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Articles arranged by Projects

Network modules/communities

  1. Szalay-Bekő, M., Palotai, R., Szappanos, B., Kovács, I.A., Papp, B. and Csermely, P. (2011) ModuLand plug-in for Cytoscape: extensively overlapping modules, community centrality and their use in biological networks. http://arxiv.org/abs/1111.3033
    Download it! PDF format
    The Cytoscape plug-in program and its User Guide can be downloaded from here: http://www.linkgroup.hu/modules.php
  2. Kovács, I.A., Palotai, R., Szalay, M.S. and Csermely, P. (2010) Community landscapes: a novel, integrative approach for the determination of overlapping network modules. PLoS ONE 7, e12528, IF: 4.4 Download it! PDF format
    www.arxiv.org/abs/0912.0161 Supporting web-site with all downloadable algorithms: www.linkgroup.hu/modules.php
    Featured in the February 2011 issue of Science Signaling
  3. 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
  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. 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
  8. 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. Farkas, I.J., Korcsmáros, T., Kovács, I.A., Mihalik, Á., Palotai, R., Simkó, G.I., Szalay, K.Z., Szalay-Bekő, M., Vellai, T., Wang, S. and Csermely, P. (2011) Network-based tools in the identification of novel drug-targets. Science Signaling 4, pt3. Download the paper! PDF format
    Download the slideshow!
  2. 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
  3. 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
  4. 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
  5. Csermely, P. (2006) Weak Links, Springer Verlag
  6. 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!
  7. Csermely, P. (2004) Strong links are important – but weak links stabilize them. Trends in Biochem. Sci. 29, 331-334Download it! PDF format
  8. 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

Network perturbation analysis

  1. Farkas, I.J., Korcsmáros, T., Kovács, I.A., Mihalik, Á., Palotai, R., Simkó, G.I., Szalay, K.Z., Szalay-Bekő, M., Vellai, T., Wang, S. and Csermely, P. (2011) Network-based tools in the identification of novel drug-targets. Science Signaling 4, pt3. Download the paper! PDF format
    Download the slideshow!
  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. Pept. Prot. Res. 10, 161-172  Download it! PDF format
    Visit it at arxiv.org!

Signalling networks

  1. Farkas, I.J., Korcsmáros, T., Kovács, I.A., Mihalik, Á., Palotai, R., Simkó, G.I., Szalay, K.Z., Szalay-Bekő, M., Vellai, T., Wang, S. and Csermely, P. (2011) Network-based tools in the identification of novel drug-targets. Science Signaling 4, pt3. Download it! PDF format
    The accompanying slideshow is available here.
  2. Korcsmáros, T. Szalay, M.S., Rovó, P., Palotai, R., Fazekas, D., Lenti, K., Farkas, I.J. Csermely, P. and Vellai, T. (2011) Signalogs: orthology-based identification of novel signaling pathway components in three metazoans. PLoS ONE 8, e19240, IF: 4,4 Download it! PDF format
  3. Tamás Korcsmáros; Illés J. Farkas; Máté S. Szalay; Petra Rovó; Dávid Fazekas; Zoltán Spiró; Csaba Böde; Katalin Lenti; Tibor Vellai; Péter Csermely (2010) Uniformly curated signaling pathways reveal tissue-specific cross-talks and support drug target discovery. Bioinformatics 26, 2042-2050, IF: 4,9; Download it! PDF format
    Supplementary material PDF format
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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

Protein structure networks

  1. Szalay-Bekő, M., Palotai, R., Szappanos, B., Kovács, I.A., Papp, B. and Csermely, P. (2011) ModuLand plug-in for Cytoscape: extensively overlapping modules, community centrality and their use in biological networks. http://arxiv.org/abs/1111.3033
    Download it! PDF format
    The Cytoscape plug-in program and its User Guide can be downloaded from here: http://www.linkgroup.hu/modules.php
  2. Csermely, P., Sandhu, K.S., Hazai, E., Hoksza, Z., Kiss, H.J.M., Miozzo, F. Veres, D.V., Piazza, F. and Nussinov, R. (2011) Disordered proteins and network disorder in network representations of protein structure, dynamics and function. Hypotheses and a comprehensive review. Curr. Prot. Pept. Sci. in press, IF: 3,9, http://arxiv.org/abs/1101.5865
    Download it! PDF format
  3. 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, 539-546, IF: 11.6, http://arxiv.org/abs/1005.0348 -- a cover story. Download it! PDF format
  4. 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
  5. Csermely, P. (2008) A network scientists highlights active sites of enzymes, cells, brains and the society. Nature 454, 5 Download it! PDF format
  6. 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!
  7. 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. Szalay-Bekő, M., Palotai, R., Szappanos, B., Kovács, I.A., Papp, B. and Csermely, P. (2011) ModuLand plug-in for Cytoscape: extensively overlapping modules, community centrality and their use in biological networks. http://arxiv.org/abs/1111.3033
    Download it! PDF format
    The Cytoscape plug-in program and its User Guide can be downloaded from here: http://www.linkgroup.hu/modules.php
  2. 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
  3. 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
  4. Hurst, L.D. and Pal, C. (2005) Dissecting dispensability. Nature Genet. 37, 214-215. Download it! PDF format
  5. 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
  6. 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. Mihalik, Á. and Csermely, P. (2011) Heat shock partially dissociates the overlapping modules of the yeast protein-protein interaction network. PLoS Comput. Biol. 7, e1002187, IF: 5.5 Download it! PDF format
    http://arxiv.org/abs/1105.2933
  2. 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
  3. 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
  4. 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
  5. Csermely, P. (2008) A network scientists highlights active sites of enzymes, cells, brains and the society. Nature 454, 5 Download it! PDF format
  6. 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!
  7. 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!
  8. 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
  9. 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
  10. 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!
  11. 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
  12. 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
  13. Csermely, P. and Soti, C. (2006) Cellular networks and the aging process. Arch. Physiol. Biochem. 112, 60-64 Download it! PDF format
  14. 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
  15. 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
  16. 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
  17. 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
  18. 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. Nussinov, R., Tsai, C.-J. and Csermely, P. (2011) Allo-network drugs: harnessing allostery in cellular networks. Trends in Pharmacol. Sci. 32, 686-693, IF: 11.0 -- a cover story. Download it! PDF format
  2. Farkas, I.J., Korcsmáros, T., Kovács, I.A., Mihalik, Á., Palotai, R., Simkó, G.I., Szalay, K.Z., Szalay-Bekő, M., Vellai, T., Wang, S. and Csermely, P. (2011) Network-based tools in the identification of novel drug-targets. Science Signaling 4, pt3. Download the paper! PDF format
    Download the slideshow!
  3. 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
  4. 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
  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. 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!
  7. 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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Published by the LINK-Group | Editor: Péter Csermely | Last updated on 12. Jan. 2011.
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