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

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Publications

2017

Kim Sneppen
Models of Life: : Epigenetics, Diversity & Cycles
Reports on Progress in Physics 0: (2017)

Orr Schlesinger, Yonatan Chemla, Mathias Heltberg, Eden Ozer, Ryan Marshall, Vincent Noireaux, Mogens H. Jensen, Lital Alfonta
Tuning of recombinant protein expression in Escherichia coli by manipulating transcription, translation initiation rates and incorporation of non-canonical amino acids
BioarXiv (preprint) https://doi.org/10.1101/100982 0: (2017)

Jan O Haerter, Namiko Mitarai, Kim Sneppen
Existence and construction of large stable food webs
BioarXiv (preprint) 0: (2017)

Sergei Maslov and Kim Sneppen
Population cycles and species diversity in dynamic Kill-the-Winner model of microbial ecosystems
Scientific Reports 7:39642 (2017)

 

2016

Stylianidou, Stella, Connor Brennan, Silas B. Nissen, Nathan J. Kuwada, and Paul A. Wiggins
SuperSegger: robust image segmentation, analysis and lineage tracking of bacterial cells
Molecular microbiology 102:690 (2016)

Florian Uekermann, Joachim Mathiesen, Namiko Mitarai
Characterization of phase transitions in a model ecosystem of sessile species
0: (2016)
1611.00171

Cilie W. Feldager, Namiko Mitarai, Hiroki Ohta
Deterministic extinction by mixing in cyclically competing species
0: (2016)
1609.08297

Mathias Heltberg, Ryan A. Kellogg, Sandeep Krishna, Savaş Tay, Mogens H. Jensen
Noise Induces Hopping between NF-κB Entrainment Modes
Cell Systems 3: p532–539. (2016)

Silas Boye Nissen, Tali Magidson, Kevin Gross, Carl T Bergstrom
Research: Publication bias and the canonization of false facts
eLife 5:e21451 (2016)

Kristian Moss Bendtsen, Florian Uekermann and Jan O. Haerter
Expert Game experiment predicts emergence of trust in professional communication networks
Proceedings of the National Academy of Sciences 113:12099 (2016)

Sřren Vedel, Harry Nunns, Andrej Košmrlj, Szabolcs Semsey, Ala Trusina
Asymmetric Damage Segregation Constitutes an Emergent Population-Level Stress Response
Cell Systems 3:187 (2016)

Kim Sneppen and Ian B. Dodd
Nucleosome dynamics and maintenance of epigenetic states of CpG islands
Physical Review E 93:062417 (2016)

Chengzhe Tian and Namiko Mitarai
Bifurcation of transition paths induced by coupled bistable systems
The Journal of Chemical Physics 144:215102 (2016)
1603.04477

Michaela J. Obersriebnig, Emil M. H. Pallesen, Kim Sneppen, Ala Trusina and Genevičve Thon
Nucleation and spreading of a heterochromatic domain in fission yeast
Nature Communications 7:11518 (2016)

Florian Uekermann and Kim Sneppen
A cross-immunization model for the extinction of old influenza strains
Scientific Reports 6:25907 (2016)

Victor Olariu, Cecilia Lövkvist and Kim Sneppen
Nanog, Oct4 and Tet1 interplay in establishing pluripotency
Scientific Reports 6:25438 (2016)

Chengzhe Tian, Mohammad Roghanian, Mikkel Girke Jřrgensen, Kim Sneppen, Michael Askvad Sřrensen, Kenn Gerdes and Namiko Mitarai
Rapid Curtailing of the Stringent Response by Toxin-Antitoxin Encoded mRNases
Journal of Bacteriology 198:1918 (2016)

Namiko Mitarai, Stanley Brown and Kim Sneppen
Population dynamics of phage and bacteria in spatially structured habitats using Phage λ and Escherichia coli
Journal of Bacteriology 198:1783 (2016)

Namiko Mitarai, Ivar Gunnarson, Buster Niels Pedersen, Christian Anker Rosiek, and Kim Sneppen
Three is much more than two in coarsening dynamics of cyclic competitions
Phys. Rev. E 93:042408 (2016)
1512.00769

Cecilia Lövkvist, Ian B. Dodd, Kim Sneppen, and Jan O. Haerter
DNA methylation in human epigenomes depends on local topology of CpG sites
Nucl. Acids Res. 44:5123 (2016)

Giulia Sormani, Jan O. Haerter, Cecilia Lövkvist and Kim Sneppen
Stabilization of epigenetic states of CpG islands by local cooperation
Molecular BioSystems 12:2142 (2016)

