Center for Models of Life - CMOL: Publications

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Publications

2010

0: (2010)

Sagar Chakraborty, Mogens H. Jensen, and Bo S. Madsen

Three-dimensional turbulent relative dispersion by Gledzer-Ohkitani-Yamada shell model

Physical Review E 81:017301 (2010)

Sagar Chakraborty, Mogens H. Jensen, and A. Sarkar

On two-dimensionalization of three-dimensional turbulence in shell models

Eur. Phys. Journ. B 73:447 (2010)

Peter B. Jensen, Lykke Pedersen, Sandeep Krishna and Mogens H. Jensen

A Wnt Oscillator Model for Somitogenesis

Biophysical Journal 98: (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)

Kim Sneppen, Sandeep Krishna, Szabolcs Semsey

Simplified Models of Biological Networks

Annual Review of Biophysics 39:Volume pub (2010)

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

Theory for stability and regulation of epigenetic landscapes

0: (2010)
1002.1600

Silja Heilmann, Kim Sneppen and Sandeep Krishna

Sustainability of Virulence in a Phage-Bacterial Ecosystem

Journal of Virology 84: (2010)

L. Lizana, M. Rosvall and K. Sneppen

Time walkers and spatial dynamics of ageing information

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

2009

Sandeeo Krishna, Szabolc Semsey and Mogens H. Jensen

Frustrated bistability as a means to engineer oscillations in biological systems

Physical Biology 6:3 (2009)

Mogens H. Jensen, Sandeep Krishna and Simone Pigolotti

The Repressor-Lattice: Feedback, Commensurability, and Dynamical Frustration

Physical Review Letters 103:118101 (2009)

K.S. Korolev, Mikkel Avlund, Oskar Hallatschek, David R. Nelson

Genetic Demixing and Evolutionary Forces in the One-Dimensional Stepping Stone Model

0: (2009)
0904.4625

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)

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)

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)

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

Why Do Phage Play Dice

Journal of Virology 83:11416 (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

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)

P. Gerlee, L. Lizana and K. Sneppen

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

Bioinformatics 25:3282 (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)

Ludvig Lizana and Tobias Ambjörnsson

Diffusion of Finite-Sized Hard-Core Interacting Particles In a One-Dimensional Box - Tagged Particle Dynamics

Phys. Rev. E 80:051103 (2009)
0907.0567

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)

A.R.A Anderson, K.A. Rejniak, P. Gerlee and V. Quaranta

Microenvironment driven invasion: a multiscale multimodel investigation

J. Math. Biol. 58:579 (2009)

P. Gerlee and A.R.A Anderson

Evolution of cell motility in an individual-based model of tumour growth

J. Theor. Biol. (in press) [preprint] 0: (2009)

P. Gerlee, T. Lundh, B. Zhang and A.R.A Anderson

Gene divergence and pathway duplication in the metabolic network of yeast and digital organisms

Royal Society Interface (in press) [preprint] 0: (2009)

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

Modeling proteasome dynamics in Parkinsons disease

Phys. Biol. 6:036005 (2009)

P. Hinow et. al (P. Gerlee)

A Spatial Model of Tumour-Host Interaction: Application of Chemotherapy

Mathematical Biosciences and Engineering (in Press) 0: (2009)
0810.1024

P. Gerlee and A.R.A Anderson

Modelling evolutionary cell behaviour using neural networks: Application to tumour growth

BioSystems 95:166 (2009)

M. Rosvall and K. Sneppen

Reinforced communication and social navigation generate groups in model networks

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

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

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)

Simone Pigolotti, Sandeep Krishna, Mogens H. Jensen

Symbolic dynamics of biological feedback networks

Phys. Rev. Lett. 102:088701 (2009)

2008

Joachim Mathiesen, Mogens H. Jensen, and J. H. Bakke

Dimensions, maximal growth sites, and optimization in the dielectric breakdown model

Physical Review E 77:066203 (2008)

Alex Nicolin, Mogens H. Jensen, Jan W. Thomsen and Roberto Carretero

Resonant energy transfer in Bose-Einstein condensates

Physica D 237:2476 (2008)

T. Ambjörnsson, L. Lizana, M. Lomholt and R. Silbey

Single-file dynamics with different diffusion constants

J. Chem. Phys. 129:185106 (2008)
0803.2485

M. Pedersen, L. Lo Leggio, J.G. Grossmann, S. Larsen and K. Hammer

Identification of quaternary structure and functional domains of the CI repressor from bacteriophage TP901-1

