Publications

- Biology - Mathematics

- Physics - Computational

- General audience

2013

1. R. Wang and R. Albert
   Effects of community structure on the dynamics of random threshold network
   Phys. Rev. E (in press, 2013).

2. R. Wang, Z. Sun and R. Albert
   Minimal functional routes in directed graphs with dependent edges
   International Transactions in Operational Research(in press, 2013).

3. A. Saadatpour, R. Albert
   Boolean modeling of biological regulatory networks: A methodology tutorial
   Methods (in press, 2013).

4. 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)

2012

1. 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

2. R. S. Wang, A. Saadatpour, R. Albert
   Boolean modeling in systems biology: an overview of methodology and applications
   Physical Biology 9 055001 (2012)

3. 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

1. 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
   PLoS Computational Biology 7:e1002267 (2011)

2. 

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

3. 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. Rev. E 84, 036117 (2011)

4. 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)

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

6. 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)

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

   2010

8. 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,
   Molecular Systems Biology 6:372 (2010)

9. Juilee Thakar, Mary Poss, Réka Albert, Gráinne H Long and Ranran Zhang
   Dynamic models of immune responses: what is the ideal level of detail?
   Theoretical Biology and Medical Modelling 7:35 (2010)

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

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

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

13. Ranran Zhang, Thomas P. Loughran, Reka Albert
    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)

14. L.Y. Cui, S. Kumara and R. Albert,
    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).

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

    2009

16. 

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

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

18. Reka Albert and Sarah M. Assmann
    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).

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

20. Ruisheng Wang, Reka Albert
    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

21. Juilee Thakar, Reka Albert
    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

    2008

22. 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

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

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

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

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

    2007

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

28. 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 evidence
    Journal of Computational Biology 14, 927-949 (2007)

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

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

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

32. 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,
    Journal of the Royal Society Interface 4, 831-840 (2007)

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

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

35. 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
    The Plant Journal 52, 14-29 (2007)

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

37. Claire Christensen and Réka Albert
    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.

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

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

    2006

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

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

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

43. 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
    BMC Bioinformatics 7 : 46  (2006)

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

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

46. Réka Albert
    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)

    2005

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

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

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

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

    2004

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

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

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

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

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

    2003

56. 

    Réka Albert and Hans G. Othmer
    ... 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)

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

58. R. Albert, H. G. Othmer, R. Dillon and C. Gadgil
    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, 2003)

    2001-2002

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

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

    2000

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

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

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

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

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

66. 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
    Phys. Rev. Lett. 84 5122-5125 (2000)

    1999

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

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

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

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

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

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

    1997-1998

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

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

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