COSBICS

Nikolov, S., Vera, J., Rath, O., Kolch, W., Wolkenhauer, O.: The role of inhibitory proteins as modulators of oscillations in NFkB signalling. IET Systems Biology2008(in press)

J.Vera, T.Millat, W.Kolch, O.Wolkenhauer: Dynamics of receptor and protein transducer homodimerisation. BMC Systems Biology (In press 2008).

Balsa-Canto, E., Alonso A.A., Banga, J.R.: Computational Procedures for Optimal Experimental Design in Biological Systems. IET Systems Biology (In press 2008).

Banga, J.R., Balsa-Canto, E.: Parameter estimation and optimal experimental design. Essays in Biochemistry (In press 2008).

Nikolov, S., Petrov, V., Kotev, V., Georgiev, G.: Mathematical description of time delays in pathways cross talk. Handbook of Research on Systems Biology Applications in Medicine, Idea Group Inc. (In press 2008).

Balsa-Canto, E., Peifer, M., Timmer, J., Banga, J.R, Fleck, C.: Hybrid optimization method with general switching strategy for parameter estimation.
BMC Systems Biology, 2:26 (2008) doi:10.1186/1752-0509-2-26.

Nikolov, S., Vera, J., Kotev, V., Wolkenhauer, O., Petrov, V.: Dynamic properties of a delayed protein cross talk model. Biosystems, 91:51–68 (2008). doi:10.1016/j.biosystems.2007.07.004.

Vera, J., Bachmann, J., Pfeifer, A.C., Becker, V., Hormiga, J.A., Torres Darias, N.V., Timmer, J., Klingmüller, U., Wolkenhauer, O.: A systems biology approach to analyse amplification in the JAK2-STAT5 signalling pathway. BMC Systems Biology 2:38 (2008). doi:10.1186/1752-0509-2-38. http://www.biomedcentral.com/1752-0509/2/38

Vera, J., Kwon, T., Schmitz, U., Millat, T., Wolkenhauer, O.: Bioinformatics analysis of interactions of receptor homodimers with intracellular protein homodimers. Rostocker Informatik Berichte, 31 ISSN 0233-0784 (2008).

Dhillon, AS., Hagan, H., Rath, O. and Kolch, W.: MAP kinase signalling pathways in cancer. Oncogene. 2007, 26, 32793290.

Balsa-Canto, E., Alonso, A.A., Banga, J.R.: Optimal Dynamic Experimental Design in Systems Biology: Applications in Cell Signaling. In Proceedings of the 10th Computer Applications on Biotechnology (CAB). IFAC. Mexico, 4-6 June, 2007.

Geier, F., Timmer, J., Fleck, C.: Reconstructing gene-regulatory networks from time series, knock-out data, and prior knowledge. BMC Systems Biology, 1, 11 (2007).

Hengl S., Kreutz C., Timmer J., Maiwald T.: Data-based identifiability analysis of non-linear dynamical models. Bioinformatics. Vol. 23(19):2612–2618, 2007.

Kim, D., Rath, O., Kolch, W. and Cho, K.H.: A hidden oncogenic positive feedback loop caused by crosstalk between Wnt and ERK Pathways. Oncogene, 26(31):4571-9 (2007).

Klingmüller, U., Schilling, M., Bohl, S., Pfeifer, A. C.: The need for standardization in systems biology. European Science Foundation (ESF) Forward Look Systems Biology: a Grand Challenge for Europe (2007).

Kotev, V.: Dynamical behavior of a time delay model of the ERK and STAT5 interaction. Bioautomation, 8: 123-132 (2007).

Kotev, V., Nikolov, S.: Stability analysis of time delay model of crosstalk between ERK and STAT5a interaction. Bioautomation, 7: 90-98 (2007).

Kreutz C., Bartolome Rodriguez M.M., Maiwald T., Seidl M., Blum H.E., Mohr L., Timmer J.: An error model for protein quantification. Bioinformatics. 23(20):2747–2753, 2007.

