Design principles of biological circuits

  • Adler M; Szekely P; Mayo A; Alon U
    Optimal Regulatory Circuit Topologies For Fold-Change Detection
    Cell Systems , (2017) [PDF]
    • Out of a million possible circuits, only very few show optimal fold change detection - possibly explaining why only a few circuit designs recur across biology.
    • Cell Systems preview
  • Towbin BD; Korem Y; Bren A; Doron S; Sorek R; Alon U;
    Optimality and Sub-Optimality in a Bacterial Growth Law
    Nature Communications , (2017) [PDF]

    Bacteria use a rule of thumb to optimize growth rate, which often works but sometimes fails

  • Omer Karin, Uri Alon
    Biphasic Response as a Mechanism Against Mutant Takeover in Tissue Homeostasis Circuits
    Molecular Systems Biology , (2017) [PDF]

    Biphasic control, where a signal is toxic at both high and low levels, eliminates mis-sensing mutants at the cost of decreased resilience to dynamic perturbations, with implications for different diseases.

  • Karin O; Swisa A; Glaser B; Dor Y; Alon U;
    Dynamical Compensation in Physiological Circuits
    Molecular Systems Biology , (2016) [PDF]

    Dynamical compensation provides robustness of the entire output trace robust to variation in key parameters and appears in endocrine and neuronal circuits

  • Aidelberg G, Towbin BD, Rothschild D, Dekel E, Bren A, Alon U,
    Hierarchy of Non-Glucose Sugars in Escherichia Coli
    Bmc Systems Biology , 8:133 (2014) [PDF]
  • Rothschild, D; Dekel, E; Hausser, J; Bren, A; Aidelberg, G; Szekely, P; Alon, U
    Linear Superposition and Prediction of Bacterial Promoter Activity Dynamics in Complex Conditions
    Plos Computational Biology , 10:e1003602 (2014) [PDF]
  • Yuval Hart, Shlomit Reich-Zeliger, Yaron E. Antebi, Irina Zaretsky, Avraham E. Mayo, Uri Alon, Nir Friedman
    Paradoxical Signaling by a Secreted Molecule Leads to Homeostasis of Cell Levels
    Cell , (2014) [PDF]
  • Adler, M; Mayo, A; Alon, U
    Logarithmic and Power Law Input-Output Relations in Sensory Systems With Fold-Change Detection
    Plos Computational Biology , 10:e1003781 (2014) [PDF]
  • Bren, A; Hart, Y; Dekel, E; Koster, D; Alon, U
    The Last Generation of Bacterial Growth in Limiting Nutrient
    Bmc Systems Biology , (2013) [PDF]
  • Hart, Y; Mayo, AE; Shoval, O; Alon, U
    Comparing Apples and Oranges: Fold-Change Detection of Multiple Simultaneous Inputs
    PLoS ONE , (2013) [PDF]
  • Hart Y, Alon U
    The Utility of Paradoxical Components in Biological Circuits
    Molecular Cell , (2013) [PDF]
  • Keren, L; Zackay, O; Lotan-Pompan, M; Barenholz, U; Dekel, E; Sasson, V; Aidelberg, G; Bren, A; Zeevi, D; Weinberger, A; Alon, U; Milo, R; Segal, E
    Promoters Maintain their Relative Activity Levels Under Different Growth Conditions
    Molecular Systems Biology , (2013) [PDF]
  • Madar D, Dekel E, Bren A, Zimmer A, Porat Z, Alon U,
    Promoter Activity Dynamics in the Lag Phase of Escherichia Coli
    Bmc Systems Biology , 7:136 (2013) [PDF]

