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Articles arranged by Projects

Network modules/communities

  1. Kov ács, I.A., Palotai, R., Szalay, M.S. and Csermely, P. (2010) Community landscapes: a novel, integrative approach for the determination of overlapping network modules. www.arxiv.org/abs/0912.0161 Supporting web-site with all downloadable algorithms: www.linkgroup.hu/modules.php
  2. Palotai, R. and Csermely, P. (2009) Network modules help the identification of key transport routes, signaling pathways in cellular and other networks. Annalen der Physik 18, 822-829, www.arxiv.org/0908.4524
    Download it! PDF format
  3. Csermely, P. (2008) A network scientists highlights active sites of enzymes, cells, brains and the society. Nature 454, 5 Download it! PDF format
  4. Csermely, P. (2008) Creative elements: network-based predictions of active centres in proteins, cellular and social networks. Trends Biochem. Sci. 33, 569-576, Download it! PDF format
    Visit it at arXiv.org!
  5. Palotai, R. Szalay, M.S. and Csermely, P. (2008) Chaperones as integrators of cellular networks: changes of cellular integrity in stress and diseases. IUBMB Life 60, 10-18, arxiv.org/0710.1622, IF: 2.3 Download it! PDF format
    Visit it at arXiv.org!
  6. Böde, C., Kovacs, I.A., Szalay M., Palotai, R., Korcsmaros, T. and Csermely, P. (2007) Network analysis of protein dynamics. FEBS Lett. 581 (15): 2776-82. IF: 3,5 Download it! PDF format
  7. Korcsmaros, T., Kovacs, I. A., Szalay, M. S. and Csermely, P (2006) Molecular chaperones: The modular evolution of cellular networks. Journal of Bioscience 32 (3): 441-446. IF: 1,5 Download it! PDF format

Network stability, dynamics and spatial games

  1. Whitacre J. M., “Degeneracy: a link between evolvability, robustness and complexity in biological systems” BMC Journal of Theoretical Biology and Medical Modeling, (accepted January, 2010)
    http://arxiv.org/ftp/arxiv/papers/0910/0910.2586.pdf
  2. Whitacre J. M. and Bender A., “Degeneracy: a design principle for robustness and evolvability” Journal of Theoretical Biology, (accepted November, 2009) DOI 10.1016/j.jtbi.2009.11.008
    http://arxiv.org/ftp/arxiv/papers/0907/0907.0510.pdf
  3. Wang, S., Szalay, M.S., Zhang, C. And Csermely, P. (2008) Learning and innovation expand cooperative network topologies, PLoS One 3, e1917 Download it! PDF format
  4. Csermely, P. (2006) Weak Links, Springer Verlag
  5. Kovacs I.A., Szalay, M.S. and Csermely, P. (2005) Water and molecular chaperones act as weak links of protein folding networks: energy landscape and punctuated equilibrium changes point towards a game theory of proteins.
    FEBS Letters, 579, 2254-2260. Download it! PDF format
    Visit it at arxiv.org!
  6. Csermely, P. (2004) Strong links are important – but weak links stabilize them. Trends in Biochem. Sci. 29, 331-334Download it! PDF format
  7. Csermely, P. (2004) The strength of weak links: from stress proteins to social networks. Hungarian Science 111, 1318-1324 (in Hungarian) Download it! PDF format

Signalling networks

  1. Tamas Korcsmaros; Illes J. Farkas; Mate S. Szalay; Petra Rovo; David Fazekas; Zoltan Spiro; Csaba Bode; Katalin Lenti; Tibor Vellai; Peter Csermely (2010) Uniformly curated signaling pathways reveal tissue-specific cross-talks and support drug target discovery.
    Bioinformatics; doi: 10.1093/bioinformatics/btq310
  2. Palotai, R. and Csermely, P. (2009) Network modules help the identification of key transport routes, signaling pathways in cellular and other networks. Annalen der Physik 18, 822-829, www.arxiv.org/0908.4524
    Download it! PDF format
  3. Csermely, P., Korcsmáros, T., Kovács, I.A., Szalay M.S. and Sőti, C. (2008) Systems biology of molecular chaperone networks. In: The biology of extracellular molecular chaperones. Novartis Foundation Symposium Series Vol. 291, Wiley, pp. 45-58. Download it! PDF format
  4. Szalay, M., Kovács, I.A., Korcsmáros, T., Böde. C. and Csermely, P. (2007) Stress-induced rearrangements of cellular networks: consequences for protection and drug design. FEBS Lett. 581, 3675-3680, Download it! PDF format
    Visit it at arXiv.org! IF: 3.5
  5. Korcsmáros, T., Szalay, M., Böde. C., Kovács, I.A., and Csermely, P. (2007) How to design multi-target drugs: Target-search options in cellular networks. Exp. Op. Drug Discovery 2: 1-10. Download it! PDF format
  6. Korcsmaros, T., Kovacs, I. A., Szalay, M. S. and Csermely, P (2006) Molecular chaperones: The modular evolution of cellular networks. Journal of Bioscience 32 (3): 441-446. IF: 1,5 Download it! PDF format

