Center for Models of Life: People

Kim Sneppen

Position: Head of Center/ Professor
Email: sneppen

nbi.dk
www: http://www.nbi.dk/~sneppen/
Phone: +45 353 25352

Publications:

L. Lizana, M. Rosvall and K. Sneppen

Time walkers and spatial dynamics of ageing information

Phys. Rev. Lett. 104:040603 (2010)
0910.4045

Silja Heilmann, Kim Sneppen and Sandeep Krishna

Sustainability of Virulence in a Phage-Bacterial Ecosystem

Journal of Virology 84: (2010)

Mille A. Micheelsen, Namiko Mitarai, Kim Sneppen, Ian. B. Dodd

Theory for stability and regulation of epigenetic landscapes

Phys. Biol. 7:026010 (2010)
1002.1600

Kim Sneppen, Sandeep Krishna, Szabolcs Semsey

Simplified Models of Biological Networks

Annual Review of Biophysics 39:Volume pub (2010)

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. 396:849–857 (2010)

Maria Werner, Szabolcs Semsey, Kim Sneppen, Sandeep Krishna

Dynamics of Uptake and Metabolism of Small Molecules in Cellular Response Systems

PLoS ONE 4:e4923 (2009)

Stefan Bornholdt, Kim Sneppen, and Hildegard Westphal

Longevity of orders is related to the longevity of their constituent genera rather than genus richness

Theory in Biosciences: doi: 10.1007/s12064-008-0053-9 0: (2009)
q-bio.PE/0608033

M. Rosvall and K. Sneppen

Reinforced communication and social navigation generate groups in model networks

Phys. Rev. E 79:026111 (2009)
0809.4803

K. Sneppen, L. Lizana, M. H. Jensen , S. Pigolotti and D. Otzen

Modeling proteasome dynamics in Parkinsons disease

Phys. Biol. 6:036005 (2009)

Sergei Maslov, Sandeep Krishna, Tin Yau Pang and Kim Sneppen

Toolbox model of evolution of prokaryotic metabolic networks and their regulation

PNAS 106:9743 (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 106:10655 (2009)

P. Gerlee, L. Lizana and K. Sneppen

Pathway identification by network pruning in the metabolic network of Escherichia coli

Bioinformatics 25:3282 (2009)

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 8:2863 (2009)

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. 394:15 (2009)
0908.4145

Mikkel Avlund, Ian B. Dodd, Szabolcs Semsey, Kim Sneppen, and Sandeep Krishna

Why Do Phage Play Dice

Journal of Virology 83:11416 (2009)

Mikkel Avlund, Ian B. Dodd, Kim Sneppen, and Sandeep Krishna

Minimal gene regulatory circuits that can count like bacteriophage lambda

J Mol Biol. 394:681 (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 191:4487 (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 391:671 (2009)

Jacob Bock Axelsen, Sebastian Bernhardsson, Kim Sneppen

One Hub-One Process: A Tool Based View on Regulatory Network Topology

BMC Systems Biology 2:25 (2008)
0711.2208

Jacob Bock Axelsen, Sandeep Krishna, Kim Sneppen

Cost and Capacity of Signaling in the Escherichia coli Protein Reaction Network

J. Stat. Mech. 0:P01018 (2008)
0711.0455

Kim Sneppen, Mille A Micheelsen & Ian B Dodd

Ultrasensitive gene regulation by positive feedback loops in nucleosome modification

Molecular Systems Biology 4:182 (2008)

Namiko Mitarai, Ian B. Dodd, Michael T. Crooks, Kim Sneppen

The Generation of Promoter-Mediated Transcriptional Noise in Bacteria

PLoS Comput. Biol. 4:e1000109 (2008)

Namiko Mitarai, Kim Sneppen, Steen Pedersen

Ribosome Collisions and Translation Efficiency: Optimization by Codon Usage and mRNA Destabilization

J. Mol. Biol. 382:236 (2008)

Mogens H.Jensen, Kim Sneppen and Luiza Angelutha

Kolmogorov Scaling from Random Force Fields

Europhysics Letters 84:10011 (2008)
0801.3717

Hiizu Nakanishi, Namiko Mitarai, Kim Sneppen

Dynamical Analysis on Gene Activity in the Presence of Repressors and an Interfering Promoter

Biophysical Journal 95:4228 (2008)

Karin Stibius and Kim Sneppen

Modeling the Two-Hybrid Detector: Experimental Bias on Protein Interaction Networks

Biophysics J. 93:1 (2007)

Sandeep Krishna, Sergei Maslov, Kim Sneppen

UV-induced mutagenesis in the Escherichia coli SOS response: A quantitative model

PLoS Comput. Biol. 3:e41 (2007)
q-bio.MN/0701013

Namiko Mitarai, Anna M. C. Andersson, Sandeep Krishna, Szabolcs Semsey, and Kim Sneppen

