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Center for Models of Life
Niels Bohr Institute
University of Copenhagen
Blegdamsvej 17
2100 Copenhagen Ø
Mail:  cmolnbi.dk

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Response dynamics of molecular networks

The molecular network in an organism consists of transcription/translation regulation, protein-protein interactions/modifications and a metabolic network, together forming a system that allows the cell to respond sensibly to the multiple signals and signal molecules that exist in its environment. We are interested in the precise characterization of response mechanisms associated to both physical and chemical shocks.

Publications

Jacob Bock Axelsen and Kim Sneppen
Quantifying the benefits of translation regulation in the unfolded protein response
Phys. Biol. 1 (2004)

Ilaria Cataudella, Ala Trusina, Kim Sneppen, Kenn Gerdes, and Namiko Mitarai
Conditional cooperativity in toxin–antitoxin regulation prevents random toxin activation and promotes fast translational recovery
Nuc. Acids Res. 40 (2012)

Ala Trusina, Feroz Papa and Chao Tang
Translation Attenuation Mechanism in Unfolded Protein Response
Evolution from Cellular to Social Scales NATO Science for Peace and Security Series B: Physics and Biophysics 0 (2008)

Ala Trusina and Chao Tang
The unfolded protein response and translation attenuation: a modelling approach
Diabetes, Obesity and Metabolism 12 (2010)

A. Trusina, F. Papa, C. Tang
Rationalizing translation attenuation in the network architecture of the unfolded protein response
PNAS 105 (2008)

P. Merksamer, A. Trusina, F. Papa
Real-time redox measurements during endoplasmic reticulum stress reveal interlinked protein folding functions
Cell 135 (2008)

W. Ma, A. Trusina, H. El-Samad,W. Lim and C. Tang
Defining Network Topologies that Can Achieve Biochemical Adaptation
Cell 138 (2009)

Christian Garde, Thomas Bjarnsholt, Michael Givskov, Tim Holm Jakobsen, Morten Hentzer, Anetta Claussen, Kim Sneppen, Jesper Ferkinghoff-Borg and Thomas Sams
Quorum Sensing Regulation in Aeromonas hydrophila
J. Mol. Biol. 396 (2010)

Kim Sneppen, Sandeep Krishna, Szabolcs Semsey
Simplified Models of Biological Networks
Annual Review of Biophysics 39 (2010)

Szabolcs Semsey, Julie-Anna M. Benjamin, Namiko Mitarai, Sandeep Krishna, Zsolt Csiszovszki, Kim Sneppen and Eric Massé
Dynamics of the recovery from sRNA-mediated gene silencing
Cell Cycle 8 (2009)

Jesper Fonslet, Kristian Rud-Petersen, Sandeep Krishna, Mogens H. Jensen
Pulses and chaos: dynamical response in a simple genetic oscillator
Int. J. Mod. Phys. B 21 (2007)

Sandeep Krishna, Szabolcs Semsey, Kim Sneppen
Combinatorics of feedback in cellular uptake and metabolism of small molecules
Proc. Natl. Acad. Sci. USA 104 (2007)

Namiko Mitarai, Anna M. C. Andersson, Sandeep Krishna, Szabolcs Semsey, and Kim Sneppen
Efficient degradation and expression prioritization with small RNAs
Phys. biol. 4 (2007)
q-bio.MN/0611069

G. Tiana, M.H. Jensen and K. Sneppen
Time delay as a key to apoptosis induction in the p53 network
Eur. Phys. J. B 29 (2002)
cond-mat/0207236

M.H. Jensen, G. Tiana and K. Sneppen
Sustained oscillations and time delays in gene expression of protein Hes1
Febs letters 541 (2003)

Sandeep Krishna, Mogens H. Jensen, Kim Sneppen
Minimal model of spiky oscillations in NF-kB signaling
Proc. Natl. Acad. Sci. (USA) 103 (2006)
q-bio.MN/0509017

Simone Pigolotti, Sandeep Krishna, Mogens H. Jensen
Oscillation patterns in negative feedback loops
Proc. Natl. Acad. Sci. (USA) 104 (2007)
q-bio.MN/0611038

Sabine Hansen, Sandeep Krishna, Szabolcs Semsey, and Sine Lo Svenningsen
Effects of Four Different Regulatory Mechanisms on the Dynamics of Gene Regulatory Cascades
Scientific Reports 5 (2015)