Maiwald, T., Kreutz, C., Pfeifer, A., Bohl, S., Klingmüller, U., Timmer, J.: Dynamic pathway modeling - Feasibility analysis and optimal experimental design. Annals New York Acad. Sci. 1115, 212-220 (2007).

Nikolov, S., Georgiev, G., Kotev, V., Wolkenhauer, O.: Stability analysis of a time delay model for the JAK-STAT signaling pathway. Series onBiomechanics, 23(1): 52-65 (2007).

Nikolov, S., Petrov, V.: Time delay model of RNA silencing. J. of Mech. in Med. and Biol., 7(3): 297-314 (2007).

Nikolov, S., Vera, J., Wolkenhauer, O., Petrov, V.: Investigation of dynamic behaviour of receptor tyrosin kinase and protein tyrosine phospatase reaction network using mathematical model. International Electronic Journal of Bioautomation (IEJB), 8(1):105-114 (2007).

Nikolov, S., Vera, J., Wolkenhauer, O., Yankulova, E., Petrov, V.: Chaos in a delayed protein cross talk model with periodic forcing, Comptes rendus de l´Academie bulgare des Sciences, vol.60, No 2, pp.127-132, 2007.

Nikolov, S., Yankulova, E., Wolkenhauer, O., Petrov, V.: Principal difference between stability and structural stability (robustness) as used in systems biology. Nonlinear Dynamics, Psychology, and Life Sciences, 11(4): 413-433 (2007).

Nikolova, E., Petrov, V.: Influence of RKIP protein complexes concentrations on the quasi-stationary behaviour of the MEK/ERK signal transduction pathway. Bioautomation, 8: 115-122 (2007).

Petrov, V., Georgiev, N., Nikolov, S., Georgiev, G.: Towards dynamical theory of breast carcinoma cell. Series on Biomechanics, 23(1): 19-34 (2007).

Petrov, V., Nikolova, E., Wolkenhauer, O.: Reduction of Nonlinear Dynamic Systems with an Application to Signal Transduction Pathways. IET Systems Biology, 2-9, Vol. 1, Issue 1, January 2007.

Rateitschak, K., Wolkenhauer, O.: Intracellular delay limits cyclic changes in gene expression (arXiv:q-bio.MN/0602009 v1, 7 Feb 2006). Mathematical Biosciences,205(2):163-79 (Feb, 2007). Epub Aug (2006) doi:10.1016/j.mbs.2006.08.010.

Rath, O., Park, S., Tang, HH., Banfield, M.J., Brady, R.L., Lee, Y.C., Dignam, J.D., Sedivy, J.M., Kolch, W., Yeung, K.C. The RKIP (Raf-1 Kinase Inhibitor Protein) conserved pocket binds to the phosphorylated N-region of Raf-1 and inhibits the Raf-1-mediated activated phosphorylation of MEK. Cell Signal., 20(5):935-41.(2008)

Ullah, M., Wolkenhauer, O.: Family tree of Markov models in systems biology. IET Systems Biology 1(4): 247-254 (2007).

Vera, J., Balsa-Canto, E., Wellstead, P., Banga, J.R., Wolkenhauer, O.: Power-Law models of signal transduction pathways. Cellular Signalling, 19: 1531-1541 (2007). 
doi:10.1016/j.cellsig.2007.01.029.

Vera, J., Sun, C., Oertel, Y., Wolkenhauer, O.: PLMaddon: A power-law module for the MatlabTM  SBToolbox. Bioinformatics, 23(19):2638-40 (2007).
doi:10.1093/bioinformatics/btm245.

Assmus, H.E., Herwig, R., Cho, K.H., Wolkenhauer, O.: Dynamics of biological systems: the role of systems biology in medical research. Expert Rev. Mol. Diagn. 6(6) 891-902, 2006.