Citation networks

  1. Csermely P., Fábián T.K.: Komplex rendszerek törvényszerűségei a pszichoszomatikában. (Complex systems and psychosomatics) In.: Vértes G., Fábián T.K. (szerk.): Fogorvosi pszichoszomatika. (Psychosomatic dentistry) Medicina, Budapest, 2007; Pp.: 61-67.
  2. Fábián T.K., Müller O., Fejérdy P., Csermely P.: Citációs gráfok a hálózatkutatásban. (citation networks and network research) KisTáska. 2006; 4(38): 8-10.

Protein structure networks

  1. Csermely, P., Palotai, R. and Nussinov, R. (2010) Induced fit, conformational selection and independent dynamic segments: an extended view of binding events. Trends Biochem. Sci. 35, in press, IF: 14.1, http://arxiv.org/abs/1005.0348 -- a cover story. Download it! PDF format
  2. Antal, M.A., Böde, C. and Csermely, P. (2009) Perturbation waves in proteins and protein networks: Applications of percolation and game theories in signaling and drug design. Curr. Prot. Pept. Sci. 10, 161-172, IF: 3.3.
    Download it! PDF format
  3. Csermely, P. (2008) A network scientists highlights active sites of enzymes, cells, brains and the society. Nature 454, 5 Download it! PDF format
  4. Csermely, P. (2008) Creative elements: network-based predictions of active centres in proteins, cellular and social networks. Trends Biochem. Sci. 33, 569-576, Download it! PDF format
    Visit it at arXiv.org!
  5. Böde, C., Kovacs, I.A., Szalay M., Palotai, R., Korcsmaros, T. and Csermely, P. (2007) Network analysis of protein dynamics. FEBS Lett. 581 (15): 2776-82. IF: 3,5 Download it! PDF format

Metabolic networks

  1. Harrison, R., Papp, B., Pal, C., Oliver, S.G. and Delneri, D. (2007) Plasticity of genetic interactions in metabolic networks of yeast. Proc. Natl. Acad. Sci. USA 104, 2307-2312 Download it! PDF format
  2. Pál, C., Papp, B., Lercher, M.J., Csermely, P., Oliver, S.G. and Hurst, L.D. (2006) Chance and necessity in the evolution of minimal metabolic networks. Nature 440, 667-670 paper Download it! PDF format
    Supplementary material PDF format
  3. Hurst, L.D. and Pal, C. (2005) Dissecting dispensability. Nature Genet. 37, 214-215. Download it! PDF format
  4. Pal, C., Papp, B. and Lercher, M.J. (2005) Adaptive evolution of bacterial metabolic networks by horizontal gene transfer. Nature Genet. 37, 1372-1375 Download it! PDF format
  5. Papp, B., Pal, C. and Hurst, L. D. (2004) Metabolic network analysis of the causes and evolution of enzyme dispensability in yeast. Nature 429, 661-664. Download it! PDF format

