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\n  \n 2019\n \n \n (3)\n \n \n
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\n \n \n
\n \n\n \n \n \n \n \n On chaotic dynamics in transcription factors and the associated effects in differential gene regulation,.\n \n \n \n\n\n \n Heltberg, M.; Krishna$^*$, S.; and Jensen$^*$, M. H.\n\n\n \n\n\n\n Nat. Commun., 10: 71 ($^*$Co-corresponding authors).. 2019.\n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
\n 
@article{chaosregulation,\r\n  title = {On chaotic dynamics in transcription factors and the associated effects in differential gene regulation,},\r\n  author = {Mathias Heltberg and Sandeep Krishna$^*$ and Mogens H. Jensen$^*$},\r\n  journal = {Nat. Commun.},\r\n  year = {2019},\r\nvolume = {10},\r\npages = {71 ($^*$Co-corresponding authors).}\r\n}\r\n\r\n
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\n\n\n
\n \n\n \n \n \n \n \n \n Metabolic constraints drive self-organization of specialized cell groups,.\n \n \n \n \n\n\n \n Varahan, S.; Sinha, V.; Walwekar, A.; Krishna, S.; and Laxman, S.\n\n\n \n\n\n\n eLife, 8: e46735.. 2019.\n \n\n\n\n
\n\n\n\n \n \n \"MetabolicPaper\n  \n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n  \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
\n 
@article{yeastcolony,\r\n  title = {Metabolic constraints drive self-organization of specialized cell groups,},\r\n  author = {Sriram Varahan and Vaibhhav Sinha and Adhish Walwekar and Sandeep Krishna and Sunil Laxman},\r\n  journal = {eLife},\r\n  year = {2019},\r\nvolume = {8},\r\nurl = {https://www.biorxiv.org/content/10.1101/573626v1},\r\npages = {e46735.},\r\nabstract = {How phenotypically distinct states in isogenic cell populations appear and stably co-exist remains an unresolved question. We find that within a clonal yeast colony developing in low glucose, cells arrange into metabolically disparate cell groups. Using this system, we model and experimentally identify metabolic constraints sufficient to drive such assembly. Beginning in a gluconeogenic state, cells in a contrary state, exhibiting high pentose phosphate pathway activity, spontaneously appear and proliferate, in a spatially constrained manner. The gluconeogenic cells in the developing colony produce a resource, which we identify as trehalose. At threshold concentrations of trehalose, cells in the new metabolic state emerge and proliferate. A self-organized system establishes, where cells in this new state are sustained by trehalose consumption, which thereby restrains other cells in the trehalose producing, gluconeogenic state. Our work suggests simple physico-chemical principles that determine how isogenic cells spontaneously self-organize into structured assemblies in complimentary, specialized states.}\r\n}\r\n\r\n
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\n How phenotypically distinct states in isogenic cell populations appear and stably co-exist remains an unresolved question. We find that within a clonal yeast colony developing in low glucose, cells arrange into metabolically disparate cell groups. Using this system, we model and experimentally identify metabolic constraints sufficient to drive such assembly. Beginning in a gluconeogenic state, cells in a contrary state, exhibiting high pentose phosphate pathway activity, spontaneously appear and proliferate, in a spatially constrained manner. The gluconeogenic cells in the developing colony produce a resource, which we identify as trehalose. At threshold concentrations of trehalose, cells in the new metabolic state emerge and proliferate. A self-organized system establishes, where cells in this new state are sustained by trehalose consumption, which thereby restrains other cells in the trehalose producing, gluconeogenic state. Our work suggests simple physico-chemical principles that determine how isogenic cells spontaneously self-organize into structured assemblies in complimentary, specialized states.\n
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\n \n\n \n \n \n \n \n \n Constraints on somite formation in developing embryos,.\n \n \n \n \n\n\n \n Juul$^*$, J. S.; Jensen, M. H.; and Krishna$^*$, S.\n\n\n \n\n\n\n J. Royal Soc. Interface, 16: doi: http://doi.org/10.1098/rsif.2019.0451 ($^*$Co-corresponding authors).. 2019.\n \n\n\n\n
\n\n\n\n \n \n \"ConstraintsPaper\n  \n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
\n 
@article{somiteconstraints,\r\n  title = {Constraints on somite formation in developing embryos,},\r\n  author = {Jonas S. Juul$^*$ and Mogens H. Jensen and Sandeep Krishna$^*$},\r\n  journal = {J. Royal Soc. Interface},\r\n  year = {2019},\r\nvolume = {16},\r\nurl = {https://www.biorxiv.org/content/10.1101/645010v1},\r\npages = {doi: http://doi.org/10.1098/rsif.2019.0451 ($^*$Co-corresponding authors).},\r\nabstract = {}\r\n}\r\n\r\n%@article{filamentrecovery,\r\n
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\n  \n 2018\n \n \n (5)\n \n \n
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\n \n\n \n \n \n \n \n \n Regulation of global transcription in E. coli by Rsd and 6S RNA,.\n \n \n \n \n\n\n \n Lal, A.; Krishna, S.; and Seshasayee, A. S. N.\n\n\n \n\n\n\n G3, 8: 2079–2089.. 2018.\n \n\n\n\n
\n\n\n\n \n \n \"RegulationPaper\n  \n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\n \n  \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
\n 
@article{rsd_and_6S,\r\n  title = {Regulation of global transcription in E. coli by Rsd and 6S RNA,},\r\n  author = {Avantika Lal and Sandeep Krishna and Aswin Sai Narain Seshasayee},\r\n  journal = {G3},\r\n  year = {2018},\r\n  doi = {10.1101/058339},\r\n  abstract = {In Escherichia coli, the housekeeping sigma factor σ70 directs RNA polymerase to transcribe growth-related genes, whereas the alternative sigma factor σ38 directs it to transcribe stress response genes during stationary phase. Two molecules hypothesized to regulate RNA polymerase activity are Rsd, which sequesters free σ70, and 6S RNA, which sequesters the RNA polymerase-σ70 holoenzyme. Despite multiple studies, their function remains controversial. Here we use genome-wide expression studies in five phases of growth, along with theoretical modeling, to investigate the functions of Rsd and 6S RNA. We show that 6S RNA and Rsd act as global regulators of gene expression throughout bacterial growth, and that both increase transcription of σ38 dependent genes. We also find several instances of crosstalk between 6S RNA and Rsd, and propose a model in which this crosstalk is important in regulating sigma factor competition.},\r\n  URL = {https://www.biorxiv.org/content/early/2016/06/10/058339},\r\n  eprint = {https://www.biorxiv.org/content/early/2016/06/10/058339.full.pdf},\r\n  volume = {8},\r\n  pages = {2079--2089.}\r\n}\r\n\r\n
\n
\n\n\n
\n In Escherichia coli, the housekeeping sigma factor σ70 directs RNA polymerase to transcribe growth-related genes, whereas the alternative sigma factor σ38 directs it to transcribe stress response genes during stationary phase. Two molecules hypothesized to regulate RNA polymerase activity are Rsd, which sequesters free σ70, and 6S RNA, which sequesters the RNA polymerase-σ70 holoenzyme. Despite multiple studies, their function remains controversial. Here we use genome-wide expression studies in five phases of growth, along with theoretical modeling, to investigate the functions of Rsd and 6S RNA. We show that 6S RNA and Rsd act as global regulators of gene expression throughout bacterial growth, and that both increase transcription of σ38 dependent genes. We also find several instances of crosstalk between 6S RNA and Rsd, and propose a model in which this crosstalk is important in regulating sigma factor competition.\n
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\n \n\n \n \n \n \n \n Detection Of Cooperatively Bound Transcription Factor Pairs Using ChIP-seq Peak Intensities And Expectation Maximization,.\n \n \n \n\n\n \n Datta, V.; Siddharthan, R.; and Krishna, S.\n\n\n \n\n\n\n PLoS ONE, 13: e0199771.. 2018.\n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
\n 
@article{cpi-em,\r\n  title = {Detection Of Cooperatively Bound Transcription Factor Pairs Using ChIP-seq Peak Intensities And Expectation Maximization,},\r\n  author = {Vishaka Datta and Rahul Siddharthan and Sandeep Krishna},\r\n  journal = {PLoS ONE},\r\n  year = {2018},\r\n  volume = {13},\r\n  pages = {e0199771.}\r\n}\r\n\r\n
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\n \n\n \n \n \n \n \n Evidence of sinks and sources in the PLC activated PIP2 cycle,.\n \n \n \n\n\n \n Suratekar, R.; Panda, A.; Raghu, P.; and Krishna, S.\n\n\n \n\n\n\n FEBS Lett., 592: 962–972.. 2018.\n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
\n 
@article{sinkssources,\r\n  title = {Evidence of sinks and sources in the PLC activated PIP2 cycle,},\r\n  author = {Rohit Suratekar and Aniruddha Panda and Padinjat Raghu and Sandeep Krishna},\r\n  journal = {FEBS Lett.},\r\n  year = {2018},\r\n  volume = {592},\r\n  pages = {962--972.}\r\n  }\r\n  \r\n
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\n \n\n \n \n \n \n \n A minimal ''push-pull\" bistability model explains oscillations between quiescent and proliferative cell states,.\n \n \n \n\n\n \n Krishna, S.; and Laxman, S.\n\n\n \n\n\n\n Mol. Biol. Cell,, 29: 2243–2258.. 2018.\n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
\n 
@article{ymc,\r\n  title = {A minimal ''push-pull" bistability model explains oscillations between quiescent and proliferative cell states,},\r\n  author = {Sandeep Krishna and Sunil Laxman},\r\n  journal = {Mol. Biol. Cell,},\r\n  year = {2018},\r\n  volume = {29},\r\n  pages = {2243--2258.}\r\n}\r\n\r\n
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\n \n\n \n \n \n \n \n Entrainment as a means of controlling phase waves in populations of coupled oscillators,.\n \n \n \n\n\n \n Juul, J.; Krishna$^*$, S.; and Jensen$^*$, M. H.\n\n\n \n\n\n\n Phys. Rev. E, 98: 062412 ($^*$Co-corresponding authors).. 2018.\n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