Balsa-Canto, E., Rodríguez-Fernández, M., Alonso, A.A., Banga, J.R.: Computational design of optimal dynamic experiments in systems biology: a case study in cell signalling. Understanding and Exploiting Systems Biology in Bioprocesses and Biomedicine (2006). Edited by: M. Canovas, J.L. Iborra, A. Manjon. pp103-117 Murcia, Spain Caja Murcia..

Balsa-Canto, E.; Peifer, M.; Fleck, C.; Timmer, J.; Banga, J.R. (2006) A hybrid optimization method for parameter estimation in systems biology. In Proceedings of 5th Vienna Symposium on Mathematical Modelling (5TH MATHMOD), Austria, 8-10 Feb.

Georgiev, N., Gospodinov, P. & Petrov, V: Multi-variate time series based reconstruction of dynamical systems. Advanced Modeling and Optimization, 8 (1): (2006).

Georgiev, N., Petrov, V., Georgiev, G.: Modelling ERK and STAT proteins interaction. Porceedings of BioPS'06, October 24-25 Sofia, pp. III.9-III.18 (2006).

Georgiev, N., Petrov, V., Georgiev, G.: Reaction-diffusion modelling ERK- and STAT- interaction dynamics. Journal on Bioinformatics and Systems Biology 2006,1-12.

Georgiev, N., Petrov, V., Nikolova, E., Georgiev, G.: Qualitative Modelling Inhomogeneous Effects in ERK and STAT Interaction Dynamics. International Electronic Journal of Bioautomation (IEJB) 5, 78-89 (2006).

Nikolov, S., Kotev, V., Georgiev, G. and Petrov, V.: Dynamical roles of time delays in protein cross talk models. Comptes Rendus de l'Academie Bulgare des Sciences, 59 (3): 261-268 (2006).

Nikolov, S., Kotev, V., Petrov, V.: Influence of Time Delay on Bifurcation Behaviour in the Protein Synthesis Model. Proceedings of BioPS'06, October 24-25 Sofia, pp. III.37-III46 (2006)

Nikolov, S., Kotev, V., Petrov, V.: Bifurcation Behaviour of Time Delay Model of Enzyme and Repressor Cross Talk. Proceedings of BioPS'06, October 24-25 Sofia, pp. III.47-III.56 (2006).

Nikolov, S., Yankulova, E., Nikolova, A., Petrov, V., Stability and Structural Stability (robustness) in Computational systems Biology, Journal of the Bulgarian Academy of Sciences, vol. 69, No 6, pp. 21-29, 2006.

Nikolova, E.: New result in Ras/Raf/MEK/ERK signal pathway dynamical model. Comptes Rendus de l'Academie Bulgare des Sciences, 59 (2): 143-150 (2006).

Nikolova, E., Petrov, V., Georgiev, N.: Space-temporal modelling of ERKPP/RKIP/RAF-1 Dynamics in RAS/RAF/MEK/ERK Signal Pathway. Proceedings of BioPS'06, October 24-25 Sofia, pp. III.1-III8 (2006).

Park, S., Rath, O., Beach, S., Xiang, X., Kelly, S.M., Luo, Z., Kolch, W., Yeung, K.C.: Regulation of RKIP binding to the N-region of the Raf-1 kinase. FEBS Letters, 580, (27): 6405-6412 (2006).

Petrov, V. & Georgiev, N.: Dynamical model of ERK- and STAT- proteins interaction, Comptes Rendus de l'Academie Bulgare des Sciences, 59 (3): 269-276 (2006).

Petrov, V., Georgiev, N.: Inhomogeneous Distributions of Concentrations in ERK- and STAT- Protein Interaction Model. Comptes Rendus de l'Academie Bulgare des Sciences, 59 (11): 1147-1156 (2006).

Vera, J., Bachmann, J., Pfeifer, A. C., Hormiga, J.A., Torres Darias, N.V., Klingmüller, U., Wolkenhauer, O.: A power-law model to describe the dynamics of the JAK2-STAT5 signalling pathway. Chapter in the book “Understanding and Exploiting Systems Biology in Bioprocesses and Biomedicine” (M. Cánovas, J. L. Iborra, A. Manjón eds.), pp. 163-173. Fundación Cajamurcia, Murcia, Spain. 2006.