Svend Bertel Dahl-Jensen, Manuel Figueiredo-Larsen, Anne Grapin-Botton and Kim Sneppen
Short-range growth inhibitory signals from the epithelium can drive non-stereotypic branching in the pancreas
Physical Biology 13:016007 (2016)

Pengfei Tian, Kresten Lindorff-Larsen, Wouter Boomsma , Mogens Hřgh Jensen , Daniel Erik Otzen
A Monte Carlo Study of the Early Steps of Functional Amyloid Formation
Plos One 11:e0146096 (2016)

Jan O. Haerter, Namiko Mitarai, and Kim Sneppen
Food Web Assembly Rules for Generalized Lotka-Volterra Equations
Plos Computational Biology 12: e1004727 (2016)
1501.04497

 

2015

Thomas C. T. Michaels, Pernille Yde, Julian C. W. Willis, Mogens H. Jensen, Daniel Otzen, Christopher M. Dobson, Alexander K. Buell and Tuomas P. J. Knowles
The length distribution of frangible biofilaments
J. Chem. Phys. 143:164901 (2015)

Andreas Rřrvig-Lund, Azra Bahadori, Szabolcs Semsey, Poul Martin Bendix, and Lene B. Oddershede
Vesicle Fusion Triggered by Optically Heated Gold Nanoparticles
Nano Letters 15:4183 (2015)

Pengfei Tian , Wouter Boomsma , Yong Wang , Daniel Erik Otzen , Mogens Hřgh Jensen , Kresten Lindorff-Larsen
What does Evolution Tell us about the Structure of a Functional Amyloid Protein?
Biophysical Journal 108:p227a (2015)

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 5:13910 (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 5:12186 (2015)

Sergei Maslov, Kim Sneppen
Diversity waves in collapse-driven population dynamics
Plos Computational Biology 11:e1004440 (2015)
1503.00529

Kim Sneppen, Szabolcs Semsey, Aswin S. Seshasayee, and Sandeep Krishna
Restriction Modification Systems as Engines of Diversity
Frontiers in Microbiology 6:528 (2015)

Szabolcs Semsey, Christopher Campion, Abdu Mohamed & Sine Lo Svenningsen
How long can bacteriophage λ change its mind?
Bacteriophage 5:e1012930 (2015)

Andrej Košmrlj, Pia Cordsen, Anders Kyrsting, Daniel E. Otzen, Lene B. Oddershede, Mogens H. Jensen
A monomer-trimer model supports intermittent glucagon fibril growth
Scientific Reports 5:9005 (2015)

David Lalaouna, Marie-Claude Carrier, Szabolcs Semsey, Jean-Simon Brouard, Jing Wang, Joseph T. Wade, Eric Massé
A 3′ External Transcribed Spacer in a tRNA Transcript Acts as a Sponge for Small RNAs to Prevent Transcriptional Noise
Molecular Cell 58:393 (2015)

Namiko Mitarai, Szabolcs Semsey, Kim Sneppen
Dynamic competition between transcription initiation and repression: Role of non-equilibrium steps in cell-to-cell heterogeneity
Phys. Rev. E 92:022710 (2015)
1502.03011

Kim Sneppen and Ian B. Dodd
Cooperative stabilization of the SIR complex provides robust epigenetic memory in a model of SIR silencing in Saccharomyces cerevisiae
Epigenetics 10:293 (2015)

Namiko Mitarai, Mogens Hřgh Jensen, Szabolcs Semsey
Coupled Positive and Negative Feedbacks Produce Diverse Gene Expression Patterns in Colonies
mBio 6:e00059-15 (2015)

Sergei Maslov, Kim Sneppen
Well-temperate phage: optimal bet-hedging against local environmental collapses
Scientific Reports 5:10523 (2015)
1308.1646

 

2014

Ninna S. Rossen , Jens M. Tarp , Joachim Mathiesen , Mogens H. Jensen , Lene Oddershede
Long-range ordered vorticity patterns in living tissue induced by cell division
Nature Communications 5:5720 (2014)

Ninna S. Rossen , Jens M. Tarp , Joachim Mathiesen , Mogens H. Jensen , Lene Oddershede
Cell Divisions Cause Long-Range Well-Ordered Vorticity Patterns in Endothelial Tissue
Biophysics Journal 106:p425a (2014)

Semsey, S, Krishna, S
Combining Theory and Experiments to Understand Sugar Regulation in Bacteria
Curr. Chem. Biol. 7:224 (2014)

