakar, and Réka Albert
    Systems-level insights into cellular regulation: inferring, analyzing and modeling intercellular networks physbio
    IET Systems Biology 1, 61-77 (2007)

  47. Isabella M. Cattadori, Réka Albert and Brian Boagt
    Variation in Host Susceptibility and Infectiousness Generated by Co-infection: The Myxoma-Trichostrongylus Retortaeformis Case in Wild Rabbits, bio
    Journal of the Royal Society Interface 4, 831-840 (2007)

  48. Claire Christensen, Anshuman Gupta, Costas D. Maranas, and Réka Albert
    Inference and graph-theoretical analysis of Bacillus Subtilis gene regulatory networks biobio
    Physica A  373, 796-810 (2007)

  49. Usha Nandini Raghavan, Réka Albert and Soundar Kumara,
    Near linear time algorithm to detect community structures in large-scale networks biobio
    Phys. Rev. E 76, 036106 (2007)

  50. Asela J. Wijeratne, Wei Zhang, Yujin Sun, Wenlei Liu, Reka Albert, Zhengui Zheng, David G. Oppenheimer, Dazhong Zhao, and Hong Ma
    Differential gene expression in Arabidopsis wild-type and mutant anthers: insights into anther cell differentiation and regulatory networks bio
    The Plant Journal 52, 14-29 (2007)

  51. H. P. Thadakamalla, R. Albert and S. R. T. Kumara
    Search in spatial scale free networks biobio
    New Journal of Physics 9, 190 (2007)

  52. Claire Christensen and Réka Albert
    Using graph concepts to understand the organization of complex systems biogen
    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.

  53. H. P. Thadakamalla, S. R. T. Kumara, and R. Albert,
    Complexity and Large-scale Networks, biogen
    Chapter 11 in Operations Research and Management Science Handbook edited by  A. R. Ravindran, CRC press, 2007.

  54. Jaewook Joo, Eric Harvill, Réka Albert
    Effects of noise on bacteriophage-mediated competition biobio
    Journal of Statistical Physics 128, 229-256 (2007).

    2006

  55. BioImageSong Li, Sarah Assmann and Réka Albert
    Predicting essential components of signal transduction networks: dynamic model of guard cell abscisic acid signaling bio
    PLoS Biology 4 (10): e312, 2006 | read synopsis

  56. Madalena Chaves, Eduardo D. Sontag and Réka Albert
    Methods of robustness analysis for Boolean models of gene control networks biobio
    IEE Proceedings in Systems Biology 153, 154-167 (2006)

  57. Jaewook Joo, Michelle Gunny, Marisa Cases, Peter Hudson, Réka Albert, Eric Harvill
    Bacteriophage-mediated competition in Bordetella bacteria biobio
    Proceedings of the Royal Society B  273, 1843-1848 (2006)

  58. Wen-Yu Chung, Réka Albert, Istvan Albert, Anton Nekrutenko and Kateryna D. Makova
    Rapid and Asymmetric Divergence of Duplicate Genes in the Human Gene Coexpression Network biobio
    BMC Bioinformatics 7 : 46  (2006)

  59. Anshuman Gupta, Costas D. Maranas, and Réka Albert
    Elucidation of directionality for co-expressed genes: predicting intra-operon termination sites | supplementary material biobio
    Bioinformatics 22 (2):209-214 , (2006)

  60. M. Chaves, E.D. Sontag, and R. Albert
    Structure and timescale analysis in genetic regulatory networks biobio
    Proc. IEEE Conf. Decision and Control, San Diego, Dec. 2006 , 2006. IEEE

  61. Réka Albert
    General Network Theorybio
    LACUS Forum 32: Networks (2006), edited by Shin Ja Hwang, William J. Sullivan, Arle R. Lommel, Houston TX, Forum 32, 320 (2006)

    2005

  62. Réka Albert
    Scale-free networks in cell biology biobio
    Journal of Cell Science 118 , 4947-4957 (2005)

  63. Hari P. Thadakamalla, Réka Albert and Soundar Kumara
    Search in weighted complex networks biogen
    Phys. Rev. E 72 , 066128 (2005)

  64. Ryan Kinney , Paolo Crucitti , Réka Albert , Vito Latora
    Modeling Cascading Failures in the North American Power Grid
    biogen
    Eur. Phys. J. B 46 , 101-107 (2005)

  65. Madalena Chaves, Réka Albert and Eduardo D. Sontag
    Robustness and fragility of Boolean models for genetic regulatory networks biobio
    Journal of Theoretical Biology, Volume 235 , pp 431-449 (2005)

    2004

  66. Hari P. Thadakamalla, Usha N. Raghavan, Soundar Kumara and Réka Albert
    Survivability of Multiagent-Based Supply Networks: A Topological Perspective biogen
    IEEE Intelligent Systems, Volume 19 , issue 5, pp 24-31 (2004)

  67. Istvan Albert and Réka Albert
    Conserved network motifs allow protein-protein interaction prediction biobio
    Bioinformatics , Vol. 20, No. 18, (2004)

