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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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Sandeep Krishna

Sandeep Krishna
Position: Reader at NCBS, India
Email: sandeepncbs.res.in
www: http://www.ncbs.res.in/sandeep

Publications:
Mathias L. Heltberg, Sandeep Krishna, Mogens H. Jensen
Time Correlations in Mode Hopping of Coupled Oscillators
Journal of Statistical Physics 0: (2017)

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)

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

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)

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

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)

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)

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

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)

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

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)

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)

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)

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

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

Silja Heilmann, Kim Sneppen and Sandeep Krishna
Sustainability of Virulence in a Phage-Bacterial Ecosystem
Journal of Virology 84: (2010)

Kim Sneppen, Sandeep Krishna, Szabolcs Semsey
Simplified Models of Biological Networks
Annual Review of Biophysics 39:43 (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)

Peter B. Jensen, Lykke Pedersen, Sandeep Krishna and Mogens H. Jensen
A Wnt Oscillator Model for Somitogenesis
Biophysical Journal 98: (2010)

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

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

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)

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)

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)

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)

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)

Sandeep Krishna, Szabolcs Semsey and Mogens H. Jensen
Frustrated bistability as a means to engineer oscillations in biological systems
Physical Biology 6:3 (2009)

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

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

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

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

G Tiana, S Krishna, S Pigolotti, M H Jensen and K Sneppen
Oscillations and temporal signalling in cells
Phys. Biol. 4:R1 (2007)

Szabolcs Semsey, Sandeep Krishna, Kim Sneppen, Sankar Adhya
Signal Integration in the Galactose Network of Escherichia coli
Molecular Microbiology 65:465 (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)

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, 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

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

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

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