Szabolcs Semsey
Mutations in transcriptional regulators allow selective engineering of signal integration logic.
MBio 5: (2014)

Kim Sneppen and Szabolcs Semsey
Mismatch repair at stop codons is directed independent of GATC methylation on the Escherichia coli chromosome
Scientific Reports 4:7346 (2014)

Charlotte Strandkvist, Jeppe Juul, Buzz Baum, Alexandre J. Kabla, Tom Duke
A kinetic mechanism for cell sorting based on local variations in cell motility
Interface Focus 0: (2014)

Simone Pigolotti, Roberto Benzi, Mogens H. Jensen, Prasad Perlekar, Federico Toschi
Stochastic competition between two populations in space
Collective Dynamics from Bacteria to Crowds, CISM International Centre for Mechanical Sciences 553:105-117 (2014)

Pengfei Tian , Wouter Boomsma , Yong Wang , Daniel E. Otzen , Mogens H Jensen , and Kresten Lindorff-Larsen
Structure of a Functional Amyloid Protein Subunit Computed Using Sequence Variation
J. Am. Chem. Soc. 0: (2014)

Bartłomiej Dybiec, Namiko Mitarai, and Kim Sneppen
Modeling rises and falls in money addicted social hierarchies
Physica Scripta 89:085002 (2014)

J. Mathiesen, L. Angheluta, M. H. Jensen
Statistics of co-occurring keywords in confined text messages on Twitter
The European Physical Journal Special Topics 223:1849 (2014)

Sine Lo Svenningsen and Szabolcs Semsey
Commitment to Lysogeny Is Preceded by a Prolonged Period of Sensitivity to the Late Lytic Regulator Q in Bacteriophage λ
Journal of bacteriology 196:3582 (2014)

Kristian Moss Bendtsen, Martin Borch Jensen, Alfred May, Lene Juel Rasmussen, Ala Trusina, Vilhelm A. Bohr, Mogens H. Jensen
Dynamics of the DNA repair proteins WRN and BLM in the nucleoplasm and nucleoli
European Biophysics Journal 0: (2014)

Kim Sneppen
Models of Life: Dynamics and Regulation in Biological Systems
Cambridge University Press 0: (2014)

Szabolcs Semsey
Mutations in Transcriptional Regulators Allow Selective Engineering of Signal Integration Logic
mBio 5:e01171-14 (2014)

Szabolcs Semsey
A Mixed Incoherent Feed-Forward Loop Allows Conditional Regulation of Response Dynamics
Plos One 9:e91243 (2014)

Jan O Haerter, Namiko Mitarai, and Kim Sneppen
Phage and bacteria support mutual diversity in a narrowing staircase of coexistence
The ISME Journal 8:2317 (2014)

Namiko Mitarai, Els Heinsalu, Kim Sneppen
Speciation, Diversification, and Coexistence of Sessile Species That Compete for Space
Plos One 9:e96665 (2014)

Ala Trusina
Stress induced telomere shortening: longer life with less mutations?
BMC Systems Biology 8: (2014)

Moseley, Christopher and Berg, Peter and Haerter, Jan O.
Probing the precipitation life cycle by iterative rain cell tracking
Journal of Geophysical Research: Atmospheres 118:13361 (2014)

Kamilla Norregaard, Magnus Andersson, Kim Sneppen, Peter Eigil Nielsen, Stanley Brown, Lene B Oddershede
Effect of supercoiling on the lambda switch
Bacteriophage 4: (2014)

Filippo Botta and Namiko Mitarai
Disturbance accelerates the transition from low- to high-diversity state in a model ecosystem
Phys. Rev. E 89:022704 (2014)

Charlotte Strandkvist, Jeppe Juul, Kristian Moss Bendtsen
Asymmetric Segregation of Damaged Cellular Components in Spatially Structured Multicellular Organisms
Plos One 9:e87917 (2014)

 

2013

Simon Holbek, Kristian Moss Bendtsen, Jeppe Juul
Moderate stem-cell telomere shortening rate postpones cancer onset in a stochastic model
Physical Review E 88: (2013)

Els Heinsalu, Emilio Hernández-Garcia, and Cristóbal López
Clustering Determines Who Survives for Competing Brownian and Lévy Walkers
Physical Review Letters 110:258101 (2013)

Subnuclear relocalization and silencing of a chromosomal region by an ectopic rDNA repeat
Jakočiūnas T, Jordö MD, Aďt-Mebarek M, Bünner CM, Verhein-Hansen J, Oddershede L, Thon G
Proc Natl Acad Sci USA 110:E4465–E447 (2013)

akočiūnas T, Holm LR, Verhein-Hansen J, Trusina A, Thon G
Two portable recombination enhancers direct donor choice in fission yeast heterochromatin
PLoS Genetics 9:e1003762 (2013)

