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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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Molecular Networks

Molecular networks guide the biochemistry of a living cell on multiple levels: its metabolic and signalling pathways are shaped by the network of interacting proteins, whose production, in turn, is controlled by the genetic regulatory network. We investigate the topological features of these networks with the goal of unraveling their design principles and the evolutionary mechanisms that governed their present day architecture.

Publications

Sergei Maslov and Kim Sneppen
Specificity and stability in topology of proteins networks
Science 296 (2002)

Hiizu Nakanishi, Margit Pedersen, Anne K. Alsing and Kim Sneppen
Modeling of the Genetic Switch of Bacteriophage TP901-1: A Heteromer of CI and MOR Ensures Robust Bistability
J. Mol. Biol. 394 (2009)
0908.4145

Mikkel Avlund, Ian B. Dodd, Kim Sneppen, and Sandeep Krishna
Minimal gene regulatory circuits that can count like bacteriophage lambda
J Mol Biol. 394 (2009)

Szabolcs Semsey, Sandeep Krishna, Janos Erdssy, Peter Horvath, Laszlo Orosz, Kim Sneppen and Sankar Adhya
Dominant Negative Autoregulation Limits Steady-State Repression Levels in Gene Networks
Journal of Bacteriology 191 (2009)

Sandeep Krishna, Laszlo Orosz, Kim Sneppen, Sankar Adhya and Szabolcs Semsey
Relation of Intracellular Signal Levels and Promoter Activities in the gal Regulon of Escherichia coli
Journal of Molecular Biology 391 (2009)

Sergei Maslov, Sandeep Krishna, Tin Yau Pang and Kim Sneppen
Toolbox model of evolution of prokaryotic metabolic networks and their regulation
PNAS 106 (2009)

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

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

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

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

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

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)

Namiko Mitarai, Mogens Høgh Jensen, Szabolcs Semsey
Coupled Positive and Negative Feedbacks Produce Diverse Gene Expression Patterns in Colonies
mBio 6 (2015)

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)

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)

P. Gerlee, L. Lizana and K. Sneppen
Pathway identification by network pruning in the metabolic network of Escherichia coli
Bioinformatics 25 (2009)

Sergei Maslov and Kim Sneppen
Computational architecture of the yeast regulatory network.
Phys. Biol. 2 (2005)

Ala Trusina, Kim Sneppen, I.B. Dodd, K.E. Shearwin and J.B. Egan.
Functional alignment of regulatory networks: A study of temerate phages
Plos Computational Biology 1 (2005)
q-bio.MN/0511047

Kasper Astrup Eriksen, Michael Hörnquist and Kim Sneppen
Visualization of large-scale correlations in gene expressions
Functional & Integrative Genomics 4 (2004)

S. Maslov and K. Sneppen
Protein interaction networks beyond artifacts
FEBS 530 (2002)

Szabolcs Semsey, Sandeep Krishna, Kim Sneppen, Sankar Adhya
Signal Integration in the Galactose Network of Escherichia coli
Molecular Microbiology 65 (2007)

Karin Stibius and Kim Sneppen
Modeling the Two-Hybrid Detector: Experimental Bias on Protein Interaction Networks
Biophysics J. 93 (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

Jacob Bock Axelsen, Sandeep Krishna, Kim Sneppen
Cost and Capacity of Signaling in the Escherichia coli Protein Reaction Network
J. Stat. Mech. 0 (2008)
0711.0455

Jacob Bock Axelsen, Sebastian Bernhardsson, Kim Sneppen
One Hub-One Process: A Tool Based View on Regulatory Network Topology
BMC Systems Biology 2 (2008)
0711.2208

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

Maria Werner, Szabolcs Semsey, Kim Sneppen, Sandeep Krishna
Dynamics of Uptake and Metabolism of Small Molecules in Cellular Response Systems
PLoS ONE 4 (2009)

Simone Pigolotti, Sandeep Krishna, Mogens H. Jensen
Symbolic dynamics of biological feedback networks
Phys. Rev. Lett. 102 (2009)

Namiko Mitarai, Julie-Anna M. Benjamin, Sandeep Krishna, Szabolcs Semsey, Zsolt Csiszovszki, Eric Massé, and Kim Sneppen
Dynamic features of gene expression control by small regulatory RNAs
Proc. Natl. Acad. Sci. USA 106 (2009)

Kristian Moss Bendtsen, Mogens H. Jensen, Sandeep Krishna, Szabolcs Semsey
The role of mRNA and protein stability in the function of coupled positive and negative feedback systems in eukaryotic cells
Scientific Reports 5 (2015)