\n 
@article{phasewaves,\r\n  title = {Entrainment as a means of controlling phase waves in populations of coupled oscillators,},\r\n  author = {Jonas Juul and Sandeep Krishna$^*$ and Mogens H. Jensen$^*$},\r\n  journal = {Phys. Rev. E},\r\n  year = {2018},\r\nvolume = {98},\r\npages = {062412 ($^*$Co-corresponding authors).}\r\n}\r\n\r\n
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\n  \n 2017\n \n \n (2)\n \n \n
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\n \n\n \n \n \n \n \n In silico evolution of lysis-lysogeny strategies reproduces observed lysogeny propensities in temperate bacteriophages,.\n \n \n \n\n\n \n Sinha, V.; Goyal, A.; Svenningsen, S. L.; Semsey, S.; and Krishna, S.\n\n\n \n\n\n\n Front. Microbiol., 8: 1386.. 2017.\n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
\n 
@article{lysislysogeny,\r\n  title = {In silico evolution of lysis-lysogeny strategies reproduces observed lysogeny propensities in temperate bacteriophages,},\r\n  author = {Vaibhhav Sinha and Akshit Goyal and Sine Lo Svenningsen and Szabolcs Semsey and Sandeep Krishna},\r\n  journal = {Front. Microbiol.},\r\n  year = {2017},\r\n  volume = {8},\r\n  pages = {1386.}\r\n}\r\n\r\n
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\n \n\n \n \n \n \n \n Time correlations in mode hopping of coupled oscillators,.\n \n \n \n\n\n \n Heltberg, M.; Krishna, S.; and Jensen, M. H.\n\n\n \n\n\n\n J. Stat. Phys., 167: 792.. 2017.\n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
\n 
@article{timecorr,\r\n  title = {Time correlations in mode hopping of coupled oscillators,},\r\n  author = {Mathias Heltberg and Sandeep Krishna and Mogens H. Jensen},\r\n  journal = {J. Stat. Phys.},\r\n  year = {2017},\r\n  volume = {167},\r\n  pages = {792.}\r\n}\r\n\r\n
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\n  \n 2016\n \n \n (2)\n \n \n
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\n \n\n \n \n \n \n \n \n Efficiency of a Stochastic Search with Punctual and Costly Restarts.\n \n \n \n \n\n\n \n Husain, K.; and Krishna, S.\n\n\n \n\n\n\n arXiv,1609.03754. 2016.\n \n\n\n\n
\n\n\n\n \n \n \"Efficiency pdf\n  \n \n \n \"Efficiency arxiv\n  \n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n  \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
\n 
@article{resetpaper,\r\n  title = {Efficiency of a Stochastic Search with Punctual and Costly Restarts},\r\n  author = {Kabir Husain and Sandeep Krishna},\r\n  journal = {arXiv},\r\n  year = {2016},\r\n  volume = {},\r\n  pages = {1609.03754},\r\n  abstract={The mean completion time of a stochastic process may be rendered finite and minimised by a\r\njudiciously chosen restart protocol, which may either be stochastic or deterministic. Here we study\r\nanalytically an arbitrary stochastic search subject to an arbitrary restart protocol, each charac-\r\nterised by a distribution of waiting times. By a direct enumeration of paths we construct the joint\r\ndistribution of completion time and restart number, in a form amenable to analytical evaluation\r\nor quadrature; thereby we optimise the search over both time and potentially costly restart events.\r\nAnalysing the effect of a punctual, i.e. almost deterministic, restart, we demonstrate that the opti-\r\nmal completion time always increases proportionately with the variance of the restart distribution;\r\nthe constant of proportionality depends only on the search process. We go on to establish simple\r\nbounds on the optimal restart time. Our results are relevant to the analysis and rational design of\r\nefficient and optimal restart protocols.},\r\n  keywords={},\r\n  url_PDF={Husain_2016_arXiv_SearchWithRestarts.pdf},\r\n  url_arXiv={http://arxiv.org/abs/1609.03754}\r\n}\r\n
\n
\n\n\n
\n The mean completion time of a stochastic process may be rendered finite and minimised by a judiciously chosen restart protocol, which may either be stochastic or deterministic. Here we study analytically an arbitrary stochastic search subject to an arbitrary restart protocol, each charac- terised by a distribution of waiting times. By a direct enumeration of paths we construct the joint distribution of completion time and restart number, in a form amenable to analytical evaluation or quadrature; thereby we optimise the search over both time and potentially costly restart events. Analysing the effect of a punctual, i.e. almost deterministic, restart, we demonstrate that the opti- mal completion time always increases proportionately with the variance of the restart distribution; the constant of proportionality depends only on the search process. We go on to establish simple bounds on the optimal restart time. Our results are relevant to the analysis and rational design of efficient and optimal restart protocols.\n
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\n \n\n \n \n \n \n \n \n Noise induces hopping between NF-kB entrainment modes.\n \n \n \n \n\n\n \n Heltberg, M.; Kellog, R. A.; Krishna, S.; Tay, S.; and Jensen, M. H.\n\n\n \n\n\n\n Cell Systems, 3: 1–8. 2016.\n \n\n\n\n
\n\n\n\n \n \n \"Noise pdf\n  \n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\n \n  \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
\n 
@article{NFkBmodehopping,\r\n  title = {Noise induces hopping between NF-kB entrainment modes},\r\n  author = {Mathias Heltberg and Ryan A. Kellog and Sandeep Krishna and Savas Tay and Mogens H. Jensen},\r\n  journal = {Cell Systems},\r\n  year = {2016},\r\n  volume = {3},\r\n  pages = {1--8},\r\n  abstract={Oscillations and noise drive many processes in\r\nbiology, but how both affect the activity of the transcription factor nuclear factor kB (NF-kB) is not understood. Here, we observe that when NF-kB oscillations are entrained by periodic tumor necrosis\r\nfactor (TNF) inputs in cells, NF-kB exhibits jumps between frequency modes, a phenomenon we call\r\n‘‘cellular mode-hopping.’’ By comparing stochastic\r\nsimulations of NF-kB oscillations to deterministic\r\nsimulations conducted inside and outside the\r\nchaotic regime of parameter space, we show that\r\nnoise facilitates mode-hopping in all regimes. However, when the deterministic system is driven by\r\nchaotic dynamics, hops between modes are erratic\r\nand short-lived, whereas in cells, the system spends\r\nseveral periods in one entrainment mode before\r\nhopping and rarely visits more than two modes.\r\nThe behavior in cells matches our simulations of\r\nnoise-induced mode-hopping outside the chaotic\r\nregime. We suggest that mode-hopping is a mechanism by which different NF-kB-dependent genes\r\nunder frequency control can be expressed at\r\ndifferent times.},\r\n  keywords={},\r\n  url_PDF={},\r\n  doi={10.1016/j.cels.2016.11.014}\r\n}\r\n\r\n
\n
\n\n\n
\n Oscillations and noise drive many processes in biology, but how both affect the activity of the transcription factor nuclear factor kB (NF-kB) is not understood. Here, we observe that when NF-kB oscillations are entrained by periodic tumor necrosis factor (TNF) inputs in cells, NF-kB exhibits jumps between frequency modes, a phenomenon we call ‘‘cellular mode-hopping.’’ By comparing stochastic simulations of NF-kB oscillations to deterministic simulations conducted inside and outside the chaotic regime of parameter space, we show that noise facilitates mode-hopping in all regimes. However, when the deterministic system is driven by chaotic dynamics, hops between modes are erratic and short-lived, whereas in cells, the system spends several periods in one entrainment mode before hopping and rarely visits more than two modes. The behavior in cells matches our simulations of noise-induced mode-hopping outside the chaotic regime. We suggest that mode-hopping is a mechanism by which different NF-kB-dependent genes under frequency control can be expressed at different times.\n
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\n  \n 2015\n \n \n (4)\n \n \n
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\n \n\n \n \n \n \n \n \n Effects of Four Different Regulatory Mechanisms on the Dynamics of Gene Regulatory Cascades,.\n \n \n \n \n\n\n \n Hansen, S.; Krishna, S.; Semsey, S.; and Svenningsen, S. L.\n\n\n \n\n\n\n Sci. Rep., 5: 12186. 2015.\n \n\n\n\n
\n\n\n\n \n \n \"Effects pdf\n  \n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\n \n  \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n \n \n \n \n \n \n \n \n\n\n\n
\n 
@article{fnuproject,\r\n  title = {Effects of Four Different Regulatory Mechanisms on the Dynamics of Gene Regulatory Cascades,},\r\n  author = {Sabine Hansen and Sandeep Krishna and Szabolcs Semsey and Sine Lo Svenningsen},\r\n  journal = {Sci. Rep.},\r\n  year = {2015},\r\n  volume = {5},\r\n  pages = {12186},\r\n  abstract = {Gene regulatory cascades (GRCs) are common motifs in cellular molecular networks. A given logical function in these cascades, such as the repression of the activity of a transcription factor, can be implemented by a number of different regulatory mechanisms. The potential consequences for the dynamic performance of the GRC of choosing one mechanism over another have not been analysed systematically. Here, we report the construction of a synthetic GRC in Escherichia coli, which allows us for the first time to directly compare and contrast the dynamics of four different regulatory mechanisms, affecting the transcription, translation, stability, or activity of a transcriptional repressor. We developed a biologically motivated mathematical model which is sufficient to reproduce the response dynamics determined by experimental measurements. Using the model, we explored the potential response dynamics that the constructed GRC can perform. We conclude that dynamic differences between regulatory mechanisms at an individual step in a GRC are often concealed in the overall performance of the GRC, and suggest that the presence of a given regulatory mechanism in a certain network environment does not necessarily mean that it represents a single optimal evolutionary solution.},\r\n  keywords={Bacterial genetics,Biological physics,Gene regulation,Genetic circuit engineering},\r\n  url_PDf={Hansen_2015_SciRep_4Regulators.pdf},\r\n  doi={10.1038/srep12186}\r\n}\r\n