Hammer, Brian K; Svenningsen, Sine Lo
Small RNA target genes and regulatory connections in the Vibrio cholerae quorum sensing system
Quorum Sensing Methods in Molecular Biology 692:189 (2013)

Ilaria Cataudella, Kim Sneppen, Kenn Gerdes, Namiko Mitarai
Conditional Cooperativity of Toxin - Antitoxin Regulation Can Mediate Bistability between Growth and Dormancy
PLoS Comput Biol 9:e1003174 (2013)

Nina Molin Hřyland-Kroghsbo, Rasmus Baadsgaard Mćrkedahl, Sine Lo Svenningsen
A quorum-sensing-induced bacteriophage defense mechanism
mBio 4: (2013)

Stefan Klumpp, Matthew Scott, Steen Pedersen, and Terence Hwa
Molecular crowding limits translation and cell growth
Proceedings of the National Academy of Sciences 110: 16754– (2013)

Joachim Mathiesen, Luiza Angheluta, Peter T. H. Ahlgren, and Mogens H. Jensen
Excitable human dynamics driven by extrinsic events in massive communities
Proc. Natl. Acad. Sct. USA 110:17259-1726 (2013)

Kamilla Norregaard, Magnus Andersson, Kim Sneppen, Peter Eigil Nielsen, Stanley Brown, and Lene B. Oddershede
DNA supercoiling enhances cooperativity and efficiency of an epigenetic switch
Proc. Natl. Acad. Sct. USA 110:17386–1739 (2013)

Mette Eriksen, Peter Horvath, Michael A. Sřrensen, Szabolcs Semsey, Lene B. Oddershede, and Liselotte Jauffred
A Novel Complex: A Quantum Dot Conjugated to an Active T7 RNA Polymerase
Journal of Nanomaterials 2013:468105 (2013)

G. Tiana and M. H. Jensen
The dynamics of genetic control in the cell: the good and bad of being late
Phil. Trans. R. Soc. A 371:20120469 (2013)

Namiko Mitarai and Steen Pedersen
Control of ribosome traffic by position-dependent choice of synonymous codons
Phys. Biol. 10:056011 (2013)
arXiv:1309.0936

Shin-ichiro Nagahiro, Hiizu Nakanishi, Namiko Mitarai
Experimental observation of shear thickening oscillation
EPL 104:28002 (2013)
1211.2886

Jeppe Juul, Ardeshir Kianercy, Sebastian Bernhardsson, and Simone Pigolotti
Replicator dynamics with turnover of players
Phys. Rev. E 88:022806 (2013)

S. Pigolotti, R. Benzi, P. Perlekar, M.H. Jensen, F. Toschi, D. R. Nelson
Growth, competition and cooperation in spatial population genetics
Theoretical Population Biology 84:72 (2013)

Lilla Sipos, Benedicte Mengel Pers, Magda Kalmár, Ildikó Tóth, Sandeep Krishna, Mogens H. Jensen, Szabolcs Semsey
Comparative Network Analysis of Preterm vs. Full-Term Infant-Mother Interactions
PLoS One 8:e67183 (2013)

Simone Pigolotti, Ludvig Lizana, Daniel Otzen, Kim Sneppen
Quality control system response to stochastic growth of amyloid fibrils
FEBS letters 587:1405 (2013)

Namiko Mitarai, Uri Alon, Mogens H. Jensen
Entrainment of noise-induced and limit cycle oscillators under weak noise
Chaos 23:023125 (2013)
1301.2440

Jeppe Juul, Kim Sneppen, and Joachim Mathiesen
Labyrinthine clustering in a spatial rock-paper-scissors ecosystem
Phys. Rev. E 87:042702 (2013)
1210.7019

Anne Katrine Alsing and Kim Sneppen
Differentiation of developing olfactory neurons analysed in terms of coupled epigenetic landscapes
Nucl. Acids Res. 41:4755 (2013)

Malte Lehmann, Kim Sneppen
Genetic Regulatory Networks that count to 3
Journal of Theoretical Biology 329:15 (2013)

Sirin W. Gangstad, Cilie W. Feldager, Jeppe Juul, and Ala Trusina
Noisy transcription factor NF-κB oscillations stabilize and sensitize cytokine signaling in space
Phys. Rev. E 87: 022702 (2013)

