Combio
An integrative approach to cellular signalling and control processes: Bringing computational biology to the bench.


2004

Ander M., Beltrao P., Di Ventura B., Ferkinghoff-Borg J., Foglierini M., Kaplan A. Lemerle C., Tomas-Oliveira I. & Serrano L. (2004). “SmartCell, a framework to simulate cellular processes that combines stochastic approximation with diffusion and localisation: analysis of simple networks”, Systems Biology IEE, 1: 129- 138.

2005

Lemerle, C., B. Di Ventura & Serrano L. (2005). “Space as the final frontier in stochastic simulations of biological systems”, FEBS Lett., 579: 1789-94.

Thomas R. & Kaufman M. (2005). “Frontier diagrams: Partition of phase space according to the signs of the eigenvalues or to the sign patterns of the circuits”, Int. J. of Bifurcation and Chaos, 15 (10).

Ciliberto, A., Novák B. & Tyson, J.J. (2005): Steady States and oscillations in the p53/Mdm2 network. Cell Cycle 4 (3): 488-493.

Ciliberto, A., Lukacs A., Toth A., Tyson, J.J. & Novák B. (2005): Rewiring the exit from mitosis. Cell Cycle 4(8), see web page: http://www.landesbioscience.com/journals/cc/abstract.php?id=1873

Lange BM, Kirfel G, Gestmann I, Herzog V, Gonzalez C. Structure and microtubule-nucleation activity of isolated Drosophila embryo centrosomes characterized by whole mount scanning and transmission electron microscopy. Histochem Cell Biol. (2005) Aug 10;:1-10 [Epub ahead of print]

Caussinus, E & Gonzalez, C Induction of tumor growth by altered stem-cell asymmetric division in Drosophila melanogaster Nature Genetics 37, 1125 - 1129 (2005)

Ciliberto, A., Novák B. & Tyson, J.J. (2005): Steady states and oscillations in the p53/Mdm2 network. Cell Cycle 4: 488-493.

Novák B., Chen, K. & Tyson, J.J. (2005): Sytems biology of the yeast cell cycle engine. Topics in Current Genetics, Vol. 13. Systems Biology: Definitions and Perspectives (eds. L. Alberghina & H.V. Westerhof) pp. 305-324, Springer Verlag GmbH.

Potapov, A.P., Voss, N., Sasse, N., Wingender, E. (2005) Topology of mammalian transcription networks. Genome Inf. Ser. 16:270-278.

2006

Dublanche, Y., Michalodimitrakis, K., Kummerer, N., Foglierini, M. and Serrano, L. Noise in transcription negative feedback loops: simulation and experimental analysis. Mol Syst Biol, 2, 41, (2006).

Di Ventura, B., Lemerle, C., Michalodimitrakis, K. and Serrano, L. From in vivo to in silico biology and back. Nature, 443, 527-533, (2006).

Csikász-Nagy A., Battogtokh, D., Chen, K.C:, Novák B. & Tyson, J.J. (2006): Analysis of a generic model of eukaryotic cell cycle regulation. Biophysical Journal 90: 4361-4379

Lovrics, A., Csikasz-Nagy A., Zsely I.G. Zador J., Turanyi T. & Novak B. (2006): Time scale and dimension analysis of a budding yeast cell cycle model. BMC Bioinformatics 7:494.

Naama Geva-Zatorsky, Nitzan Rosenfeld, Shalev Itzkovitz, Ron Milo, Alex Sigal., Erez Dekel, Talia Yarnitzky, Yuvalal Liron, Paz Polak, Galit Lahav and Uri Alon, Oscillations and variability in the p53 system. Molecular Systems Biology, (2006).

Castoldi M. and I.Vernos (2006) Chromokinesin Xklp1 contributes to the regulation of microtubule density and organization during spindle assembly. Mol Biol Cell. Mar;17(3):1451-60.

Christodoulou A., Lederer C.W., Surrey T., Vernos I., and N. Santama (2006) Motor protein KIFC5A interacts with Nubp1 and Nubp2 and is implicated in the regulation of centrosome duplication. J. Cell Sci. 119, 2035-2047

Brunet S., Zimmermann T., Reynaud E., Vernos I., E. Karsenti and R. Pepperkok (2006) Detection and quantification of protein-microtubules interactions using GFP photo-conversion Traffic, 7: 1283-1289

Vernos I. (2006) Only one spindle, if you please ...Nat Cell Biol. 2006 Sep;8(9):901-2.

Andreas Wodarz and Cayetano Gonzalez (2006) Connecting Cancer to the Asymmetric Division of Stem Cells. Cell, 124 (6): 1121-1123. Review.

Krull, M., Pistor, S., Voss, N., Kel, A., Reuter, I., Kroneberg, D., Michael, H., Schwarzer, K., Potapov, A., Choi, C., Kel-Margoulis, O., Wingender, E. (2006) TRANSPATH®: An information resource for storing and visualizing signaling pathways and their pathological aberrations. Nucleic Acids Res. 34:D546-D551.

Kel, A., Voss, N., Jauregui, R., Kel-Margoulis, O. and Wingender, E. Beyond microarrays: Find key transcription factors controlling signal transduction pathways BMC Bioinformatics, 7(Suppl. 2), S13 (2006)

Waleev, T., Shtokalo, D., Konovalova, T., Voss, N., Cheremushkin, E., Stegmaier, P., Kel-Margoulis, O., Wingender, E. and Kel, A. Composite Module Analyst: Identification of transcription factor binding site combinations using genetic algorithm. Nucleic Acids Res. 34, W541-W545 (2006)

Kel, A., Konovalova, T., Waleev, T., Cheremushkin, E., Kel-Margoulis, O. and Wingender, E. Composite Module Analyst: a fitness-based tool for identification of transcription factor binding site combinations Bioinformatics 22, 1190-1197 (2006)

2007

Zámborszky, J., Hong, C.I. & Csikász-Nagy, A. (2007) Computational Analysis of Mammalian Cell Division Gated by a Circadian Clock: Quantized Cell Cycles and Cell Size Control. Proc. Natl. Acad. Sci. USA.

Csikász-Nagy, A., Novák B. & Tyson, J.J. (2007): Reverse Engineering Models of Cell Cycle Regulation. in Cellular Oscillatory Mechanisms (M. Maroto & N. Monk) Landes Bioscience (in press).

Rebollo E., Sampaio P., Januschke J., Varmark H., Llamazares S., and Gonzalez C. (2007) Functionally Unequal Centrosomes Drive Spindle Orientation in Asymmetrically Dividing Drosophila Neural Stem Cells. Developmental Cell.

Wingender, E., Crass, T., Hogan, J. D, Kel, A.E., Kel-Margoulis, O.V. and Potapov, A.P. (2007) Integrative content-driven concepts for bioinformatics "beyond the cell" J. Biosci. 32, 169-180.

M. Janson, R. Loughlin, I. Loiodice, C. Fu, D. Brunner, F. Nédélec and P. Tran. Crosslinkers and Motors Organize Dynamic Microtubules to Form Stable Bipolar Arrays in Fission Yeast. Cell 128; 357-68; Jan 2007.