\n
\n\n\n
\n Gene regulatory cascades (GRCs) are common motifs in cellular molecular networks. A given logical function in these cascades, such as the repression of the activity of a transcription factor, can be implemented by a number of different regulatory mechanisms. The potential consequences for the dynamic performance of the GRC of choosing one mechanism over another have not been analysed systematically. Here, we report the construction of a synthetic GRC in Escherichia coli, which allows us for the first time to directly compare and contrast the dynamics of four different regulatory mechanisms, affecting the transcription, translation, stability, or activity of a transcriptional repressor. We developed a biologically motivated mathematical model which is sufficient to reproduce the response dynamics determined by experimental measurements. Using the model, we explored the potential response dynamics that the constructed GRC can perform. We conclude that dynamic differences between regulatory mechanisms at an individual step in a GRC are often concealed in the overall performance of the GRC, and suggest that the presence of a given regulatory mechanism in a certain network environment does not necessarily mean that it represents a single optimal evolutionary solution.\n
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\n\n\n
\n \n\n \n \n \n \n \n \n Restriction Modification Systems as Engines of Diversity,.\n \n \n \n \n\n\n \n Sneppen, K.; Semsey, S.; Seshasayee, A.; and Krishna, S.\n\n\n \n\n\n\n Front. Microbiol., 6: 528. 2015.\n \n\n\n\n
\n\n\n\n \n \n \"Restriction pdf\n  \n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\n \n  \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n
\n 
@article{RMsystems,\r\n  title = {Restriction Modification Systems as Engines of Diversity,},\r\n  author = {Kim Sneppen and Szabolcs Semsey and Aswin Seshasayee and Sandeep Krishna},\r\n  journal = {Front. Microbiol.},\r\n  year = {2015},\r\n  volume = {6},\r\n  pages = {528},\r\n  abstract = {Restriction modification (RM) systems provide protection against a broad spectrum of phages. However, the likelihood of a phage permanently bypassing this can be as high as 0.1 per infection (Korona et al., 1993) which makes for a relatively weak defense. Here we argue that, apart from providing such transient defenses, RM systems can facilitate long-term coexistence of many bacterial strains. We show that this diversity can be as large as the burst size of the phage but no larger—a curious correspondence between a number at the level of species and another number at the level of individuals. Such a highly diverse and stably coexisting ecosystem is robust to substantial variation in both bacterial growth rates and strength of their RM systems, which might be one reason why quite weak RM systems exist in the wild.},\r\n  keywords={bacteriophage defense,epigenetic labeling,phage-bacteria interaction,ecosystem diversity,mathematical modeling,population dynamics},\r\n  url_Pdf = {Sneppen_2015_FrontMicrobiol_RMSystems.pdf},\r\n  doi={10.3389%2Ffmicb.2015.00528},\r\n}\r\n
\n
\n\n\n
\n Restriction modification (RM) systems provide protection against a broad spectrum of phages. However, the likelihood of a phage permanently bypassing this can be as high as 0.1 per infection (Korona et al., 1993) which makes for a relatively weak defense. Here we argue that, apart from providing such transient defenses, RM systems can facilitate long-term coexistence of many bacterial strains. We show that this diversity can be as large as the burst size of the phage but no larger—a curious correspondence between a number at the level of species and another number at the level of individuals. Such a highly diverse and stably coexisting ecosystem is robust to substantial variation in both bacterial growth rates and strength of their RM systems, which might be one reason why quite weak RM systems exist in the wild.\n
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\n\n\n
\n \n\n \n \n \n \n \n \n Why do bacteria regulate public goods by quorum sensing?-How the shapes of cost and benefit functions determine the form of optimal regulation,.\n \n \n \n \n\n\n \n Heilmann, S.; Krishna, S.; and Kerr, B.\n\n\n \n\n\n\n Front. Microbiol., 6: 767. 2015.\n \n\n\n\n
\n\n\n\n \n \n \"Why pdf\n  \n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\n \n  \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n
\n 
@article{costsbenefits,\r\n  title = {Why do bacteria regulate public goods by quorum sensing?-How the shapes of cost and benefit functions determine the form of optimal regulation,},\r\n  author = {Silja Heilmann and Sandeep Krishna and Benjamin Kerr},\r\n  journal = {Front. Microbiol.},\r\n  year = {2015},\r\n  volume = {6},\r\n  pages = {767},\r\n  abstract={Many bacteria secrete compounds which act as public goods. Such compounds are often under quorum sensing (QS) regulation, yet it is not understood exactly when bacteria may gain from having a public good under QS regulation. Here, we show that the optimal public good production rate per cell as a function of population size (the optimal production curve, OPC) depends crucially on the cost and benefit functions of the public good and that the OPC will fall into one of two categories: Either it is continuous or it jumps from zero discontinuously at a critical population size. If, e.g., the public good has accelerating returns and linear cost, then the OPC is discontinuous and the best strategy thus to ramp up production sharply at a precise population size. By using the example of public goods with accelerating and diminishing returns (and linear cost) we are able to determine how the two different categories of OPSs can best be matched by production regulated through a QS signal feeding back on its own production. We find that the optimal QS parameters are different for the two categories and specifically that public goods which provide accelerating returns, call for stronger positive signal feedback.},\r\n  keywords={quorum sensing, cooperation, cost and benefit functions, bacteria, public good production and regulation},\r\n  url_PDF={Heilmann_2015_FrontMicrobiol_QuorumSensing.pdf},\r\n  doi={10.3389/fmicb.2015.00767}\r\n}\r\n
\n
\n\n\n
\n Many bacteria secrete compounds which act as public goods. Such compounds are often under quorum sensing (QS) regulation, yet it is not understood exactly when bacteria may gain from having a public good under QS regulation. Here, we show that the optimal public good production rate per cell as a function of population size (the optimal production curve, OPC) depends crucially on the cost and benefit functions of the public good and that the OPC will fall into one of two categories: Either it is continuous or it jumps from zero discontinuously at a critical population size. If, e.g., the public good has accelerating returns and linear cost, then the OPC is discontinuous and the best strategy thus to ramp up production sharply at a precise population size. By using the example of public goods with accelerating and diminishing returns (and linear cost) we are able to determine how the two different categories of OPSs can best be matched by production regulated through a QS signal feeding back on its own production. We find that the optimal QS parameters are different for the two categories and specifically that public goods which provide accelerating returns, call for stronger positive signal feedback.\n
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\n\n\n
\n \n\n \n \n \n \n \n \n The role of mRNA and protein stability in the function of coupled positive and negative feedback systems in eukaryotic cells,.\n \n \n \n \n\n\n \n Bendtsen, K. M.; Jensen, M. H.; Krishna, S.; and Semsey, S.\n\n\n \n\n\n\n Sci. Rep., 5: 13910. 2015.\n \n\n\n\n
\n\n\n\n \n \n \"The pdf\n  \n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\n \n  \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n \n \n \n \n \n \n \n \n\n\n\n
\n 
@article{tetpaper,\r\n  title = {The role of mRNA and protein stability\r\nin the function of coupled positive and negative feedback systems in eukaryotic cells,},\r\n  author = {Kristian Moss Bendtsen and Mogens H. Jensen and Sandeep Krishna and Szabolcs Semsey},\r\n  journal = {Sci. Rep.},\r\n  year = {2015},\r\n  volume = {5},\r\n  pages = {13910},\r\n  abstract={Oscillators and switches are important elements of regulation in biological systems. These are composed of coupling negative feedback loops, which cause oscillations when delayed, and positive feedback loops, which lead to memory formation. Here, we examine the behavior of a coupled feedback system, the Negative Autoregulated Frustrated bistability motif (NAF). This motif is a combination of two previously explored motifs, the frustrated bistability motif (FBM) and the negative auto regulation motif (NAR), which both can produce oscillations. The NAF motif was previously suggested to govern long term memory formation in animals, and was used as a synthetic oscillator in bacteria. We build a mathematical model to analyze the dynamics of the NAF motif. We show analytically that the NAF motif requires an asymmetry in the strengths of activation and repression links in order to produce oscillations. We show that the effect of time delays in eukaryotic cells, originating from mRNA export and protein import, are negligible in this system. Based on the reported protein and mRNA half-lives in eukaryotic cells, we find that even though the NAF motif possesses the ability for oscillations, it mostly promotes constant protein expression at the biologically relevant parameter regimes.},\r\n  keywords={Biochemical reaction networks,Dynamical systems,Kinetics,Modularity},\r\n  url_PDF={Bendtsen_2015_SciRep_CoupledFeedback.pdf},\r\n  doi={10.1038/srep13910}\r\n}\r\n