Szabolcs Semsey, Liselotte Jauffred, Zsolt Csiszovszki, János Erdőssy, Viktor Stéger, Sabine Hansen and Sandeep Krishna
The effect of LacI autoregulation on the performance of the lactose utilization system in Escherichia coli
Nucleic Acids Research 41:6381 (2013)

Peter Berg, Christopher Moseley & Jan O. Haerter
Strong increase in convective precipitation in response to higher temperatures
Nature Geoscience 6:181 (2013)

Haerter, Jan O., Cecilia Lövkvist, Ian B. Dodd, and Kim Sneppen
Collaboration between CpG sites is needed for stable somatic inheritance of DNA methylation states
Nucleic Acids Research 27: (2013)

 

2012

Masayo Inoue, Namiko Mitarai, and Ala Trusina.
Circuit architecture explains functional similarity of bacterial heat shock responses
Phys. Biol. 9:066003 (2012)
1209.2504

Spisák, S, Kalmár, A, Galamb, O, Wichmann, B, Sipos, F, Péterfia, B, Csabai, I, Kovalszky, I, Semsey, S, Tulassay, Z, and Molnár, B
Genome-wide screening of genes regulated by DNA methylation in colon cancer development.
PLoS One 7:e46215 (2012)

S. Pigolotti, R. Benzi, M.H. Jensen and D. Nelson
Population Genetics in Compressible Flows
Phys. Rev. Lett. 108:128102 (2012)

S. Chakraborty, M.H. Jensen, S. Krishna, B. Mengel, S. Pigolotti, V. Sekara and S. Semsey,
Limit-cycle oscillations and stable patterns in repressor lattices
Phys.Rev.E 86:031905 (2012)

Zsolt Csiszovszki, Dale E. A. Lewis, Phuoc Le, Kim Sneppen and Szabolcs Semsey
Specific contacts of the −35 region of the galP1 promoter by RNA polymerase inhibit GalR-mediated DNA looping repression
Nucl. Acids Res 40:10064 (2012)

Kim Sneppen and Ian B. Dodd
A Simple Histone Code Opens Many Paths to Epigenetics
PLoS Comput Biol 8:e1002643 (2012)

Florian Uekermann and Kim Sneppen
Spreading of multiple epidemics with cross immunization
Phys. Rev. E 86:036108 (2012)

C. Piani and J. O. Haerter
Two dimensional bias correction of temperature and precipitation copulas in climate models
Geophysical Research Letters 0: (2012)

Jan O. Haerter, Bjorn Jamtveit, Joachim Mathiesen
Communication dynamics in finite capacity social networks
Phys. Rev. Lett. 109:168701 (2012)
1209.1479

A. G. Lerner,J-P Upton,P.V.K. Praveen,R. Ghosh,Y. Nakagawa,A. Igbaria,S. Shen,V. Nguyen,B.J. Backes,M. Heiman,N. Heintz,P. Greengard,S. Hui,Q. Tang, A. Trusina,S. A. Oakes,F. R. Papa
IRE1α Induces Thioredoxin-Interacting Protein to Activate the NLRP3 Inflammasome and Promote Programmed Cell Death under Irremediable ER Stress
Cell Metabolism 6:250 (2012)

Kim Sneppen and Namiko Mitarai
Multistability with a Metastable Mixed State
Phys. Rev. Lett. 109:100602 (2012)

Jeppe Juul, Kim Sneppen, and Joachim Mathiesen
Clonal selection prevents tragedy of the commons when neighbors compete in a rock-paper-scissors game
Phys. Rev. E 85:061924 (2012)

R. Benzi, M.H. Jensen, D.R. Nelson, P. Perlekar, S. Pigolotti and F. Toschi
Population dynamics in compressible flows
Eur. Phys. J. Special Topics 204:57 (2012)

Mogens H. Jensen and Sandeep Krishna
Inducing phase-locking and chaos in cellular oscillators by modulating the driving stimuli
Febs Letters 586:1664 (2012)

Jan O. Haerter and Kim Sneppen
Spatial Structure and Lamarckian Adaptation Explain Extreme Genetic Diversity at CRISPR Locus
mBio 3:e00126-12 (2012)

Silja Heilmanna, Kim Sneppena, Sandeep Krishna
Coexistence of phage and bacteria on the boundary of self-organized refuges
Proc. Natl. Acad. Sci. USA 109:12828 (2012)

Namiko Mitarai, Joachim Mathiesen, Kim Sneppen
Emergence of diversity in a model ecosystem
Phys. Rev. E 86:011929 (2012)
1204.3398