  68. Réka Albert
    Boolean modeling of genetic regulatory networks biobio
    In: Complex Networks editors: E. Ben-Naim, H. Frauenfelder and Z. Toroczkai), (Springer Verlag 2004)

  69. Réka Albert, Yu-Wen Chiu and Hans G. Othmer
    Dynamic receptor team formation can explain the high signal transduction gain in E. coli biobio
    Biophysics Journal 86, 2650-59 (2004)

  70. Réka Albert, Istvan Albert and Gary L. Nakarado
    Structural Vulnerability of the North American Power Grid biobio
    Phys. Rev. E 69, 025103(R) (2004)

    2003

  71. Pattern

    Réka Albert and Hans G. Othmer
    ... but no kinetic details are needed
    Siam News, Dec. (2003) biobio
    (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)

  72. Réka Albert and Hans G. Othmer
    The topology of the regulatory interactions predicts the expression pattern of the Drosophila segment polarity genes biobio
    Journal of Theoretical Biology 223, 1-18 (2003)

  73. R. Albert, H. G. Othmer, R. Dillon and C. Gadgil
    Spatial Pattern Formation and Morphogenesis in Development: Recent Progress for Two Model Systems biobio
    in Morphogenesis and Pattern Formation in Biological Systems: Experiments and Models , editors: T. Sekimura, S. Noji, N. Ueno and P.K. Maini (Springer Verlag, 2003)

    2001-2002

  74. ISIRéka Albert and Albert-László Barabási ,
    Statistical mechanics of complex networks, bio
    Rev. Mod. Phys. 74, 47-97 (2002)
    selected by ISI as Fast Breaking Paper in Dec 2002

  75. I. Albert, P. Tegzes, R. Albert, J. G. Sample, A-L. Barabási, T. Vicsek and P. Schiffer, bio
    Stick-slip fluctuations in granular drag
    Phys. Rev. E 64, 031307 (2001)

    2000

  76. Nature Cover1R. Albert, A-L. Barabási and H. Jeong
    The Internet's Achilles' heel: Error and attack tolerance in complex networks bio
    Nature 406, 378-382 (2000) (cover story)

  77. Réka Albert and Albert-László Barabási
    Topology of complex networks: local events and universality bio
    Phys. Rev. Lett. 85, 5234 (2000)

  78. H. Jeong, B. Tombor, R. Albert, Z. N. Oltvai and A-L. Barabási
    Topological properties of metabolic networks biobio
    Nature, 407, 651s-654 (2000)

  79. A.-L. Barabási, R. Albert, and H. Jeong
    Scale-free characteristics of random networks:
    The topology of the World Wide Web
    bio
    Physica A 281 69-77 (2000)

  80. Réka Albert and Albert-László Barabási
    Dynamics of Complex Systems: Calculating the Period of Boolean Networks biobio
    Phys. Rev. Lett. 84 5660-5663 (2000)

  81. I. Albert, P. Tegzes, R. Albert, B. Kahng, J. G. Sample, M. Pfeifer, A-L. Barabási, T. Vicsek and P. Schiffer
    Jamming and Fluctuations in Granular Drag bio
    Phys. Rev. Lett. 84 5122-5125 (2000)

    1999

  82. Albert-Laszlo Barabási, Reka Albert and Hawoong Jeong
    Mean-field theory for scale-free random networks bio
    Physica A 272 173-187 (1999)

  83. Albert-László Barabási and Reka Albert
    Emergence of scaling in random networks biogen
    Science 286 509-512 (1999)

  84. R. Albert, H. Jeong and A-L. Barabási,
    The Diameter of the World-Wide Web biogen
    Nature 401 130-131 (1999)

  85. P. Tegzes, R. Albert, M. Paskvan, A-L. Barabási, T. Vicsek and P. Schiffer
    Liquid-Induced Transitions in Granular Media bio
    Phys. Rev. E 60 5823-5827 (1999)

  86. A-L. Barabási, R. Albert and P. Schiffer
    Physics of Sandcastles bio
    Physica A 266 340-345 (1999)

  87. R. Albert, M.A. Pfeifer, P. Schiffer, A-L. Barabási
    Slow drag in a granular medium bio
    Phys. Rev. Lett. 82 205-208 (1999)

    1997-1998

  88. NatureCover2D.J. Hornbaker, R. Albert, I. Albert, A-L. Barabási and P. Schiffer
    What keeps sandcastles standing? biogen
    Nature 387 765 (1997) (cover story)

  89. R. Albert, A-L. Barabási, N. Carle and A. Dougherty
    Driven interfaces in disordered media: determination of universality classes from experimental data bio
    Phys. Rev. Lett. 81 2926-2929 (1998)

  90. R. Albert, I. Albert, D.J. Hornbaker, P. Schiffer, and A-L. Barabási
    Maximum angle of stability in wet and dry spherical granular media bio
    Phys. Rev. E 56 R6271-R6274 (1997).