Signalling networks

Background

Link to the SignaLink website
containing the related manuscript,
its supplement and the database.

The Network Biology (NetBiol) Group is at the Department of Genetics of the Eötvös Loránd University. The NetBiol Group works in close cooperation with the LINK-Group led by Prof. Peter Csermely and with the experimental C. elegans lab led by Tibor Vellai. Our completed research projects include

1. the development of a signaling pathway database, SignaLink, which focuses especially on signaling cross-talk,
2. the identification of novel signaling proteins (signalogs),
3. the development of the PathwayLinker webservice that analyzes the signaling pathway memberships of proteins as well as their interactors for experiment design and evaluation,
4. a systems-level examination of the interaction and regulatory network of NRF2, a major transcription factor important in antioxidant response and cancer therapy.

Current research interest

Autophagy, the major catabolic process of eukaryotic cells degrading and recycling damaged macromolecules and organelles, is implicated in several diseases, e.g., cancer and neurodegenerative disorders. In anticancer therapy, medical downregulation of autophagy would be important as radiotherapy and certain cytotoxic drugs were found to induce autophagy and protect the cancer cells. Autophagy is regulated by a complex signaling network, including several pathways and cross-talks between them. Currently, we are using network based approaches and dynamical modeling to uncover key signaling components important in the robustness of the autophagy-regulating signaling network. These key proteins would be unexpected autophagy regulators and possible novel chemotherapic drug targets for intervening autophagy.

If you have any questions regarding the above mentioned project or about our results, please write to: korcsmaros [at] netbiol.elte.hu.

• A collection of groups working with signaling networks
• A collection of useful and important biological sites in network science

The list of publications:

1. Csályi, K., Fazekas, D., Kadlecsik, T., Türei, D., Gul, L., Horváth, B., Dezső Módos, D., Demeter, A., Pápai, N., Lenti, K., Csermely, P., Vellai, T., Korcsmáros, T. and Varga, M. (2016) SignaFish: a zebrafish-specific signaling pathway resource. Zebrafish, 13, 541-544, IF: 2.0 Download it!
2. Nussinov, R. Tsai, C-J., Janga, H., Korcsmáros, T. and Csermely, P. (2016) Oncogenic KRAS signaling and YAP1/β-catenin: Similar cell cycle control in tumor initiation. Sem. Cell Dev. Biol. 58, 79-85, IF: 6.3 Download it!
3. Csermely, P., Korcsmaros, T. and Nussinov, R. (2016) Intracellular and intercellular signaling networks in cancer initiation, development and precision anti-cancer therapy. RAS acts as contextual signaling hub. Sem. Cell Dev. Biol. 58, 55-59, IF: 6.3 Download it!
4. Modos, D., Brooks, J., Fazekas, D., Ari, E., Vellai, T., Csermely, P., Korcsmáros, T. and Lenti, K. (2016) Identification of critical paralog groups with indispensable roles in the regulation of signaling flow. Sci. Rep. 6, in press, IF: 5,2
5. Adami, H.-O., Csermely, P., Veres, D.V., Emilsson, L., Loberg, M., Bretthauer, M. and Kalager, M. 2016. Are rapidly growing cancers more lethal? Eur. J. Cancer. in press, IF: 6.2 Download it!
6. Korcsmaros, T., Modos, D., Bulusu, K., Fazekas, D., Kubisch, J., Brooks, J., Marczell, I., Szabo, P., Vellai, T., Csermely, P., Lenti, K. and Bender, A. (2016) Neighbours of cancer-related proteins have key influence on pathogenesis and could increase the drug target space for anti-cancer therapies. Systems Biology and Applications, in press.
7. Korcsmaros, T. Dunai, Z.A., Vellai, T. and Csermely, P. (2013). Teaching the bioinformatics of signaling networks - an integrated approach to facilitate multidisciplinary learning. Briefings Bioinformatics 14, 618-632, IF: 5.2 Download it!
8. Türei, D., Papp, D., Fazekas, D., Földvári-Nagy, L., Módos, D., Lenti, K., Csermely, P. and Korcsmaros, T. (2013) NRF2-ome, an integrated web resource to discover protein interaction and regulatory networks of NRF2. Oxidative Medicine and Cellular Longevity, 737591, IF: 2.8 Download it!
9. Diána Papp, Katalin Lenti, Dezső Módos, Dávid Fazekas, Zoltán Dúl, Dénes Türei, László Földvári-Nagy, Ruth Nussinov, Péter Csermely, Tamás Korcsmáros (2012) The NRF2-related interactome and regulome contain multifunctional proteins and fine-tuned autoregulatory loops. FEBS Letters 586, 1795-1802, IF: 3.6 Download it!
10. Farkas IJ, Szántó-Várnagy Á, Korcsmáros T (2012) Linking proteins to
    signaling pathways for experiment design and evaluation. PLoS ONE 7,
    e36202 IF: 4.4
    Download it!
11. 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!
    Download the slideshow!
12. 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!
13. Tamás Korcsmáros; Illes 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!
14. 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!
15. Korcsmáros, T., Kovács, 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!
16. 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!
    Visit it at arXiv.org! IF: 3.5
17. 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!