J. Mol. Biol. 376:983 (2008)

M. Pedersen and K. Hammer

The role of MOR and the CI operator sites on the genetic switch of the

J. Mol. Biol 384:577 (2008)

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)

Mogens H.Jensen, Kim Sneppen and Luiza Angelutha

Kolmogorov Scaling from Random Force Fields

Europhysics Letters 84:10011 (2008)
0801.3717

Namiko Mitarai, Kim Sneppen, Steen Pedersen

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

J. Mol. Biol. 382:236 (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)

Kim Sneppen, Mille A Micheelsen & Ian B Dodd

Ultrasensitive gene regulation by positive feedback loops in nucleosome modification

Molecular Systems Biology 4:182 (2008)

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

2007

M. T Borup , A. Trusina, A. Andersson

Aging mechanism as the "down side" of adaptation: A network approach

J Theor Biol. 250:66 (2007)

Alexandru I. Nicolin, Mogens H. Jensen, and Riccordo Carretero-Gonzalez

Mode locking of a driven Bose-Einstein condensate

Physics Review E 75:036208 (2007)

Poul Olesen and Mogens H. Jensen

Exact Periodic Solutions of Shells Models of Turbulence

Nonlinearity 20:2333 (2007)

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 21:4083 (2007)

Sandeep Krishna, Szabolcs Semsey, Kim Sneppen

Combinatorics of feedback in cellular uptake and metabolism of small molecules

PNAS 104:20815 (2007)

Jacob Bock Axelsen, Joseph Lotem, Leo Sachs and Eytan Domany

Genes overexpressed in different human solid cancers exhibit different tissue-specific expression profiles

Proc Natl Acad Sci USA 104:13122 (2007)

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

Oscillations and temporal signalling in cells

Phys. Biol. 4:R1 (2007)

M. Rosvall, K. Sneppen

Dynamics of Opinions and Social Structures

0: (2007)
0708.0368

Jakob Enemark, Kim Sneppen

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

JSTAT 0:P11007 (2007)
0704.3808

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

Modelling transcriptional interference and DNA looping in gene regulation

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

Szabolcs Semsey, Sandeep Krishna, Kim Sneppen, Sankar Adhya

Signal Integration in the Galactose Network of Escherichia coli

Molecular Microbiology 65:465 (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)

Karin Stibius and Kim Sneppen

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

Biophysics J. 93:1 (2007)

Sergei Maslov, Kim Sneppen, Iaroslav Ispolatov

Spreading out of perturbations in reversible reaction networks

New J. Phys. 9:273 (2007)
q-bio.MN/0611026

Simone Pigolotti, Sandeep Krishna, Mogens H. Jensen

Oscillation patterns in negative feedback loops

Proc. Natl. Acad. Sci. (USA) 104:6533-6537 (2007)
q-bio.MN/0611038

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

Kjaerulff, S., Andersen, NR., Borup, MT. and Nielsen, O.

Cdk-phosphorylation of the Ste11 transcription factor constrains differentiation specific transcription to G1.

Genes Dev.(in press) 0:0 (2007)

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

Efficient degradation and expression prioritization with small RNAs

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

2006

Jesper Ferkinghoff-Borg, Mogens H. Jensen, Joachim Mathiesen and Poul Olesen

Scale Free Cluster Distributions from Conserving Merging-Fragmentation Processes

Europhys. Lett. 73:422 (2006)

Jesper Ferkinghoff-Borg, Mogens H. Jensen, Poul Olesen and Joachim Mathiesen

Diffusion, Fragmentation and Merging: Rate Equations, Distributions and Critical Points

Physica D 222:88 (2006)

Simone Pigolotti, Mogens H. Jensen and Angelo Vulpiani

Absorbing processes in Richardson diffusion: Analytical results

Physics of Fluids 18:048104 (2006)

Dirk Helbing, Anders Johansson, Joachim Mathiesen, Mogens H. Jensen, and Alex Hansen

Analytical approach to continuous and intermittent bottleneck flows

Physical Review Letters 97:168001 (2006)

Anders Johansen, Ingve Simonsen and Mogens H. Jensen

Optimal investment horizons for stocks and markets

Physica A 370:64 (2006)