Efficient degradation and expression prioritization with small RNAs

Phys. biol. 4:164 (2007)
q-bio.MN/0611069

G Tiana, S Krishna, S Pigolotti, M H Jensen and K Sneppen

Oscillations and temporal signalling in cells

Phys. Biol. 4:R1 (2007)

Ian B. Dodd, Mille A. Micheelsen, Kim Sneppen and Geneviève Thon

Theoretical Analysis of Epigenetic Cell Memory by Nucleosome Modification

Cell 129:813-822 (2007)

Szabolcs Semsey, Sandeep Krishna, Kim Sneppen, Sankar Adhya

Signal Integration in the Galactose Network of Escherichia coli

Molecular Microbiology 65:465 (2007)

I.B. Dodd, K.E. Shearwin and K. Sneppen

Modelling transcriptional interference and DNA looping in gene regulation

J. Mol. Biol. 369:1200 (2007)

Jakob Enemark, Kim Sneppen

Analyzing a stochastic model for evolving regulatory networks by unbiased gene duplication

JSTAT 0:P11007 (2007)
0704.3808

Sandeep Krishna, Szabolcs Semsey, Kim Sneppen

Combinatorics of feedback in cellular uptake and metabolism of small molecules

PNAS 104:20815 (2007)

Sandeep Krishna, Mogens H. Jensen, Kim Sneppen

Minimal model of spiky oscillations in NF-kB signaling

Proc. Natl. Acad. Sci. (USA) 103:10840 (2006)
q-bio.MN/0509017

Jacob Bock Axelsen, Sebastian Bernhardsson, Martin Rosvall, Kim Sneppen, Ala Trusina

Degree Landscapes in Scale-Free Networks

Phys. Rev. E 74:036119 (2006)
physics/0512075

Sandeep Krishna, Anna M. C. Andersson, Szabolcs Semsey, Kim Sneppen

Structure and function of negative feedback loops at the interface of genetic and metabolic networks

Nucleic Acids Research 34:2455 (2006)
q-bio.MN/0604029

Martin Rosvall og Kim Sneppen

Modeling self-organization of communication and topology in social networks

Phys. Rev. E 74:16108 (2006)
physics/0512105

Martin Rosvall og Kim Sneppen

Self-Assembling of information in networks

Europhys. Lett. 74:1109 (2006)
abs/physics/0603218

Szabolcs Semsey, Anna M. C. Andersson, Sandeep Krishna, Mogens Høgh Jensen, Eric Massé, and Kim Sneppen

Genetic regulation of fluxes: Iron homeostasis of Escherichia coli

Nucleic Acids Research 34:4960 (2006)
q-bio.MN/0609042

Martin Rosvall, Ian B. Dodd, Sandeep Krishna, Kim Sneppen

Network models of phage-bacteria coevolution

Phys. Rev. E 74:66105 (2006)
q-bio.PE/0609031

K. Sneppen, A. Trusina, M. Rosvall

Hide and Seek on Complex Networks

Europhys. Lett. 69:853 (2005)
cond-mat/0407055

M. Rosvall, A. Gronlund, P. Minnhagen, K. Sneppen

Searchability of Networks

Phys. Rev. E 72:46117 (2005)
cond-mat/0505400

M. Rosvall, P. Minnhagen, K. Sneppen

Navigating Networks with Limited Information

Phys. Rev. E. 71:66111 (2005)
cond-mat/0412051

Sneppen K, Dodd IB, Shearwin KE, Palmer AC, Schubert RA, Callen BP, Egan JB

A mathematical model for transcriptional interference by RNA polymerase traffic in Escherichia coli

J. Mol. Biol. 346:399 (2005)

R. Donangelo, A. Hansen, K. Sneppen and S. R. Souza

Need, Greed and Noise: Competing strategies in a trading model

Physica A 348:496 (2005)
cond-mat/0408531

Beom Jun Kim, Petter Minhagen, Ala Trusina og Kim Sneppen

Scale Free networks from Aggregation and Creation of Vertices

European Physical Journal B 43:369 (2005)

Sergei Maslov and Kim Sneppen

Computational architecture of the yeast regulatory network.

Phys. Biol. 2:94 (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 1:7 (2005)
q-bio.MN/0511047

K.Sneppen and G. Zocchi

Physics in molecular biology, Course Book for master/Phd course in Biological Physics, 300 pages

0:0 (2005)

A. Gronlund, K. Sneppen and P. Minnhagen.

Correlations in Networks associated to Preferential Growth

Physica Scripta 71:680 (2005)
cond-mat/0401537

M. Rosvall, A. Trusina, P. Minnhagen, K. Sneppen

Networks and Cities: An Information Perspective

Phys. Rev. Lett 94:28701 (2005)
cond-mat/0407054

A. Trusina, M. Rosvall, K. Sneppen

Communication Boundaries in Networks

Phys. Rev. Lett. 94:238701 (2004)
cond-mat/0412064

Ala Trusina, Sergei Maslov, Petter Minnhagen, Kim Sneppen

Hierarchy and Anti-Hierarchy in Real and Scale Free networks

Phys. Rev. Lett. 92:178702 (2004)
cond-mat/0308339

Jacob Bock Axelsen and Kim Sneppen

Quantifying the benefits of translation regulation in the unfolded protein response

