Adaptive dynamics with a single two-state proteinAttila Csikasz-Nagy
Microsoft Research University of Trento Centre for Computational and Systems Biology, Piazza Manci 17, Povo Trento, Italy
J R Soc Interface 5:S41-7. 2008
..The analysis of coupled BioNetUnits will show how the presented dynamics at single unit will change upon increased system complexity and how such systems would mediate biological functions...
- Molecular network dynamics of cell cycle control: transitions to start and finish
Attila Csikasz-Nagy
The Microsoft Research, University of Trento Centre for Computational and Systems Biology, 38123, Povo Trento, Italy
Methods Mol Biol 761:277-91. 2011
..Here we review the basic physiological and molecular transitions in the cell cycle and present how the system-level emergent properties were found by the help of mathematical/computational modeling...
- Response dynamics of phosphorelays suggest their potential utility in cell signalling
Attila Csikasz-Nagy
Microsoft Research University of Trento Centre for Computational and Systems Biology CoSBi, Povo Trento, Italy
J R Soc Interface 8:480-8. 2011
..In addition, our analysis suggests that middle layers of phosphorelays could embed thresholds. We discuss the consequence of these findings in relation to why cells might use phosphorelays along with enzymatic kinase cascades...
- Computational systems biology of the cell cycle
Attila Csikasz-Nagy
The Microsoft Research University of Trento Centre for Computational and Systems Biology, Piazza Manci 17, Povo Trento I 38100, Italy
Brief Bioinform 10:424-34. 2009
..Here we review past and present of computational modeling of cell-cycle regulation, and discuss possible future directions of the field...
- Cell cycle regulation by feed-forward loops coupling transcription and phosphorylation
Attila Csikasz-Nagy
The Microsoft Research, University of Trento Centre for Computational and Systems Biology, Povo, Trento, Italy
Mol Syst Biol 5:236. 2009
..The signal-transduction properties of FFLs allow one (or a few) Cdk signal(s) to drive a host of cell cycle responses in correct temporal sequence...
- Transcriptional regulation is a major controller of cell cycle transition dynamics
Alessandro Romanel
The Microsoft Research University of Trento Centre for Computational and Systems Biology, Trento, Italy
PLoS ONE 7:e29716. 2012
..Based on these observations, we propose two transcriptional control modes of cell cycle regulation that either STOP or let the cycle GO in case of a transcriptional failure. We discuss the biological relevance of such differences...
- Stochastic Petri Net extension of a yeast cell cycle model
Ivan Mura
The Microsoft Research University of Trento, Centre for Computational and Systems Biology, Piazza Manci 17, Povo Trento I 38100, Italy
J Theor Biol 254:850-60. 2008
..The SPN model fine-tunes the simulation results, enriching the breadth and the quality of its outcome...
- Regulating the total level of a signaling protein can vary its dynamics in a range from switch like ultrasensitivity to adaptive responses
Orkun S Soyer
Microsoft Research University of Trento Centre for Computational and Systems Biology, Italy
FEBS J 276:3290-8. 2009
..We discuss relevant biological examples in which regulating total protein levels could be exploited to alter signaling behavior...
- Prosperity is associated with instability in dynamical networks
Matteo Cavaliere
The Microsoft Research University of Trento Centre for Computational and Systems Biology, Povo Trento 38123, Italy
J Theor Biol 299:126-38. 2012
..Cooperation is prosperous when the network has frequent formation and fragmentation...
- Role of mRNA Gestation and Senescence in Noise Reduction during the Cell Cycle
Attila Csikasz-Nagy
The Microsoft Research University of Trento Centre for Computational and Systems Biology, Povo, Italy
In Silico Biol 10:81-8. 2010
..This result suggests that the complex process of transcription can be more accurately approximated by multi-step linear processes...
- Role of mRNA Gestation and Senescence in Noise Reduction during the Cell Cycle
Attila Csikasz-Nagy
The Microsoft Research University of Trento Centre for Computational and Systems Biology, Povo, Italy
Stud Health Technol Inform 162:236-43. 2011
..This result suggests that the complex process of transcription can be more accurately approximated by multi-step linear processes...