Sřren Bang Nielsen, Pernille Yde, Lise Giehm, Sabrina Sundbye, Gunna Christiansen, Joachim Mathiesen, Mogens Hřgh Jensen, Poul Henning Jensen, Daniel E. Otzen
Multiple Roles of Heparin in the Aggregation of p25α
Journal of Molecular Biology 421:601 (2012)

Kristian Moss Bendtsen, Jeppe Juul, Ala Trusina
Fragile DNA Repair Mechanism Reduces Ageing in Multicellular Model
PLoS ONE 7:e36018 (2012)

Bartlomiej Dybiec, Namiko Mitarai, Kim Sneppen
Information spreading and development of cultural centers
Phys. Rev. E 85:056116 (2012)

Weihan Li, Sandeep Krishna, Simone Pigolotti, Namiko Mitarai, and Mogens H. Jensen.
Switching between oscillations and homeostasis in competing negative and positive feedback motifs
J. Theor. Biol. 307:205 (2012)
1204.3760

Namiko Mitarai and Hiizu Nakanishi
Granular flow: Dry and wet
Eur. Phys. J. Special Topics 204:5 (2012)

Hiizu Nakanishi, Shin-ichiro Nagahiro, and Namiko Mitarai.
Fluid dynamics of dilatant fluid
Phys. Rev. E 85:011401 (2012)
1112.4593

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. 40:6424 (2012)

Benedicte Mengel, Sandeep Krishna, Mogens H. Jensen, Ala Trusina
Nested feedback loops in gene regulation
Physica A 391:100 (2012)

Sebastian Bernhardsson, Namiko Mitarai, Kim Sneppen
Protein Localization with Flexible DNA or RNA
Plos One 7:e29218 (2012)

 

2011

Cui Chen, Jan O. Haerter, Stefan Hagemann, Claudio Piani
On the contribution of statistical bias correction to the uncertainty in the projected hydrological cycle
GEOPHYSICAL RESEARCH LETTERS 38:L20403 (2011)

Kristian Moss Bendtsen, János Erdőssy, Zsolt Csiszovszki, Sine Lo Svenningsen, Kim Sneppen, Sandeep Krishna and Szabolcs Semsey
Direct and indirect effects in the regulation of overlapping promoters
Nucleic Acid Research 39:6879 (2011)

Simone Pigolotti, Sandeep Krishna and Mogens H. Jensen
Symbolic Dynamics in Genetic Oscillation Patterns
"The Complexity of Dynamical Systems: a multidisciplinary perspective" eds. J. Dubbeldam, D. Lenstra, and K. Green, Wiley Publishing 0:99 (2011)

Mogens H. Jensen, Simone Pigolotti and Sandeep Krishna
Genetic oscillation patterns
Eur. Phys. Jour. ST 178:45 (2011)

M.F. Gruber, C.J. Johnson, C.Y. Tang, Mogens H. Jensen, L. Yde and C. Helix-Nielsen
Computational fluid dynamics simulations of flow and concentration polarization in forward osmosis membrane systems
Journal of Membrane Science 379:488 (2011)

Hiizu Nakanishi and Namiko Mitarai
Shear Thickening Oscillation in a Dilatant Fluid
J. Phys. Soc. Jpn. 80:033801 (2011)
1010.5063

Brown, S., and Mathiasen, S.
Particle-dissociating peptides
Adv. Mater. 23:132 (2011)

Pia Cordsen, Simone Pigolotti, and Mogens H. Jensen
Ecological oscillations induced by a shared predator and the “Winner peaks first” rule
Phys. Rev. E 84:031915 (2011)

Lykke Pedersen, Mogens Hřgh Jensen, Sandeep Krishna
Dickkopf1 - A New Player in Modelling the Wnt Pathway
Plos One 6:e25550 (2011)

Sebastian Bernhardsson, Philip Gerlee and Ludvig Lizana
Structural correlations in bacterial metabolic networks
BMC Evolutionary Biology 11:20 (2011)

Anne Alsing, Margit Pedersen, Kim Sneppen, Karin Hammer
Key Players in the Genetic Switch of Bacteriophage TP901-1
Biophysical Journal 100:313 (2011)

Ian B. Dodd and Kim Sneppen
Barriers and Silencers: A Theoretical Toolkit for Control and Containment of Nucleosome-Based Epigenetic States
Journal of Molecular Biology 0: (2011)

Pernille Yde, Benedicte Mengel, Mogens H Jensen, Sandeep Krishna and Ala Trusina
Modeling the NF-κB mediated inflammatory response predicts cytokine waves in tissue
BMC Systems Biology 5:115 (2011)