Raul Donangelo, Mogens H. Jensen, Ingve Simonsen, Kim Sneppen

Synchronization Model for Stock Market Asymmetry

J. Stat. Mech. 0:L11001 (2006)
physics/0604137

Ingve Simonsen, Peter Toke Heden Ahlgren, Mogens H. Jensen, Raul Donangelo, Kim Sneppen

Fear and its implications for stock markets

EPJB 57:1434 (2006)
physics/0609046

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

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

Mia T. Borup

Stress-induced switch to pseudohyphal growth in S. pombe

Cell Cycle 5:2138 (2006)

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

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

Martin Rosvall og Kim Sneppen

Self-Assembling of information in networks

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

Martin Rosvall og Kim Sneppen

Modeling self-organization of communication and topology in social networks

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

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

2005

Hans C. Fogedby and Mogens H. Jensen

Weak noise approach to the logistic map

Journal Statistical Physics 121:759 (2005)

Poul Olesen, Jesper Ferkinghoff-Borg, Mogens H. Jensen, and Joachim Mathiesen

Diffusion, Fragmentation and Coagulation Processes: Analytical and Numerical Results

Physical Review E 72:031103 (2005)

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

Correlations in Networks associated to Preferential Growth

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

K.Sneppen and G. Zocchi

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

0:0 (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

Sergei Maslov and Kim Sneppen

Computational architecture of the yeast regulatory network.

Phys. Biol. 2:94 (2005)

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)

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

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)

M. Rosvall, P. Minnhagen, K. Sneppen

Navigating Networks with Limited Information

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

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

Searchability of Networks

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

K. Sneppen, A. Trusina, M. Rosvall

Hide and Seek on Complex Networks

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

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

Networks and Cities: An Information Perspective

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

2004

Mogens H.Jensen, Anders Johansen, F. Petroni and Ingve Simonsen

Inverse Statistics in the Foreign Exchange Market

Physica A 340:678 (2004)

Thomas C. Halsey and Mogens H. Jensen

Hurricanes and butterflies

Nature 428:127 (2004)

Karin Stibius Jensen

Analysis and modelling of protein interaction networks - A study of the two-hybrid network

Thesis 0: (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

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

Variability alignment identifies functional regions in tubulin paralogs

Protein Science 13:25 (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

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

Diffusion on complex networks: a way to probe their

Physica A 336:163 (2004)

Kasper Astrup Eriksen, Michael Hörnquist and Kim Sneppen

Visualization of large-scale correlations in gene expressions

Functional & Integrative Genomics 4:241 (2004)

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

A simple model for self organization of bipartite networks

Europhys. Lett. 67:394 (2004)

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

Self Organized Scale-Free Networks from Mergin and Regeneration

: (2004)
nlin.AO/0403006

Jacob Bock Axelsen and Kim Sneppen

Quantifying the benefits of translation regulation in the unfolded protein response

Phys. Biol. 1:159 (2004)

"The urban maze"
(news@nature.com) : (2004)

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

A. Trusina, M. Rosvall, K. Sneppen

Communication Boundaries in Networks

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

2003

M. A. Micheelsen, C. Rischel, J. Ferkinghoff-Borg, R. Guerois and L. Serrano

Mean first-passage time analysis reveals rate-limiting steps, parallel pathways and dead ends in a simple model of protein folding

Europhys. Lett. 61:561 (2003)
cond-mat/0303604

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

Localization of Denaturation Bubbles in random DNA Sequences

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

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

Sustained oscillations and time delays in gene expression of protein Hes1

Febs letters 541:176 (2003)

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)

Martin Rosvall and Kim Sneppen

Modeling Dynamics of Information Networks

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

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

Modularity and Extreme Edges of the Interet

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

2002

R. Donangelo and K. Sneppen

Cooperativity in a trading model with memory and production

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

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

Stability puzzles in lambda phage

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

S. Maslov and K. Sneppen

Protein interaction networks beyond artifacts

FEBS 530:255 (2002)

E. Aurell and K. Sneppen

Epigenetics as a first exit problem

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

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

Sergei Maslov and Kim Sneppen

Specificity and stability in topology of proteins networks

Science 296:910 (2002)

Background papers

Bergqvist S, Alverdi V, Mengel B, Hoffmann A, Ghosh G, Komives EA.

Kinetic enhancement of NF-kB:DNA dissociation by IkBa

PNAS 106:19328 (2009)

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)