\n
\n\n\n
\n Oscillators and switches are important elements of regulation in biological systems. These are composed of coupling negative feedback loops, which cause oscillations when delayed, and positive feedback loops, which lead to memory formation. Here, we examine the behavior of a coupled feedback system, the Negative Autoregulated Frustrated bistability motif (NAF). This motif is a combination of two previously explored motifs, the frustrated bistability motif (FBM) and the negative auto regulation motif (NAR), which both can produce oscillations. The NAF motif was previously suggested to govern long term memory formation in animals, and was used as a synthetic oscillator in bacteria. We build a mathematical model to analyze the dynamics of the NAF motif. We show analytically that the NAF motif requires an asymmetry in the strengths of activation and repression links in order to produce oscillations. We show that the effect of time delays in eukaryotic cells, originating from mRNA export and protein import, are negligible in this system. Based on the reported protein and mRNA half-lives in eukaryotic cells, we find that even though the NAF motif possesses the ability for oscillations, it mostly promotes constant protein expression at the biologically relevant parameter regimes.\n
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\n  \n 2014\n \n \n (1)\n \n \n
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\n \n \n
\n \n\n \n \n \n \n \n \n Road rules for traffic on DNA – systematic analysis of transcriptional roadblocking in vivo,.\n \n \n \n \n\n\n \n Hao, N.; Krishna, S.; Ahlgren-Berg, A.; Cutts, E. E; Shearwin, K. E; and Dodd, I. B\n\n\n \n\n\n\n Nucl. Acids Res., 42: 8861–8872. 2014.\n \n\n\n\n
\n\n\n\n \n \n \"Road pdf\n  \n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\n \n  \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n \n \n \n \n \n \n \n \n\n\n\n
\n 
@article{roadrules,\r\n  title = {Road rules for traffic on DNA -- systematic analysis of transcriptional roadblocking in vivo,},\r\n  author = {Nan Hao and Sandeep Krishna and Alexandra Ahlgren-Berg and Erin E Cutts and Keith E Shearwin and Ian B Dodd},\r\n  journal = {Nucl. Acids Res.},\r\n  year = {2014},\r\n  volume = {42},\r\n  pages = {8861--8872},\r\n  abstract = {Genomic DNA is bound by many proteins that could\r\npotentially impede elongation of RNA polymerase\r\n(RNAP), but the factors determining the magnitude of\r\ntranscriptional roadblocking in vivo are poorly understood.\r\nThrough systematic experiments and modeling,\r\nwe analyse how roadblocking by the lac repressor\r\n(LacI) in Escherichia coli cells is controlled by\r\npromoter firing rate, the concentration and affinity\r\nof the roadblocker protein, the transcription-coupled\r\nrepair protein Mfd, and promoter–roadblock spacing.\r\nIncreased readthrough of the roadblock at higher\r\nRNAP fluxes requires active dislodgement of LacI\r\nby multiple RNAPs. However, this RNAP cooperation\r\neffect occurs only for strong promoters because\r\nroadblock-paused RNAP is quickly terminated by\r\nMfd. The results are most consistent with a single\r\nRNAP also sometimes dislodging LacI, though we\r\ncannot exclude the possibility that a single RNAP\r\nreads through by waiting for spontaneous LacI dissociation.\r\nReducing the occupancy of the roadblock\r\nsite by increasing the LacI off-rate (weakening the\r\noperator) increased dislodgement strongly, giving a\r\nstronger effect on readthrough than decreasing the\r\nLacI on-rate (decreasing LacI concentration). Thus,\r\nprotein binding kinetics can be tuned to maintain site\r\noccupation while reducing detrimental roadblocking.},\r\n  keywords={Bacterial genetics,Biological physics,Gene regulation,Genetic circuit engineering},\r\n  url_PDf={Hao_2014_NuclAcidsRes_Roadblocking.pdf},\r\n  doi={10.1093/nar/gku627}\r\n}\r\n
\n
\n\n\n
\n Genomic DNA is bound by many proteins that could potentially impede elongation of RNA polymerase (RNAP), but the factors determining the magnitude of transcriptional roadblocking in vivo are poorly understood. Through systematic experiments and modeling, we analyse how roadblocking by the lac repressor (LacI) in Escherichia coli cells is controlled by promoter firing rate, the concentration and affinity of the roadblocker protein, the transcription-coupled repair protein Mfd, and promoter–roadblock spacing. Increased readthrough of the roadblock at higher RNAP fluxes requires active dislodgement of LacI by multiple RNAPs. However, this RNAP cooperation effect occurs only for strong promoters because roadblock-paused RNAP is quickly terminated by Mfd. The results are most consistent with a single RNAP also sometimes dislodging LacI, though we cannot exclude the possibility that a single RNAP reads through by waiting for spontaneous LacI dissociation. Reducing the occupancy of the roadblock site by increasing the LacI off-rate (weakening the operator) increased dislodgement strongly, giving a stronger effect on readthrough than decreasing the LacI on-rate (decreasing LacI concentration). Thus, protein binding kinetics can be tuned to maintain site occupation while reducing detrimental roadblocking.\n
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\n  \n 2013\n \n \n (5)\n \n \n
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\n \n\n \n \n \n \n \n Combining theory and experiments to understand sugar regulation in bacteria,.\n \n \n \n\n\n \n Semsey, S.; and Krishna, S.\n\n\n \n\n\n\n Curr. Chem. Biol., 7: 224–233.. 2013.\n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
\n 
@article{shahidreview,\r\n  title = {Combining theory and experiments to understand sugar regulation in bacteria,},\r\n  author = {Szabolcs Semsey and Sandeep Krishna},\r\n  journal = {Curr. Chem. Biol.},\r\n  year = {2013},\r\n  volume = {7},\r\n  pages = {224--233.}\r\n}\r\n\r\n
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\n \n\n \n \n \n \n \n Comparative Network Analysis of Preterm vs. Full-Term Infant-Mother Interactions,.\n \n \n \n\n\n \n Sipos, L.; Pers, B. M.; Kalmar, M.; Toth, I.; Krishna, S.; Jensen, M. H; and Semsey, S.\n\n\n \n\n\n\n PLoS ONE, 8: e67183.. 2013.\n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
\n 
@article{mombaby,\r\n  title = {Comparative Network Analysis of Preterm vs. Full-Term Infant-Mother Interactions,},\r\n  author = {Lilla Sipos and Benedicte Mengel Pers and Magda Kalmar and Ildiko Toth and Sandeep Krishna and Mogens H Jensen and Szabolcs Semsey},\r\n  journal = {PLoS ONE},\r\n  year = {2013},\r\n  volume = {8},\r\n  pages = {e67183.}\r\n}\r\n\r\n
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\n \n\n \n \n \n \n \n The effect of LacI autoregulation on the performance of the lactose utilization system in Escherichia coli,.\n \n \n \n\n\n \n Semsey, S.; Pedersen, L. J.; Csiszovszki, Z.; Erdossy, J.; Steger, V.; Hansen, S.; and Krishna, S.\n\n\n \n\n\n\n Nucl. Acids Res., 41: 6381–6390.. 2013.\n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
\n 
@article{lacautoreg,\r\n  title = {The effect of LacI autoregulation on the performance of the lactose utilization system in Escherichia coli,},\r\n  author = {Szabolcs Semsey and Liselotte Jauffred Pedersen and Zsolt Csiszovszki and Janos Erdossy and Viktor Steger and Sabine Hansen and Sandeep Krishna},\r\n  journal = {Nucl. Acids Res.},\r\n  year = {2013},\r\n  volume = {41},\r\n  pages = {6381--6390.}\r\n}\r\n\r\n
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\n \n\n \n \n \n \n \n Genomic analysis reveals a bi-layered epistatic control of ``expensive\" genes in Escherichia coli K-12,.\n \n \n \n\n\n \n Srinivasan, R.; Chandraprakash, D.; Krishnamurthi, R.; Singh, P.; Scolari, V.; Krishna, S.; and Seshasayee, A.\n\n\n \n\n\n\n Mol. Biosyst., 9: 2021–2033.. 2013.\n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
\n 
@article{expensivegenes,\r\n  title = {Genomic analysis reveals a bi-layered epistatic control of ``expensive" genes in Escherichia coli K-12,},\r\n  author = {Rajalakshmi Srinivasan and Deepti Chandraprakash and Revathy Krishnamurthi and Parul Singh and Vittore Scolari and Sandeep Krishna and Aswin Seshasayee},\r\n  journal = {Mol. Biosyst.},\r\n  year = {2013},\r\n  volume = {9},\r\n  pages = {2021--2033.}\r\n}\r\n\r\n
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\n \n\n \n \n \n \n \n Flux-based classification of reactions reveals a functional bow-tie organization of complex metabolic networks,.\n \n \n \n\n\n \n Singh, S.; Samal, A.; Giri, V.; Krishna, S.; Raghuram, N.; and Jain, S.\n\n\n \n\n\n\n Phys. Rev. E, 87: 052708.. 2013.\n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
\n 
@article{bowtie,\r\n  title = {Flux-based classification of reactions reveals a functional bow-tie organization of complex metabolic networks,},\r\n  author = {Shalini Singh and Areejit Samal and Varun Giri and Sandeep Krishna and Nandula Raghuram and Sanjay Jain},\r\n  journal = {Phys. Rev. E},\r\n  year = {2013},\r\n  volume = {87},\r\n  pages = {052708.}\r\n}\r\n
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\n  \n 2012\n \n \n (6)\n \n \n
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\n \n\n \n \n \n \n \n A life on the edge: Coexistence of virulent phage and bacteria on the boundary of self-organized refuges,.\n \n \n \n\n\n \n Heilmann, S.; Sneppen, K.; and Krishna, S.\n\n\n \n\n\n\n Proc. Natl. Acad. Sci. (USA), 109: 12828–12833.. 2012.\n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