Hagan, S., Al-Mulla, F., Mallon, E., Oien, K., Ferrier, R., Gusterson, B., Curto Garcia J.J., Kolch, W.: Reduction of Raf-1Kinase Inhibitor Protein Expression Correlates with Breast Cancer Metastasis. Clin Cancer Res 11(20) October 15 (2005).

Mesarovic, M., Sreenath, S.N., Wolkenhauer, O.: Multilevel, hierarchical systems paradigm of systems biology. Proceedings of the Congress: Foundations of Systems Biology and Engineering (FOSBE). UCSB, Santa Barbara, California, August 2005.

Nikolov, S., Kotev, V. & Petrov, V.: An alternative approach to investigating a time delay model of JAK/STAT signalling pathway. Comptes Rendus de l'Academie Bulgare des Sciences, 58 (8): 889-896 (2005).

Nikolov, S., Kotev, V. and Petrov, V: Stability analysis of a time delay model of the JAK-STAT signalling pathway. Proceedings of the 10th jubilee congress of theoretical and applied mechanics, Varna, Bulgaria, 13-16 September 2005: 156-162 (2005).

Nikolova, E.: Reduction of dimensionality of Ras/Raf/MEK/ERK signal pathway dynamical model. Proceedings of the 10th Jubilee Congress on Theoretical and Applied Mechanics, Varna, Bulgaria, 2: 170-175 (2005).

Petrov, V., Georgiev, G.: On the spatialdescription of cell signalling with application to ERK and STAT pathways stability. Comptes Rendus de l'Academie Bulgare des Sciences, 58 (12): 1391-1398 (2005).

Petrov, V., Georgiev, N., Nikolova, E.: Izchislitelna systemna biologia na kletuchno signalizirane. Journal of the Bulgarian Academy of Sciences, 2: 45-51 (2005) (in Bulgarian).

Petrov, V., Georgiev, N., Nikolova, E.: Systems biology of cell signalling pathways. Proceedings of the 10th Jubilee Congress on Theoretical and Applied Mechanics, Varna, Bulgaria, 2: 120-123 (2005).

Petrov, V., Nikolova, E. & Wolkenhauer, O.: Driver identification of the RAS/RAF/MEK/ERK signal transduction pathways. Comptes Rendus de l'Academie Bulgare des Sciences, 58 (6): 639-644 (2005).

Petrov, V., Peifer, M., Timmer, J.: Structural stability analysis of a cell cycle control model. Comptes Rendus de l'Academie Bulgare des Sciences, 58 (1): 19-24 (2005).

Rateitschak, K., Wolkenhauer, O.: Steady state - limit cycle - steady state transitions in gene transcription networks with distributed time delay. Proceedings of the Congress: International Conference for Systems Biology (ICSB). Boston, October 2005.

Soebiyanto, R.P., Sreenath, S.N., Mesarovic, M.D., Wolkenhauer, O.: From networks to systems to complex systems: A signalling pathway coordination case study. Proceedings of the Congress: 44th IEEE Conference on Decision and Control and European Control Conference (ECC). Sevilla, Spain, 12-15 December 2005.

Wellstead, P., Mason, O., O'Connor, W.T., Cho, K.-H., Bullinger, E., Wolkenhauer, O., Duncan, S.: Towards a systems understanding of the cerebral motor circuit. Proceedings of the Congress: 23. Foundations of Systems Biology and Engineering (FOSBE). UCSB, Santa Barbara, California, August 2005.

Wolkenhauer, O., Mesarovic, M., Wellstead, P.: A pledge for more theory in cell signalling experiments: When fishing for drug targets is not sufficient. Proceedings of the Ernst Schering Foundation Workshop "Systems Biology - Applications and Perspectives" (2005).