Jeppe Juul and Kim Sneppen
Locally self-organized quasicritical percolation in a multiple-disease model
Phys. Rev. E 84:036119 (2011)
1107.0528

Joachim Mathiesen, Namiko Mitarai, Kim Sneppen, and Ala Trusina
Ecosystems with mutually exclusive interactions self-organize to a state of high diversity
Phys. Rev. Lett. 107 107:188101 (2011)
1108.2011

J.O. Haerter, A. Trusina, K. Sneppen
Bacterial CRISPR defense system buffers phage diversity
Journal of Virology 85:10554 (2011)

Bendtsen KM, Erdossy J, Csiszovszki Z, Svenningsen SL, Sneppen K, Krishna S, Semsey S.
Direct and indirect effects in the regulation of overlapping promoters.
Nucleic Acids Res. 39:6879 (2011)

Csiszovszki Z, Krishna S, Orosz L, Adhya S, Semsey S.
Structure and function of the d-galactose network in enterobacteria.
MBio 2:pii: e0005 (2011)

L. Lizana, N. Mitarai, H. Nakanishi, and K. Sneppen
Modeling the spatial dynamics of culture spreading in the presence of cultural strongholds
Phys. Rev. E 83:066116 (2011)
1101.3998

Margit Pedersen, Sřren Nissen, Namiko Mitarai, Sine Lo Svenningsen, Kim Sneppen, and Steen Pedersen
The Functional Half-Life of an mRNA Depends on the Ribosome Spacing in an Early Coding Region
J. Mol. Biol. 407:35 (2011)

S. Bornholdt, M. H. Jensen and K. Sneppen
Emergence and Decline of Scientific Paradigms
PHYSICAL REVIEW LETTERS 106:058701 (2011)

CH Bang-Berthelsen*, L Pedersen*, T Flřyel, PH Hagedorn, T Gylvin (*: Contributed equally)
Independent component and pathway-based analysis of miRNA-regulated gene expression in a model of type 1 diabetes.
BMC genomics 12: (2011)

L Larsen, MW Rosenstierne, LW Gaarn, A Bagge, L Pedersen, CM Dahmcke, JH Nielsen, and LT Dalgaard
Expression and Localization of microRNAs in Perinatal Rat Pancreas: Role of miR-21 in Regulation of Cholesterol Metabolism
PLoS ONE 6:e25997 (2011)

Pernille Yde, Mogens Hogh Jensen, and Ala Trusina
Analyzing inflammatory response as excitable media
Phys. Rev. E 84:051913 (2011)

 

2010

Tu, Kimberly C; Long, Tao; Svenningsen, Sine L; Wingreen, Ned S; Bassler, Bonnie L
Negative Feedback Loops Involving Small Regulatory RNAs Precisely Control the Vibrio harveyi Quorum-Sensing Response
Molecular Cell 37:567 (2010)

Anna Akesson, Kristian Moss Bendtsen, Manja A. Beherens, Jan Skov Pedersen, Viveka Alfredsson and Marite´ Cardenas Gomez
The effect of PAMAM G6 dendrimers on the structure of lipid vesicles
Physical Chemistry Chemical Physics 12:12267 (2010)

Mikkel Avlund, Sandeep Krishna, Szabolcs Semsey, Ian B. Dodd, Kim Sneppen
Minimal Gene Regulatory Circuits for a Lysis-Lysogeny Choice in the Presence of Noise
PLoS ONE 5:e15037 (2010)

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

Sneppen K, Trusina A, Jensen MH, and Bornholdt S
A minimal model for multiple epidemics and immunity spreading.
Plos One 5:e13326 (2010)

J. Mathiesen, B. Jamtveit, K. Sneppen.
Organizational structure and communication networks in a university environment
Phys. Rev. E 82:016104 (2010)
1006.4652

E. Jettestuen, A. Nermoen, G. Hestmark, E. Timdal, and J. Mathiesen
Competition on the Rocks: Community Growth and Tessellation
PLoS ONE 5:e12820 (2010)

Benedicte Mengel, Alexander Hunziker, Lykke Pedersen, Ala Trusina, Mogens H Jensen and Sandeep Krishna
Modeling oscillatory control in NF-κB, p53 and Wnt signaling
Current Opinion in Genetics & Development 20:571 (2010)

Sneppen K, Pedersen S, Krishna S, Dodd I, Semsey S.
Economy of operon formation: cotranscription minimizes shortfall in protein complexes.
MBio 1: e00177 (2010)