\n 
@article{edge,\r\n  title = {A life on the edge: Coexistence of virulent phage and bacteria on the boundary of self-organized refuges,},\r\n  author = {Silja Heilmann and Kim Sneppen and Sandeep Krishna},\r\n  journal = {Proc. Natl. Acad. Sci. (USA)},\r\n  year = {2012},\r\n  volume = {109},\r\n  pages = {12828--12833.}\r\n}\r\n\r\n
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\n \n\n \n \n \n \n \n Inducing phase-locking and chaos in cellular oscillators by modulating the driving stimuli,.\n \n \n \n\n\n \n Jensen, M. H; and Krishna, S.\n\n\n \n\n\n\n FEBS Lett., 586: 1664–1668.. 2012.\n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
\n 
@article{arnold,\r\n  title = {Inducing phase-locking and chaos in cellular oscillators by modulating the driving stimuli,},\r\n  author = {Mogens H Jensen and Sandeep Krishna},\r\n  journal = {FEBS Lett.},\r\n  year = {2012},\r\n  volume = {586},\r\n  pages = {1664--1668.}\r\n}\r\n\r\n
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\n \n\n \n \n \n \n \n Context-dependent conservation of DNA methyltransferases in bacteria,.\n \n \n \n\n\n \n Seshasayee, A. S. N.; Singh, P.; and Krishna, S.\n\n\n \n\n\n\n Nucl. Acids. Res., 40: 7066–7073.. 2012.\n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
\n 
@article{restrictionmodification,\r\n  title = {Context-dependent conservation of DNA methyltransferases in bacteria,},\r\n  author = {Aswin Sai Narain Seshasayee and Parul Singh and Sandeep Krishna},\r\n  journal = {Nucl. Acids. Res.},\r\n  year = {2012},\r\n  volume = {40},\r\n  pages = {7066--7073.}\r\n}\r\n\r\n
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\n \n\n \n \n \n \n \n Limit cycle oscillations and stable patterns in repressor lattices,.\n \n \n \n\n\n \n Chakraborty, S.; Jensen, M. H; Krishna, S.; Mengel, B.; Pigolotti, S.; Sekara, V.; and Semsey, S.\n\n\n \n\n\n\n Phys. Rev. E, 86: 031905.. 2012.\n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
\n 
@article{latticePRE,\r\n  title = {Limit cycle oscillations and stable patterns in repressor lattices,},\r\n  author = {Sagar Chakraborty and Mogen H Jensen and Sandeep Krishna and Benedicte Mengel and Simone Pigolotti and Vedran Sekara and Szabolcs Semsey},\r\n  journal = {Phys. Rev. E},\r\n  year = {2012},\r\n  volume = {86},\r\n  pages = {031905.}\r\n}\r\n\r\n
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\n \n\n \n \n \n \n \n Effects of growth and mutation on pattern formation in tissues,.\n \n \n \n\n\n \n Mengel, B.; Krishna, S.; Chakraborty, S.; Pigolotti, S.; Sekara, V.; Semsey, S.; and Jensen, M. H\n\n\n \n\n\n\n PLoS ONE, 7: e48772. 2012.\n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
\n 
@article{latticetissues,\r\n  title = {Effects of growth and mutation on pattern formation in tissues,},\r\n  author = {Benedicte Mengel and Sandeep Krishna and Sagar Chakraborty and Simone Pigolotti and Vedran Sekara and Szabolcs Semsey and Mogens H Jensen},\r\n  journal = {PLoS ONE},\r\n  year = {2012},\r\n  volume = {7},\r\n  pages = {e48772}\r\n}\r\n\r\n
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\n \n\n \n \n \n \n \n Switching between oscillations and homeostasis in competing negative and positive feedback motifs,.\n \n \n \n\n\n \n Li, W.; Krishna, S.; Pigolotti, S.; Mitarai, N.; and Jensen, M.\n\n\n \n\n\n\n J. Theor. Biol., 307: 205–210.. 2012.\n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
\n 
@article{oscandfixedpoint,\r\n  title = {Switching between oscillations and homeostasis in competing negative and positive feedback motifs,},\r\n  author = {Weihan Li and Sandeep  Krishna and Simone Pigolotti and Namiko Mitarai and Mogens Jensen},\r\n  journal = {J. Theor. Biol.},\r\n  year = {2012},\r\n  volume = {307},\r\n  pages = {205--210.}\r\n}\r\n\r\n
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\n  \n 2011\n \n \n (7)\n \n \n
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\n \n\n \n \n \n \n \n Symbolic dynamics in genetic oscillation patterns,.\n \n \n \n\n\n \n Pigolotti, S.; Krishna, S.; and Jensen, M. H.\n\n\n \n\n\n\n In Dubbeldam, J.; Green, K.; and Lenstra, D., editor(s), The complexity of dynamical systems: A multi-disciplinary perspective, pages 99–116.. Wiley-VCH, 2011.\n \n\n\n\n
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@incollection{book6,\r\n  title = {Symbolic dynamics in genetic oscillation patterns,},\r\n  author = {S. Pigolotti and S. Krishna and M. H. Jensen},\r\n  editor = {J. Dubbeldam and K. Green and D. Lenstra},\r\n  booktitle = {The complexity of dynamical systems: A multi-disciplinary perspective},\r\n  publisher = {Wiley-VCH},\r\n  year = {2011},\r\n  pages = {99--116.}\r\n}\r\n
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\n \n\n \n \n \n \n \n Nested feedback loops in gene regulation,.\n \n \n \n\n\n \n Mengel, B.; Krishna, S.; Jensen, M. H; and Trusina, A.\n\n\n \n\n\n\n Physica A, 391: 100–106.. 2011.\n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
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@article{nfkbnested,\r\n  title = {Nested feedback loops in gene regulation,},\r\n  author = {Benedicte Mengel and Sandeep Krishna and Mogens H Jensen and Ala Trusina},\r\n  journal = {Physica A},\r\n  year = {2011},\r\n  volume = {391},\r\n  pages = {100--106.}\r\n}\r\n\r\n
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\n \n\n \n \n \n \n \n Structure and function of the D-galactose network in enterobacteria,.\n \n \n \n\n\n \n Csiszovszki, Z.; Krishna, S; Orosz, L; Adhya, S; and Semsey, S\n\n\n \n\n\n\n mBio, 2: e00053-11.. 2011.\n \n\n\n\n
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@article{ypestis,\r\n  title = {Structure and function of the D-galactose network in enterobacteria,},\r\n  author = {Zsolt Csiszovszki and S Krishna and L Orosz and S Adhya and S Semsey},\r\n  journal = {mBio},\r\n  year = {2011},\r\n  volume = {2},\r\n  pages = {e00053-11.}\r\n}\r\n\r\n
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\n \n\n \n \n \n \n \n Direct and indirect effects in the regulation of overlapping promoters,.\n \n \n \n\n\n \n Bendtsen, K. M.; Erdossy, J.; Csiszovszki, Z.; Svenningsen, S. L.; Sneppen, K.; Krishna, S.; and Semsey, S.\n\n\n \n\n\n\n Nucl. Acids Res., 39: 6879–6885.. 2011.\n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
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@article{overlappingpromoters,\r\n  title = {Direct and indirect effects in the regulation of overlapping promoters,},\r\n  author = {Kristian Moss Bendtsen and Janos Erdossy and Zsolt Csiszovszki and Sine Lo Svenningsen and Kim Sneppen and Sandeep Krishna and Szabolcs Semsey},\r\n  journal = {Nucl. Acids Res.},\r\n  year = {2011},\r\n  volume = {39},\r\n  pages = {6879--6885.}\r\n}\r\n\r\n
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\n \n\n \n \n \n \n \n Dickkopf1 - A New Player in Modelling the Wnt Pathway,.\n \n \n \n\n\n \n Pedersen, L.; Jensen, M. H.; and Krishna, S.\n\n\n \n\n\n\n PLoS ONE, 6: e25550.. 2011.\n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
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@article{dkk1,\r\n  title = {Dickkopf1 - A New Player in Modelling the Wnt Pathway,},\r\n  author = {Lykke Pedersen and Mogens Høgh Jensen and Sandeep Krishna},\r\n  journal = {PLoS ONE},\r\n  year = {2011},\r\n  volume = {6},\r\n  pages = {e25550.}\r\n}\r\n\r\n
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\n \n\n \n \n \n \n \n Modeling the NF-kB mediated inflammatory response predicts cytokine waves in tissue,.\n \n \n \n\n\n \n Yde, P.; Mengel, B.; Jensen, M. H; Krishna, S.; and Trusina, A.\n\n\n \n\n\n\n BMC Sys. Biol., 5: 115.. 2011.\n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
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@article{nfkbwaves,\r\n  title = {Modeling the NF-kB mediated inflammatory response predicts cytokine waves in tissue,},\r\n  author = {Pernille Yde and Benedicte Mengel and Mogens H Jensen and Sandeep Krishna and Ala Trusina},\r\n  journal = {BMC Sys. Biol.},\r\n  year = {2011},\r\n  volume = {5},\r\n  pages = {115.}\r\n}\r\n\r\n
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\n \n\n \n \n \n \n \n Can we recognize an innovation? Perspective from an evolving network model,.\n \n \n \n\n\n \n Jain, S.; and Krishna, S.\n\n\n \n\n\n\n In Meyer-Ortmanns, H.; and Thurner, S., editor(s), Principles of Evolution: From the Planck Epoch to Complex Multicellular Life, pages 145–172.. Springer, Berlin, 2011.\n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
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@incollection{bookinnovation,\r\n  title = {Can we recognize an innovation? Perspective from an evolving network model,}, \r\n  author = {S. Jain and S. Krishna},\r\n  editor = {Hildegard Meyer-Ortmanns and Stefan Thurner},\r\n  booktitle = {Principles of Evolution: From the Planck Epoch to Complex Multicellular Life},\r\n  publisher = {Springer, Berlin},\r\n  year = {2011},\r\n  pages = {145--172.}\r\n}\r\n
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\n  \n 2010\n \n \n (10)\n \n \n
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\n \n\n \n \n \n \n \n Stress-specific response of the p53-Mdm2 feedback loop,.\n \n \n \n\n\n \n Hunziker, A.; Jensen, M. H.; and Krishna, S.\n\n\n \n\n\n\n BMC Syst. Biol., 4: 94.. 2010.\n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
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@article{p53paper,\r\n  title = {Stress-specific response of the p53-Mdm2 feedback loop,},\r\n  author = {A. Hunziker and M. H. Jensen and S. Krishna},\r\n  journal = {BMC Syst. Biol.},\r\n  year = {2010},\r\n  volume = {4},\r\n  pages = {94.}\r\n}\r\n
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\n \n\n \n \n \n \n \n A Wnt Oscillator Model for Somitogenesis,.\n \n \n \n\n\n \n Jensen, P. B.; Pedersen, L.; Krishna, S.; and Jensen, M. H.\n\n\n \n\n\n\n Biophys. J., 98: 943–950.. 2010.\n \n\n\n\n