Phys. Biol. 1:159 (2004)

Beom Jun Kim, Ala Trusina, Petter Minnhagen, Kim Sneppen

Self Organized Scale-Free Networks from Mergin and Regeneration

: (2004)
nlin.AO/0403006

K. Sneppen, M. Rosvall, A. Trusina and P. Minnhagen

A simple model for self organization of bipartite networks

Europhys. Lett. 67:394 (2004)

Kasper Astrup Eriksen, Michael Hörnquist and Kim Sneppen

Visualization of large-scale correlations in gene expressions

Functional & Integrative Genomics 4:241 (2004)

I. Simonsen , K.A. Eriksen , S. Maslov and K. Sneppen

Diffusion on complex networks: a way to probe their

Physica A 336:163 (2004)

P. Minnhagen, M. Rosvall, K. Sneppen and A. Trusina.

Self-organization of structures and networks from merging and small-scale fluctuations

Physica A 340:724 (2004)
cond-mat/0406752

D.K. Fygenson, D.J. Needleman and K. Sneppen

Variability alignment identifies functional regions in tubulin paralogs

Protein Science 13:25 (2004)

S. Maslov, K. Sneppen and A. Zaliznyak

Detection of topological patterns in complex networks: correlation profile of the internet

Physica A 333:529 (2004)
cond-mat/0205379

Sergei Maslov, Kim Sneppen, Kasper A. Eriksen, Koon-Kiu Yan

Upstream Plasticity and Downstream Robustness in Evolution of Molecular Networks.

BMC Evolutionary Biology 4:9 (2004)

Kasper Astrup Eriksen, Ingve Simonsen, Sergei Maslov, Kim Sneppen

Modularity and Extreme Edges of the Interet

Phys. Rev. Lett. 90:148701 (2003)

Martin Rosvall and Kim Sneppen

Modeling Dynamics of Information Networks

Phys. Rev. Lett. 91:178791 (2003)
cond-mat/0308399

K.T. Bæk, S. Svenningsen, H. Eisen, K. Sneppen and S. Brown

Single-cell analysis of lambda immunity regulation

J. Mol. Biol. 334:363 (2003)

M.H. Jensen, G. Tiana and K. Sneppen

Sustained oscillations and time delays in gene expression of protein Hes1

Febs letters 541:176 (2003)

T. Hwa, E. Marinari, K. Sneppen, Lei-han Tang

Localization of Denaturation Bubbles in random DNA Sequences

PNAS 100:4411 (2003)
cond-mat/0302603

Sergei Maslov and Kim Sneppen

Specificity and stability in topology of proteins networks

Science 296:910 (2002)

G. Tiana, M.H. Jensen and K. Sneppen

Time delay as a key to apoptosis induction in the p53 network

Eur. Phys. J. B 29:135 (2002)
cond-mat/0207236

E. Aurell and K. Sneppen

Epigenetics as a first exit problem

Phys. Rev. Lett 88:48101 (2002)
cond-mat/0103080

S. Maslov and K. Sneppen

Protein interaction networks beyond artifacts

FEBS 530:255 (2002)

E. Aurell, S. Brown, J. Johansen, K. Sneppen

Stability puzzles in lambda phage

Phys. Rev. E 65:51914 (2002)
cond-mat/0010286

R. Donangelo and K. Sneppen

Cooperativity in a trading model with memory and production

Physica A 316:581 (2002)
cond-mat/0309549

K.B. Arnvig, S. Pedersen and K. Sneppen

Thermodynamics of Heat Shock Response

Phys. Rev. Lett. 84:3005 (2000)
cond-mat/9912402

S. Bornholdt and K.Sneppen

Robustness as an evolutionary principle

Proc Roy. Soc. London B 267:2281 (2000)
http://xxx.lanl.gov/pdf/cond-mat/0003333

T. Sams, K. Sneppen, M. H. Jensen, C. Ellegaard, B. E. Christensen and U. Trane

Morphological instability in a growing yeast colony

Phys. Rev. Lett. 79:313 (1997)

Per Bak og Kim Sneppen

Punctuated equilibrium and criticality in a simple model of evoluton

Phys. Rev. Lett. 71:4083 (1994)

K. Sneppen

Self-organized pinning and interface growth in a random medium

Phys. Rev. Lett. 69:3539 (1992)

K. Sneppen, J. Krug, M. H. Jensen, C. Jayaprakash, and T. Bohr.

Dynamic scaling and crossover analysis for the Kuramoto - Sivashinsky equation

Phys. Rev. A 46:0 (1992)

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