Protein interaction networks, stress, apoptosis and aging

  1. Simkó, G. I., Gyurkó, D., Veres, D. V., Nánási, T. and Csermely, P. (2009) Network strategies to understand the aging process and help age-related drug design. Visit it at arXiv.org!
    Download Genome Medicine 1, 90! PDF format
  2. Antal, M.A., Böde, C. and Csermely, P. (2009) Perturbation waves in proteins and protein networks: Applications of percolation and game theories in signaling and drug design. Curr. Prot. Pept. Sci. 10, 161-172, IF: 3.3.
    Download it! PDF format
  3. Kiss H.J.M., Mihalik, Á., Nánási, T. Ory, B., Spiró, Z., Soti, C. és Csermely, P. (2009) Ageing as a price of cooperation and complexity: Self-organization of complex systems causes the ageing of constituent networks. Bio Essays 31, 651-664 . Visit it at arXiv.org! Available from Nature Precedings
    Download it! PDF format
  4. Csermely, P. (2008) A network scientists highlights active sites of enzymes, cells, brains and the society. Nature 454, 5 Download it! PDF format
  5. Csermely, P. (2008) Creative elements: network-based predictions of active centres in proteins, cellular and social networks. Trends Biochem. Sci. 33, 569-576. Download it! PDF format
    Visit it at arXiv.org!
  6. Palotai, R. Szalay, M.S. and Csermely, P. (2008) Chaperones as integrators of cellular networks: changes of cellular integrity in stress and diseases. IUBMB Life 60, 10-18, arxiv.org/0710.1622, IF: 2.3 Download it! PDF format
    Visit it at arXiv.org!
  7. Csermely, P., Blatch, G. and Soti, C. (2007) Chaperones as parts of cellular networks. Adv. Exp. Med. Biol. 594, 55-63 Download it! PDF format
  8. Rutherford, S. L., Knapp, J. R. and Csermely, P. (2007) Hsp90 and developmental networks. Adv. Exp. Med. Biol. 594, 190-197 Download it! PDF format
  9. Csermely, P. and Soti, C. (2007) Aging cellular networks: chaperones as major participants. Exp. Gerontol. 42, 113-119, Download it! PDF format
    Visit it at arXiv.org!
  10. Korcsmaros, T., Kovacs, I. A., Szalay, M. S. and Csermely, P (2006) Molecular chaperones: The modular evolution of cellular networks. Journal of Bioscience 32 (3): 441-446. IF: 1,5 Download it! PDF format
  11. Szalay, M., Kovács, I.A., Korcsmáros, T., Böde. C. and Csermely, P. (2007) Stress-induced rearrangements of cellular networks: consequences for protection and drug design. FEBS Lett. 581, 3675-3680, Download it! PDF format
    Visit it at arXiv.org! IF: 3.5
  12. Csermely, P. and Soti, C. (2006) Cellular networks and the aging process. Arch. Physiol. Biochem. 112, 60-64 Download it! PDF format
  13. Nardai, G., Vegh, E., Prohaszka, Z. and Csermely, P. (2006) Chaperone-related immune dysfunctions: An emergent property of distorted chaperone-networks. Trends Immunol. 27, 74-79 Download it! PDF format
  14. Soti, Cs., Pal, Cs., Papp, B. and Csermely, P. (2005) Chaperones as regulatory elements of cellular networks. Curr. Op. Cell Biol. 17, 210-215 Download it! PDF format
  15. Sreedhar, A.S., Mihály, K., Pató, B., Schnaider, T., Steták, A., Kis-Petik, K., Fidy, J., Simonics, T., Maráz, A. and Csermely, P. (2003) Hsp90 inhibition accelerates cell lysis: anti-Hsp90 ribozyme reveals a complex mechanism of Hsp90 inhibitors involving both superoxide- and Hsp90-dependent events. J. Biol. Chem. 278, 35231-35240 Download it! PDF format
  16. Nardai, G., Csermely, P. and Soti, Cs. (2002) Chaperone function and chaperone overload in the aged, Exp. Gerontol, 37, 1255-1260 Download it! PDF format
  17. Csermely, P. (2001) Chaperone-overload as a possible contributor to “civilization diseases”: atherosclerosis, cancer, diabetes. Trends in Genetics, 17, 701-704 Download it! PDF format
    Supplementary material PDF format

Networks and drug design

  1. Spiro, Z., Kovacs I.A. and Csermely, P. (2008) Insights from networks of drugs, therapies, targets and diseases and the prediction of novel drug targets. J. Biol. 7, 20.
    Visit the extended version at arXiv.org!
     Download it! PDF format
  2. Antal, M.A., Böde, C. and Csermely, P. (2009) Perturbation waves in proteins and protein networks: Applications of percolation and game theories in signaling and drug design. Curr. Prot. Pept. Sci. 10, 161-172, IF: 3.3.
    Download it! PDF format
  3. Korcsmáros, T., Szalay, M., Böde. C., Kovács, I.A., and Csermely, P. (2007) How to design multi-target drugs: Target-search options in cellular networks. Exp. Op. Drug Discovery 2: 1-10. Download it! PDF format
  4. Agoston, V., Csermely, P. and Pongor, S. (2005) Multiple, weak hits confuse complex systems. Phys. Rev. E. 71, 051909, Download it! PDF format
    Visit it at arXiv.org!
  5. Csermely, P., Ágoston, V. and Pongor, S. (2005) The efficiency of multi-target drugs: the network approach might help drug design. Trends Pharmacol. Sci. 26, 178-182 Download it! PDF format
    Visit it at arXiv.org!

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