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@article{pub33,\r\n  title = {A Wnt Oscillator Model for Somitogenesis,},\r\n  author = {P. B. Jensen and L. Pedersen and S. Krishna and M. H. Jensen},\r\n  journal = {Biophys. J.},\r\n  year = {2010},\r\n  volume = {98},\r\n  pages = {943--950.}\r\n}\r\n\r\n
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\n \n\n \n \n \n \n \n Simplified models of biological networks,.\n \n \n \n\n\n \n Sneppen, K.; Krishna, S.; and Semsey, S.\n\n\n \n\n\n\n Annu. Rev. Biophys., 39: 43–59.. 2010.\n \n\n\n\n
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@article{pub40,\r\n  title = {Simplified models of biological networks,},\r\n  author = {K. Sneppen and S. Krishna and S. Semsey},\r\n  journal = {Annu. Rev. Biophys.},\r\n  year = {2010},\r\n  volume = {39},\r\n  pages = {43--59.}\r\n}\r\n
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\n \n\n \n \n \n \n \n Sustainability of Virulence in a Phage-Bacterial Ecosystem,.\n \n \n \n\n\n \n Heilmann, S.; Sneppen, K.; and Krishna, S.\n\n\n \n\n\n\n J. Virol., 84: 3016–3022.. 2010.\n \n\n\n\n
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@article{coex,\r\n  title = {Sustainability of Virulence in a Phage-Bacterial Ecosystem,},\r\n  author = {S. Heilmann and K. Sneppen and S. Krishna},\r\n  journal = {J. Virol.},\r\n  year = {2010},\r\n  volume = {84},\r\n  pages = {3016--3022.}\r\n}\r\n
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\n \n\n \n \n \n \n \n Genetic flexibility of regulatory networks,.\n \n \n \n\n\n \n Hunziker, A.; Tuboly, C.; Horvath, P.; Krishna, S.; and Semsey, S.\n\n\n \n\n\n\n Proc. Natl. Acad. Sci. (USA), 107: 12998-13003.. 2010.\n \n\n\n\n
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@article{logicgates,\r\n  title = {Genetic flexibility of regulatory networks,},\r\n  author = {Alexander Hunziker and Csaba Tuboly and Peter Horvath and Sandeep Krishna and Szabolcs Semsey},\r\n  journal = {Proc. Natl. Acad. Sci. (USA)},\r\n  year = {2010},\r\n  volume = {107},\r\n  pages = {12998-13003.}\r\n}\r\n\r\n
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\n \n\n \n \n \n \n \n Stop-and-go kinetics in amyloid fibrillation,.\n \n \n \n\n\n \n Ferkhgingoff-Borg, J.; Fonslet, J.; Andersen, C. B.; Krishna, S.; Pigolotti, S.; Yogi, H.; Goto, Y.; Otzen, D.; and Jensen, M. H.\n\n\n \n\n\n\n Phys. Rev. E, 82: 010901(R).. 2010.\n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
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@article{fibril,\r\n  title = {Stop-and-go kinetics in amyloid fibrillation,},\r\n  author = {Jesper Ferkhgingoff-Borg and Jesper Fonslet and Christian B. Andersen and Sandeep Krishna and Simone Pigolotti and Hisashi Yogi and Yuji Goto and Daniel Otzen and Mogens H. Jensen},\r\n  journal = {Phys. Rev. E},\r\n  year = {2010},\r\n  volume = {82},\r\n  pages = {010901(R).}\r\n}\r\n\r\n
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\n \n\n \n \n \n \n \n Timing of Gene Transcription in the Galactose Utilization System of Escherichia coli,.\n \n \n \n\n\n \n Horvath, P.; Hunziker, A.; Erdossy, J.; Krishna, S.; and Semsey, S.\n\n\n \n\n\n\n J. Biol. Chem., 285: 38062-38068.. 2010.\n \n\n\n\n
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@article{galtiming,\r\n  title = {Timing of Gene Transcription in the Galactose Utilization System of Escherichia coli,},\r\n  author = {Peter Horvath and Alexander Hunziker and Janos Erdossy and Sandeep Krishna and Szabolcs Semsey},\r\n  journal = {J. Biol. Chem.},\r\n  year = {2010},\r\n  volume = {285},\r\n  pages = {38062-38068.}\r\n}\r\n\r\n
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\n \n\n \n \n \n \n \n Economy of Operon Formation: Cotranscription Minimizes Shortfall in Protein Complexes,.\n \n \n \n\n\n \n Sneppen, K.; Pedersen, S.; Krishna, S.; Dodd, I. B.; and Semsey, S.\n\n\n \n\n\n\n mBio, 1: e00177-10.. 2010.\n \n\n\n\n
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@article{operon,\r\n  title = {Economy of Operon Formation: Cotranscription Minimizes Shortfall in Protein Complexes,},\r\n  author = {Kim Sneppen and Steen Pedersen and Sandeep Krishna and Ian B. Dodd and Szabolcs Semsey},\r\n  journal = {mBio},\r\n  year = {2010},\r\n  volume = {1},\r\n  pages = {e00177-10.}\r\n}\r\n\r\n
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\n \n\n \n \n \n \n \n Modelling oscillatory control in NF-kB, p53 and Wnt signalling,.\n \n \n \n\n\n \n Mengel, B.; Hunziker, A.; Pedersen, L.; Trusina, A.; Jensen, M. H.; and Krishna, S.\n\n\n \n\n\n\n Curr. Opin. Gen. Devel., 20: 656–664.. 2010.\n \n\n\n\n
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@article{oscreview10,\r\n  title = {Modelling oscillatory control in NF-kB, p53 and Wnt signalling,},\r\n  author = {Benedicte Mengel and Alexander Hunziker and Lykke Pedersen and Ala Trusina and Mogens H. Jensen and Sandeep Krishna},\r\n  journal = {Curr. Opin. Gen. Devel.},\r\n  year = {2010},\r\n  volume = {20},\r\n  pages = {656--664.}\r\n}\r\n\r\n
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\n \n\n \n \n \n \n \n Minimal Gene Regulatory Circuits for a Lysis-Lysogeny Choice in the Presence of Noise,.\n \n \n \n\n\n \n Avlund, M.; Krishna, S.; Semsey, S.; Dodd, I. B.; and Sneppen, K.\n\n\n \n\n\n\n PLoS ONE, 5: e15037.. 2010.\n \n\n\n\n
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@article{lambdanoise,\r\n  title = {Minimal Gene Regulatory Circuits for a Lysis-Lysogeny Choice in the Presence of Noise,},\r\n  author = {Mikkel Avlund and Sandeep Krishna and Szabolcs Semsey and Ian B. Dodd and Kim Sneppen},\r\n  journal = {PLoS ONE},\r\n  year = {2010},\r\n  volume = {5},\r\n  pages = {e15037.}\r\n}\r\n\r\n
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\n  \n 2009\n \n \n (13)\n \n \n
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\n \n\n \n \n \n \n \n Signalling and feedback in biological networks,.\n \n \n \n\n\n \n Krishna, S.; Jensen, M. H.; and Sneppen, K.\n\n\n \n\n\n\n In Ganguly, N.; Deutsch, A.; and Mukherjee, A., editor(s), Dynamics on and of Complex Networks: Applications to Biology, Computer Science, Economics, and the Social Sciences, pages 73–93.. Birkhauser, Springer, Boston, 2009.\n \n\n\n\n
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@incollection{pub23,\r\n  title = {Signalling and feedback in biological networks,},\r\n  author = {S. Krishna and M. H. Jensen and K. Sneppen},\r\n  editor = {N. Ganguly and A. Deutsch and A. Mukherjee},\r\n  booktitle = {Dynamics on and of Complex Networks: Applications to Biology, Computer Science, Economics, and the Social Sciences},\r\n  publisher = {Birkhauser, Springer, Boston},\r\n  year = {2009},\r\n  pages = {73--93.}\r\n}\r\n
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\n \n\n \n \n \n \n \n Dynamics of uptake and metabolism of small molecules in cellular response systems,.\n \n \n \n\n\n \n Werner, M.; Krishna, S.; Semsey, S.; and Sneppen, K.\n\n\n \n\n\n\n PLoS ONE, 4: e4923.. 2009.\n \n\n\n\n
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@article{pub25,\r\n  title = {Dynamics of \r\nuptake and metabolism of small molecules in cellular response systems,},\r\n  author = {M. Werner and S. Krishna and S. Semsey and K. Sneppen},\r\n  journal = {PLoS ONE},\r\n  year = {2009},\r\n  volume = {4},\r\n  pages = {e4923.}\r\n}\r\n
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\n \n\n \n \n \n \n \n Symbolic dynamics of biological feedback networks,.\n \n \n \n\n\n \n Pigolotti, S.; Krishna, S.; and Jensen, M. H.\n\n\n \n\n\n\n Phys. Rev. Lett., 102: 088701.. 2009.\n \n\n\n\n
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@article{pub26,\r\n  title = {Symbolic dynamics of biological feedback networks,},\r\n  author = {S. Pigolotti and S. Krishna and M. H. Jensen},\r\n  journal = {Phys. Rev. Lett.},\r\n  year = {2009},\r\n  volume = {102},\r\n  pages = {088701.}\r\n}\r\n\r\n
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\n \n\n \n \n \n \n \n Why do phage play dice?.\n \n \n \n\n\n \n Avlund, M.; Dodd, I.; Semsey, S.; Sneppen, K.; and Krishna, S.\n\n\n \n\n\n\n J. Virol., 83: 11416–11420.. 2009.\n \n\n\n\n
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@article{pub28,\r\n  title = {Why do phage play dice?},\r\n  author = {M. Avlund and I. Dodd and S. Semsey and K. Sneppen and S. Krishna},\r\n  journal = {J. Virol.},\r\n  year = {2009},\r\n  volume = {83},\r\n  pages = {11416--11420.}\r\n}\r\n
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\n \n\n \n \n \n \n \n Toolbox model for the evolution of metabolism and its regulation,.\n \n \n \n\n\n \n Maslov, S.; Krishna, S.; Pang, T. Y.; and Sneppen, K.\n\n\n \n\n\n\n Proc. Natl. Acad. Sci. (USA), 106: 9743–9748.. 2009.\n \n\n\n\n
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@article{pub29,\r\n  title = {Toolbox model for the evolution of metabolism and its regulation,},\r\n  author = {S. Maslov and S. Krishna and T. Y. Pang and K. Sneppen},\r\n  journal = {Proc. Natl. Acad. Sci. (USA)},\r\n  year = {2009},\r\n  volume = {106},\r\n  pages = {9743--9748.}\r\n}\r\n
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\n \n\n \n \n \n \n \n Frustrated bistability as a means for engineering spiky genetic oscillations,.\n \n \n \n\n\n \n Krishna, S.; Semsey, S.; and Jensen, M. H.\n\n\n \n\n\n\n Phys. Biol., 6: 036009.. 2009.\n \n\n\n\n
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@article{pub30,\r\n  title = {Frustrated bistability as a means for engineering spiky genetic oscillations,},\r\n  author = {S. Krishna and S. Semsey and M. H. Jensen},\r\n  journal = {Phys. Biol.},\r\n  year = {2009},\r\n  volume = {6},\r\n  pages = {036009.}\r\n}\r\n\r\n
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\n \n\n \n \n \n \n \n Minimal gene regulatory circuits that can count like bacteriophage lambda,.\n \n \n \n\n\n \n Avlund, M.; Dodd, I.; Sneppen, K.; and Krishna, S.\n\n\n \n\n\n\n J. Mol. Biol., 394: 681–693.. 2009.\n \n\n\n\n