Peter Horvath, Alexander Hunziker, Janos Erdossy, Sandeep Krishna and Szabolcs Semsey
Timing of gene transcription in the galactose utilization system of Escherichia coli
JBC 285:38062 (2010)

Alexander Hunziker, Mogens H Jensen, Sandeep Krishna
Stress-specific response of the p53-Mdm2 feedback loop
BMC Systems Biology 4:94 (2010)

Alexander Hunziker, Csaba Tuboly, Péter Horváth, Sandeep Krishna, and Szabolcs Semsey
Genetic flexibility of regulatory networks
Proc. Natl. Acad. Sci. USA 107:12998 (2010)

Pedersen M, Ligowska M, Hammer K
Characterization of the CI repressor pretein encoded by the temperate lactococcal phage TP901-1
J Bacteriol. 192:2102 (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 39:43 (2010)

K.S. Korolev, Mikkel Avlund, Oskar Hallatschek, David R. Nelson
Genetic Demixing and Evolutionary Forces in the One-Dimensional Stepping Stone Model
Review of Modern Physics 82:1691 (2010)
0904.4625

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

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

HG Hansen, J Overgaard, M Lajer, F Hubalek, P Hřjrup, L Pedersen, L Tarnow, P Rossing, F Pociot, and JN McGuire
Finding diabetic nephropathy biomarkers in the plasma peptidome by high-throughput magnetic bead-processing and MALDI-TOF-MS analysis. Proteomics
Clinical Applications 4: (2010)

 

2009

Svenningsen, Sine L; Tu, Kimberly C; Bassler, Bonnie L
Gene dosage compensation calibrates four regulatory RNAs to control Vibrio cholerae quorum sensing,The EMBO journal
The EMBO journal 28:429 (2009)

Namiko Mitarai and Hiizu Nakanishi
Simple Model for Wet Granular Materials with Liquid Clusters
Europhys. Lett. 88:64001 (2009)
0908.1477v2

B. Jamtveit, E. Jettestuen, J. Mathiesen
Scaling properties of European research units
Proc. Nat. Acad. Sci. USA 106:13160 (2009)

Sandeep Krishna, Szabolcs 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)

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)

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)

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

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 0:83 (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

L Pedersen and H Flyvbjerg
Comment on "Direct Measurement of the Oscillation Frequency in an Optical-Tweezers Trap by Parametric Excitation"
PRL 98:189801 (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
Proc. Natl. Acad. Sci. USA 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 Genevičve 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 Hřgh 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)

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. Bćk, 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

Peter Berg, Christopher Moseley & Jan O. Haerter
Strong increase in convective precipitation in response to higher temperatures
Nature Geoscience 6:181 (2013)

Shin-ichiro Nagahiro, Hiizu Nakanishi, Namiko Mitarai
Experimental observation of shear thickening oscillation
EPL 104:28002 (2013)
1211.2886

Stefan Klumpp, Matthew Scott, Steen Pedersen, and Terence Hwa
Molecular crowding limits translation and cell growth
Proceedings of the National Academy of Sciences 110: 16754– (2013)

Ilaria Cataudella, Kim Sneppen, Kenn Gerdes, Namiko Mitarai
Conditional Cooperativity of Toxin - Antitoxin Regulation Can Mediate Bistability between Growth and Dormancy
PLoS Comput Biol 9:e1003174 (2013)

Bendtsen KM, Erdossy J, Csiszovszki Z, Svenningsen SL, Sneppen K, Krishna S, Semsey S.
Direct and indirect effects in the regulation of overlapping promoters.
Nucleic Acids Res. 39:6879 (2011)

M.F. Gruber, C.J. Johnson, C.Y. Tang, Mogens H. Jensen, L. Yde and C. Helix-Nielsen
Computational fluid dynamics simulations of flow and concentration polarization in forward osmosis membrane systems
Journal of Membrane Science 379:488 (2011)

Mogens H. Jensen, Simone Pigolotti and Sandeep Krishna
Genetic oscillation patterns
Eur. Phys. Jour. ST 178:45 (2011)

Kristian Moss Bendtsen, János Erdőssy, Zsolt Csiszovszki, Sine Lo Svenningsen, Kim Sneppen, Sandeep Krishna and Szabolcs Semsey
Direct and indirect effects in the regulation of overlapping promoters
Nucleic Acid Research 39:6879 (2011)

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)

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 and Kim Sneppen
Punctuated equilibrium and criticality in a simple model of evoluton
Phys. Rev. Lett. 71:4083 (1993)

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)