    Commentary by Daniel Schultz and Roy Kishony

  • Silander, OK; Nikolic, N; Zaslaver, A; Bren, A; Kikoin, I; Alon, U; Ackermann, M
    A Genome-Wide Analysis of Promoter-Mediated Phenotypic Noise in Escherichia Coli
    Plos Genetics , (2012)
  • Hart, Y; Antebi, YE; Mayo, AE; Friedman, N; Alon, U
    Design Principles of Cell Circuits With Paradoxical Components
    Proceedings of the National Academy of Sciences of the United States of America , (2012) [PDF] [SOM]
  • Sasson, V; Shachrai, I; Bren, A; Dekel, E; Alon, U
    Mode of Regulation and the Insulation of Bacterial Gene Expression
    Molecular Cell , (2012) [PDF] [SOM]
  • Hart, Y; Madar, D; Yuan, J; Bren, A; Mayo, AE; Rabinowitz, JD; Alon, U
    Robust Control of Nitrogen Assimilation by a Bifunctional Enzyme in E. Coli
    Molecular Cell , (2011) [PDF]
  • Madar D, Hart Y, Yuan J, Bren A, Mayo AE, Rabinowitz JD, Alon U,
    Robust Control of Nitrogen Assimilation by a Bifunctional Enzyme in e. Coli
    Febs Journal , (2011)
  • Shoval, O; Alon, U; Sontag, E
    Symmetry Invariance For Adapting Biological Systems
    Siam Journal on Applied Dynamical Systems , (2011)
  • Hart, Y; Mayo, AE; Milo, R; Alon, U
    Robust Control of Pep Formation Rate in the Carbon Fixation Pathway of c-4 Plants by a Bifunctional Enzyme
    Bmc Systems Biology , 5:171 (2011) [PDF]
  • Guy Shinar, Martin Feinberg
    Structural Sources of Robustness in Biochemical Reaction Networks
    Science , (2010) [PDF]
  • Shachrai, I; Zaslaver, A; Alon, U; Dekel, E
    Cost of Unneeded Proteins in e. Coil is Reduced After Several Generations in Exponential Growth
    Molecular Cell , (2010) [PDF]
  • Shoval, O; Goentoro, L; Hart, Y; Mayo, A; Sontag, E; Alon, U
    Fold-Change Detection and Scalar Symmetry of Sensory Input Fields
    Proceedings of the National Academy of Sciences of the United States of America , (2010) [PDF]
  • Noor, E; Eden, E; Milo, R; Alon, U
    Central Carbon Metabolism as a Minimal Biochemical Walk Between Precursors For Biomass and Energy
    Molecular Cell , (2010) [PDF]
  • Shinar, G; Alon, U; Feinberg, M
    Sensitivity and Robustness in Chemical Reaction Networks
    Siam Journal on Applied Mathematics , (2009) [PDF]
  • Shinar, G; Rabinowitz, JD; Alon, U
    Robustness in Glyoxylate Bypass Regulation
    Plos Computational Biology , (2009) [PDF]
  • Zaslaver, A; Kaplan, S; Bren, A; Jinich, A; Mayo, A; Dekel, E; Alon, U; Itzkovitz, S
    Invariant Distribution of Promoter Activities in Escherichia Coli
    Plos Computational Biology , (2009) [PDF]
  • Goentoro, L; Shoval, O; Kirschner, MW; Alon, U
    The Incoherent Feedforward Loop Can Provide Fold-Change Detection in Gene Regulation
    Molecular Cell , (2009) [PDF]
  • Shinar, G; Milo, R; Martinez, MR; Alon, U
    Input-Output Robustness in Simple Bacterial Signaling Systems
    Proceedings of the National Academy of Sciences of the United States of America , (2007) [PDF]
  • Zaslaver, A; Bren, A; Ronen, M; Itzkovitz, S; Kikoin, I; Shavit, S; Liebermeister, W; Surette, MG; Alon, U
    A Comprehensive Library of Fluorescent Transcriptional Reporters For Escherichia Coli
    Nature Methods , (2006) [PDF]
  • Shinar, G; Dekel, E; Tlusty, T; Alon, U
    Rules For Biological Regulation Based on Error Minimization
    Proceedings of the National Academy of Sciences of the United States of America , (2006) [PDF]
  • Zaslaver, A; Mayo, AE; Rosenberg, R; Bashkin, P; Sberro, H; Tsalyuk, M; Surette, MG; Alon, U
    Just-in-Time Transcription Program in Metabolic Pathways
    Nature Genetics , (2004) [PDF]

    See features in:

    • Nature Reviews Genetics : [PDF]
    • Journal of Cell Biology : [PDF]
  • Kalir S, Alon U
    Using a Quantitative Blueprint to Reprogram the Dynamics of the Flagella Gene Network
    Cell , (2004) [PDF]
  • Rosenfeld, N; Alon, U
    Response Delays and the Structure of Transcription Networks
    Journal of Molecular Biology , (2003) [PDF]
  • Setty, Y; Mayo, AE; Surette, MG; Alon, U
    Detailed Map of a Cis-Regulatory Input Function
    Proceedings of the National Academy of Sciences of the United States of America , (2003) [PDF]
  • Rosenfeld, N; Elowitz, MB; Alon, U
    Negative Autoregulation Speeds the Response Times of Transcription Networks
    Journal of Molecular Biology , (2002) [PDF]
  • Ronen, M; Rosenberg, R; Shraiman, BI; Alon, U
    Assigning Numbers to the Arrows: Parameterizing a Gene Regulation Network by Using Accurate Expression Kinetics
    Proceedings of the National Academy of Sciences of the United States of America , (2002) [PDF]

    See also JCB news:  [PDF]

  • Kalir, S; McClure, J; Pabbaraju, K; Southward, C; Ronen, M; Leibler, S; Surette, MG; Alon, U
    Ordering Genes in a Flagella Pathway by Analysis of Expression Kinetics From Living Bacteria
    Science , (2001) [PDF]
  • Alon U, Surette MG, Barkai N, Leibler S.
    Robustness in Bacterial Chemotaxis
    Nature , (1999) [PDF]