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@article{pub34,\r\n  title = {Minimal gene regulatory circuits that can count like bacteriophage\r\nlambda,},\r\n  author = {M. Avlund and I. Dodd and K. Sneppen and S. Krishna},\r\n  journal = {J. Mol. Biol.},\r\n  year = {2009},\r\n  volume = {394},\r\n  pages = {681--693.}\r\n}\r\n\r\n
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\n \n\n \n \n \n \n \n Dynamic features of gene expression control by small regulatory RNAs,.\n \n \n \n\n\n \n Mitarai, N.; Benjamin, J. M.; Krishna, S.; Semsey, S.; Csiszovszki, Z.; Masse, E.; and Sneppen, K.\n\n\n \n\n\n\n Proc. Natl. Acad. Sci. (USA), 106: 10655–10659.. 2009.\n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
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@article{pub35,\r\n  title = {Dynamic features of gene expression control by small regulatory RNAs,},\r\n  author = {N. Mitarai and J.-A. M. Benjamin and S. Krishna and S. Semsey and Z. Csiszovszki and E. Masse and K. Sneppen},\r\n  journal = {Proc. Natl. Acad. Sci. (USA)},\r\n  year = {2009},\r\n  volume = {106},\r\n  pages = {10655--10659.}\r\n}\r\n
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\n \n\n \n \n \n \n \n Relation of Intracellular Signal Levels and Promoter Activities in the gal Regulon of Escherichia coli,.\n \n \n \n\n\n \n Krishna, S.; Orosz, L.; Sneppen, K.; Adhya, S.; and Semsey, S.\n\n\n \n\n\n\n J. Mol. Biol., 391: 671–678.. 2009.\n \n\n\n\n
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@article{pub36,\r\n  title = {Relation of Intracellular Signal Levels and Promoter Activities in the gal Regulon of Escherichia coli,},\r\n  author = {S. Krishna and L. Orosz and K. Sneppen and S. Adhya and S. Semsey},\r\n  journal = {J. Mol. Biol.},\r\n  year = {2009},\r\n  volume = {391},\r\n  pages = {671--678.}\r\n}\r\n
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\n \n\n \n \n \n \n \n Dynamics of the recovery from sRNA-mediated gene silencing,.\n \n \n \n\n\n \n Mitarai, N.; Benjamin, J. M.; Krishna, S.; Semsey, S.; Csiszovszki, Z.; Masse, E.; and Sneppen, K.\n\n\n \n\n\n\n Cell Cycle, 8: 2863–2864.. 2009.\n \n\n\n\n
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@article{pub37,\r\n  title = {Dynamics of the recovery from sRNA-mediated gene silencing,},\r\n  author = {N. Mitarai and J.-A. M. Benjamin and S. Krishna and S. Semsey and Z. Csiszovszki and E. Masse and K. Sneppen},\r\n  journal = {Cell Cycle},\r\n  year = {2009},\r\n  volume = {8},\r\n  pages = {2863--2864.}\r\n}\r\n
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\n \n\n \n \n \n \n \n Dominant Negative Autoregulation Limits Steady-State Repression Levels in Gene Networks,.\n \n \n \n\n\n \n Semsey, S.; Krishna, S.; Erdossy, J.; Horvath, P.; Orosz, L.; Sneppen, K.; and Adhya, S.\n\n\n \n\n\n\n J. Bacteriol., 191: 4487–4491.. 2009.\n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
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@article{pub38,\r\n  title = {Dominant Negative Autoregulation Limits Steady-State Repression Levels in Gene Networks,},\r\n  author = {S. Semsey and S. Krishna and J. Erdossy and P. Horvath and L. Orosz and K. Sneppen and S. Adhya},\r\n  journal = {J. Bacteriol.},\r\n  year = {2009},\r\n  volume = {191},\r\n  pages = {4487--4491.}\r\n}\r\n
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\n \n\n \n \n \n \n \n Repressor lattice: Feedback, commensurability, and dynamical frustration,.\n \n \n \n\n\n \n Jensen, M. H.; Krishna, S.; and Pigolotti, S.\n\n\n \n\n\n\n Phys. Rev. Lett., 103: 11810.. 2009.\n \n\n\n\n
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@article{pub39,\r\n  title = {Repressor lattice: Feedback,\r\ncommensurability, and dynamical frustration,},\r\n  author = {M. H. Jensen and S. Krishna and S. Pigolotti},\r\n  journal = {Phys. Rev. Lett.},\r\n  year = {2009},\r\n  volume = {103},\r\n  pages = {11810.}\r\n}\r\n
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\n \n\n \n \n \n \n \n Genetic oscillation patterns,.\n \n \n \n\n\n \n Jensen, M. H.; Pigolotti, S.; and Krishna, S.\n\n\n \n\n\n\n Eur. Phys. J. Special Topics, 178: 45–56.. 2009.\n \n\n\n\n
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@article{geilo,\r\n  title = {Genetic oscillation patterns,},\r\n  author = {M. H. Jensen and S. Pigolotti and S. Krishna},\r\n  journal = {Eur. Phys. J. Special Topics},\r\n  year = {2009},\r\n  volume = {178},\r\n  pages = {45--56.}\r\n}\r\n\r\n
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\n  \n 2008\n \n \n (2)\n \n \n
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\n \n\n \n \n \n \n \n Cost and capacity of signalling in the Escherichia coli reaction network,.\n \n \n \n\n\n \n Axelsen, J. B.; Krishna, S.; and Sneppen, K.\n\n\n \n\n\n\n J. Stat. Mech.,, P01018.. 2008.\n \n\n\n\n
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@article{pub22,\r\n  title = {Cost and capacity of signalling in the Escherichia coli reaction network,},\r\n  author = {J. B. Axelsen and S. Krishna and K. Sneppen},\r\n  journal = {J. Stat. Mech.,},\r\n  year = {2008},\r\n  volume = {P01018.},\r\n  pages = {}\r\n}\r\n
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\n \n\n \n \n \n \n \n Dynamical genetic regulation,.\n \n \n \n\n\n \n Jensen, M. H.; Krishna, S.; Sneppen, K.; and Tiana, G.\n\n\n \n\n\n\n In Skjeltorp, A.; and Belushkin, V., editor(s), Evolution from cellular to social scales, pages 61–81.. Springer, Dordrecht, 2008.\n \n\n\n\n
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@incollection{pub24,\r\n  title = {Dynamical genetic regulation,},\r\n  author = {M. H. Jensen and S. Krishna and K. Sneppen and G. Tiana},\r\n  editor = {A. Skjeltorp and V. Belushkin},\r\n  booktitle = {Evolution from cellular to social scales},\r\n  publisher = {Springer, Dordrecht},\r\n  year = {2008},\r\n  pages = {61--81.}\r\n}\r\n
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\n  \n 2007\n \n \n (8)\n \n \n
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\n \n\n \n \n \n \n \n UV induced mutagenesis in Escherichia coli: a quantitative model,.\n \n \n \n\n\n \n Krishna, S.; Maslov, S.; and Sneppen, K.\n\n\n \n\n\n\n PLoS Comput. Biol., 3: 451–462.. 2007.\n \n\n\n\n
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@article{pub14,\r\n  title = {UV induced mutagenesis in Escherichia coli: a quantitative model,},\r\n  author = {S. Krishna and S. Maslov and K. Sneppen},\r\n  journal = {PLoS Comput. Biol.},\r\n  year = {2007},\r\n  volume = {3},\r\n  pages = {451--462.}\r\n}\r\n
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\n \n\n \n \n \n \n \n Oscillation patterns in negative feedback loops,.\n \n \n \n\n\n \n Pigolotti, S.; Krishna, S.; and Jensen, M. H.\n\n\n \n\n\n\n Proc. Natl. Acad. Sci. (USA), 104: 6533–6537.. 2007.\n \n\n\n\n
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@article{pub15,\r\n  title = {Oscillation patterns in negative feedback loops,},\r\n  author = {S. Pigolotti and S. Krishna and M. H. Jensen},\r\n  journal = {Proc. Natl. Acad. Sci. (USA)},\r\n  year = {2007},\r\n  volume = {104},\r\n  pages = {6533--6537.}\r\n}\r\n
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\n \n\n \n \n \n \n \n A universal power law and proportionate change process characterize the evolution of metabolic networks,.\n \n \n \n\n\n \n Singh, S.; Samal, A.; Giri, V.; Krishna, S.; Raghuram, N.; and Jain, S.\n\n\n \n\n\n\n Eur. Phys. J. B, 57: 75–80.. 2007.\n \n\n\n\n
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@article{pub16,\r\n  title = {A universal power law and proportionate change process characterize the evolution of metabolic networks,},\r\n  author = {S. Singh and A. Samal and V. Giri and S. Krishna and N. Raghuram and S. Jain},\r\n  journal = {Eur. Phys. J. B},\r\n  year = {2007},\r\n  volume = {57},\r\n  pages = {75--80.}\r\n}\r\n
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\n \n\n \n \n \n \n \n Signal integration in the galactose network of Escherichia coli,.\n \n \n \n\n\n \n Semsey, S.; Krishna, S.; Sneppen, K.; and Adhya, S.\n\n\n \n\n\n\n Mol. Microbiol., 65: 465–476.. 2007.\n \n\n\n\n
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@article{pub17,\r\n  title = {Signal integration in the galactose network of Escherichia coli,},\r\n  author = {S. Semsey and S. Krishna and K. Sneppen and S. Adhya},\r\n  journal = {Mol. Microbiol.},\r\n  year = {2007},\r\n  volume = {65},\r\n  pages = {465--476.}\r\n}\r\n
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\n \n\n \n \n \n \n \n Pulses and chaos: dynamical response in a simple genetic oscillator,.\n \n \n \n\n\n \n Fonslet, J.; Rud-Petersen, K.; Krishna, S.; and Jensen, M. H.\n\n\n \n\n\n\n Int. J. Mod. Phys. B,, 21: 4083–4090.. 2007.\n \n\n\n\n
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@article{pub18,\r\n  title = {Pulses and chaos: dynamical response in a simple genetic oscillator,},\r\n  author = {J. Fonslet and K. Rud-Petersen and S. Krishna and M. H. Jensen},\r\n  journal = {Int. J. Mod. Phys. B,},\r\n  year = {2007},\r\n  volume = {21},\r\n  pages = {4083--4090.}\r\n}\r\n
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\n \n\n \n \n \n \n \n Efficient degradation and expression prioritization with small RNAs,.\n \n \n \n\n\n \n Mitarai, N.; Andersson, A. M. C.; Krishna, S.; Semsey, S.; and Sneppen, K.\n\n\n \n\n\n\n Phys. Biol., 4: 164–171.. 2007.\n \n\n\n\n
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@article{pub19,\r\n  title = {Efficient degradation and expression prioritization with small RNAs,},\r\n  author = {N. Mitarai and A. M. C. Andersson and S. Krishna and S. Semsey and K. Sneppen},\r\n  journal = {Phys. Biol.},\r\n  year = {2007},\r\n  volume = {4},\r\n  pages = {164--171.}\r\n}\r\n
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\n \n\n \n \n \n \n \n Combinatorics of feedback in cellular uptake and metabolism of small molecules.\n \n \n \n\n\n \n Krishna, S.; Semsey, S.; and Sneppen, K.\n\n\n \n\n\n\n Proc. Natl. Acad. Sci. (USA), 104: 20815–20819.. 2007.\n \n\n\n\n
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@article{pub20,\r\n  title = {Combinatorics of feedback in cellular uptake and metabolism of small molecules},\r\n  author = {S. Krishna and S. Semsey and K. Sneppen},\r\n  journal = {Proc. Natl. Acad. Sci. (USA)},\r\n  year = {2007},\r\n  volume = {104},\r\n  pages = {20815--20819.}\r\n}\r\n
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\n \n\n \n \n \n \n \n Oscillations and temporal signalling in cells,.\n \n \n \n\n\n \n Tiana, G.; Krishna, S.; Pigolotti, S.; Jensen, M. H.; and Sneppen, K.\n\n\n \n\n\n\n Phys. Biol., 4: R1–R17.. 2007.\n \n\n\n\n
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@article{pub21,\r\n  title = {Oscillations and temporal signalling in cells,},\r\n  author = {G. Tiana and S. Krishna and S. Pigolotti and M. H. Jensen and K. Sneppen},\r\n  journal = {Phys. Biol.},\r\n  year = {2007},\r\n  volume = {4},\r\n  pages = {R1--R17.}\r\n}\r\n
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\n  \n 2006\n \n \n (6)\n \n \n
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\n \n\n \n \n \n \n \n Minimal model of spiky oscillations in NF-kB signalling,.\n \n \n \n\n\n \n Krishna, S.; Jensen, M. H.; and Sneppen, K.\n\n\n \n\n\n\n Proc. Natl. Acad. Sci. (USA), 103: 10840–10845.. 2006.\n \n\n\n\n
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@article{pub8,\r\n  title = {Minimal model of spiky oscillations in NF-kB signalling,},\r\n  author = {S. Krishna and M. H. Jensen and K. Sneppen},\r\n  journal = {Proc. Natl. Acad. Sci. (USA)},\r\n  year = {2006},\r\n  volume = {103},\r\n  pages = {10840--10845.}\r\n}\r\n
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\n \n\n \n \n \n \n \n Low degree metabolites explain essential reactions and enhance modularity in biological networks,.\n \n \n \n\n\n \n Samal, A.; Singh, S.; Giri, V.; Krishna, S.; Raghuram, N.; and Jain, S.\n\n\n \n\n\n\n BMC Bioinformatics, 7: 118.. 2006.\n \n\n\n\n
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@article{pub9,\r\n  title = {Low degree metabolites explain essential reactions and enhance modularity in biological networks,},\r\n  author = {A. Samal and S. Singh and V. Giri and S. Krishna and N. Raghuram and S. Jain},\r\n  journal = {BMC Bioinformatics},\r\n  year = {2006},\r\n  volume = {7},\r\n  pages = {118.}\r\n}\r\n
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\n \n\n \n \n \n \n \n Structure and function of negative feedback loops at the interface of genetic and metabolic networks,.\n \n \n \n\n\n \n Krishna, S.; Andersson, A. M. C.; Semsey, S.; and Sneppen, K.\n\n\n \n\n\n\n Nucl. Acids Res., 34: 2455–2462.. 2006.\n \n\n\n\n
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@article{pub10,\r\n  title = {Structure and function of negative feedback loops at the interface of genetic and metabolic networks,},\r\n  author = {S. Krishna and A. M. C. Andersson and S. Semsey and K. Sneppen},\r\n  journal = {Nucl. Acids Res.},\r\n  year = {2006},\r\n  volume = {34},\r\n  pages = {2455--2462.}\r\n}\r\n
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\n \n\n \n \n \n \n \n Genetic regulation of fluxes: iron homeostasis of Escherichia coli,.\n \n \n \n\n\n \n Semsey, S.; Andersson, A. M. C.; Krishna, S.; Jensen, M. H.; Massé, E.; and Sneppen, K.\n\n\n \n\n\n\n Nucl. Acids Res., 34: 4960–4967.. 2006.\n \n\n\n\n
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@article{pub11,\r\n  title = {Genetic regulation of fluxes: iron homeostasis of Escherichia coli,},\r\n  author = {S. Semsey and A. M. C. Andersson and S. Krishna and M. H. Jensen and E. Mass\\'e and K. Sneppen},\r\n  journal = {Nucl. Acids Res.},\r\n  year = {2006},\r\n  volume = {34},\r\n  pages = {4960--4967.}\r\n}\r\n
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\n \n\n \n \n \n \n \n Can we recognize an innovation? Perspective from an evolving network model,.\n \n \n \n\n\n \n Jain, S.; and Krishna, S.\n\n\n \n\n\n\n In B. K. Chakrabarti, A. C.; and Chatterjee, A., editor(s), Econophysics and Sociophysics: Trends and Perspectives, pages 561–588.. Wiley-VCH, Weinheim, 2006.\n \n\n\n\n
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@incollection{pub12,\r\n  title = {Can we recognize an innovation? Perspective from an evolving network model,}, \r\n  author = {S. Jain and S. Krishna},\r\n  editor = {B. K. Chakrabarti, A. Chakraborti and A. Chatterjee},\r\n  booktitle = {Econophysics and Sociophysics: Trends and Perspectives},\r\n  publisher = {Wiley-VCH, Weinheim},\r\n  year = {2006},\r\n  pages = {561--588.}\r\n}\r\n
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\n \n\n \n \n \n \n \n Network models of phage-bacteria coevolution,.\n \n \n \n\n\n \n Rosvall, M.; Dodd, I.; Krishna, S.; and Sneppen, K.\n\n\n \n\n\n\n Phys. Rev. E, 74: 066105.. 2006.\n \n\n\n\n
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@article{pub13,\r\n  title = {Network models of phage-bacteria coevolution,},\r\n  author = {M. Rosvall and I. Dodd and S. Krishna and K. Sneppen},\r\n  journal = {Phys. Rev. E},\r\n  year = {2006},\r\n  volume = {74},\r\n  pages = {066105.}\r\n}\r\n
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\n  \n 2005\n \n \n (1)\n \n \n
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\n \n\n \n \n \n \n \n Stochastic simulations of the origins and implications of long-tailed distributions in gene expression,.\n \n \n \n\n\n \n Krishna, S.; Banerjee, B.; Ramakrishnan, T. V.; and Shivashankar, G. V.\n\n\n \n\n\n\n Proc. Natl. Acad. Sci. (USA), 102: 4771–4776.. 2005.\n \n\n\n\n
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@article{pub7,\r\n  title = {Stochastic simulations of the origins and implications of long-tailed distributions in gene expression,},\r\n  author = {S. Krishna and B. Banerjee and T. V. Ramakrishnan and G. V. Shivashankar},\r\n  journal = {Proc. Natl. Acad. Sci. (USA)},\r\n  year = {2005},\r\n  volume = {102},\r\n  pages = {4771--4776.}\r\n}\r\n
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\n \n\n \n \n \n \n \n Graph theory and the evolution of autocatalytic networks,.\n \n \n \n\n\n \n Jain, S.; and Krishna, S.\n\n\n \n\n\n\n In Bornholdt, S.; and Schuster, H. G., editor(s), Handbook of graphs and networks, pages 355–395.. Wiley-VCH, Weinheim, 2002.\n \n\n\n\n
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@incollection{pub4,\r\n  title = {Graph theory and the evolution of autocatalytic networks,},\r\n  author = {S. Jain and S. Krishna},\r\n  editor = {S. Bornholdt and H. G. Schuster},\r\n  booktitle = {Handbook of graphs and networks},\r\n  publisher = {Wiley-VCH, Weinheim},\r\n  year = {2002},\r\n  pages = {355--395.}\r\n}\r\n
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\n \n\n \n \n \n \n \n Crashes, recoveries and ``core-shifts\" in a model of evolving networks,.\n \n \n \n\n\n \n Jain, S.; and Krishna, S.\n\n\n \n\n\n\n Phys. Rev. E, 65: 026103.. 2002.\n \n\n\n\n
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@article{pub5,\r\n  title = {Crashes, recoveries and ``core-shifts" in a model of evolving networks,},\r\n  author = {S. Jain and S. Krishna},\r\n  journal = {Phys. Rev. E},\r\n  year = {2002},\r\n  volume = {65},\r\n  pages = {026103.}\r\n}\r\n
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\n \n\n \n \n \n \n \n Large extinctions in an evolutionary model: the role of innovation and keystone species,.\n \n \n \n\n\n \n Jain, S.; and Krishna, S.\n\n\n \n\n\n\n Proc. Natl. Acad. Sci. (USA), 99: 2055–2060.. 2002.\n \n\n\n\n
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@article{pub6,\r\n  title = {Large extinctions in an evolutionary model: the role of innovation and keystone species,},\r\n  author = {S. Jain and S. Krishna},\r\n  journal = {Proc. Natl. Acad. Sci. (USA)},\r\n  year = {2002},\r\n  volume = {99},\r\n  pages = {2055--2060.}\r\n}\r\n
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\n  \n 2001\n \n \n (1)\n \n \n
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\n \n\n \n \n \n \n \n A model for the emergence of cooperation, interdependence and structure in evolving networks,.\n \n \n \n\n\n \n Jain, S.; and Krishna, S.\n\n\n \n\n\n\n Proc. Natl. Acad. Sci. (USA), 98: 543–547.. 2001.\n \n\n\n\n
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@article{pub3,\r\n  title = {A model for the emergence of cooperation, interdependence and structure in evolving networks,},\r\n  author = {S. Jain and S. Krishna},\r\n  journal = {Proc. Natl. Acad. Sci. (USA)},\r\n  year = {2001},\r\n  volume = {98},\r\n  pages = {543--547.}\r\n}\r\n
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\n \n\n \n \n \n \n \n Emergence and growth of complex networks in adaptive systems,.\n \n \n \n\n\n \n Jain, S.; and Krishna, S.\n\n\n \n\n\n\n Comput. Phys. Commun., 121: 116–121.. 1999.\n \n\n\n\n
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@article{pub2,\r\n  title = {Emergence and growth of complex networks in adaptive systems,},\r\n  author = {S. Jain and S. Krishna},\r\n  journal = {Comput. Phys. Commun.},\r\n  year = {1999},\r\n  volume = {121},\r\n  pages = {116--121.}\r\n}\r\n
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\n \n\n \n \n \n \n \n Autocatalytic sets and the growth of complexity in an evolutionary model,.\n \n \n \n\n\n \n Jain, S.; and Krishna, S.\n\n\n \n\n\n\n Phys. Rev. Lett., 81: 5684–5687.. 1998.\n \n\n\n\n
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@article{pub1,\r\n  title = {Autocatalytic sets and the growth of complexity in an evolutionary model,},\r\n  author = {S. Jain and S. Krishna},\r\n  journal = {Phys. Rev. Lett.},\r\n  year = {1998},\r\n  volume = {81},\r\n  pages = {5684--5687.}\r\n}\r\n
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