Design principles of biological circuits

  • Miri Adler, Uri Alon
    Fold-Change Detection in Biological Systems
    Current Opinion in Systems Biology , (2018) [PDF]
  • 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

  • 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]
  • 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]
  • Anat Bren; Yuval Hart; Erez Dekel; Daniel Koster; Uri Alon
    The Last Generation of Bacterial Growth in Limiting Nutrient
    Bmc Systems Biology , 7:000007820 (2013) [PDF]
  • Yuval Hart; Avraham E. Mayo; Oren Shoval; Uri Alon
    Comparing Apples and Oranges: Fold-Change Detection of Multiple Simultaneous Inputs
    PLoS ONE , 8:000018118 (2013) [PDF]
  • Hart Y, Alon U
    The Utility of Paradoxical Components in Biological Circuits
    Molecular Cell , (2013) [PDF]
  • Leeat Keren; Ora Zackay; Maya Lotan-Pompan; Uri Barenholz; Erez Dekel; Vered Sasson; Guy Aidelberg; Anat Bren; Danny Zeevi; Adina Weinberger; Uri Alon; Ron Milo; Eran Segal
    Promoters Maintain their Relative Activity Levels Under Different Growth Conditions
    Molecular Systems Biology , 9:000021320 (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

  • Vered Sasson; Irit Shachrai; Anat Bren; Erez Dekel; Uri Alon
    Mode of Regulation and the Insulation of Bacterial Gene Expression
    Molecular Cell , 46:000033772 (2012) [PDF] [SOM]
  • Olin K. Silander; Nela Nikolic; Alon Zaslaver; Anat Bren; Ilya Kikoin; Uri Alon; Martin Ackermann
    A Genome-Wide Analysis of Promoter-Mediated Phenotypic Noise in Escherichia Coli
    Plos Genetics , 8:000036466 (2012)
  • Yuval Hart; Yaron E. Antebi; Avraham E. Mayo; Nir Friedman; Uri Alon
    Design Principles of Cell Circuits With Paradoxical Components
    Proceedings of the National Academy of Sciences of the United States of America , 109:000018115 (2012) [PDF] [SOM]
  • Yuval Hart; Daniel Madar; Jie Yuan; Anat Bren; Avraham E. Mayo; Joshua D. Rabinowitz; Uri Alon
    Robust Control of Nitrogen Assimilation by a Bifunctional Enzyme in E. Coli
    Molecular Cell , 41:000018116 (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)
  • Oren Shoval; Uri Alon; Eduardo Sontag
    Symmetry Invariance For Adapting Biological Systems
    Siam Journal on Applied Dynamical Systems , 10:000036279 (2011)
  • Yuval Hart; Avraham E. Mayo; Ron Milo; Uri Alon
    Robust Control of Pep Formation Rate in the Carbon Fixation Pathway of c-4 Plants by a Bifunctional Enzyme
    Bmc Systems Biology , 5:000018117 (2011) [PDF]
  • Guy Shinar, Martin Feinberg
    Structural Sources of Robustness in Biochemical Reaction Networks
    Science , (2010) [PDF]
  • Irit Shachrai; Alon Zaslaver; Uri Alon; Erez Dekel
    Cost of Unneeded Proteins in e. Coil is Reduced After Several Generations in Exponential Growth
    Molecular Cell , 38:000035032 (2010) [PDF]
  • Oren Shoval; Lea Goentoro; Yuval Hart; Avi Mayo; Eduardo Sontag; Uri Alon
    Fold-Change Detection and Scalar Symmetry of Sensory Input Fields
    Proceedings of the National Academy of Sciences of the United States of America , 107:000036280 (2010) [PDF]
  • Elad Noor; Eran Eden; Ron Milo; Uri Alon
    Central Carbon Metabolism as a Minimal Biochemical Walk Between Precursors For Biomass and Energy
    Molecular Cell , 39:000028865 (2010) [PDF]
  • Guy Shinar; Uri Alon; Martin Feinberg
    Sensitivity and Robustness in Chemical Reaction Networks
    Siam Journal on Applied Mathematics , 69:000036033 (2009) [PDF]
  • Guy Shinar; Joshua D. Rabinowitz; Uri Alon
    Robustness in Glyoxylate Bypass Regulation
    Plos Computational Biology , 5:000036041 (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]
  • Lea Goentoro; Oren Shoval; Marc W. Kirschner; Uri Alon
    The Incoherent Feedforward Loop Can Provide Fold-Change Detection in Gene Regulation
    Molecular Cell , 36:000015713 (2009) [PDF]
  • Guy Shinar; Ron Milo; Maria Rodriguez Martinez; Uri Alon
    Input-Output Robustness in Simple Bacterial Signaling Systems
    Proceedings of the National Academy of Sciences of the United States of America , 104:000036040 (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]
  • Guy Shinar; Erez Dekel; Tsvi Tlusty; Uri Alon
    Rules For Biological Regulation Based on Error Minimization
    Proceedings of the National Academy of Sciences of the United States of America , 103:000036034 (2006) [PDF]
  • Kalir S, Alon U
    Using a Quantitative Blueprint to Reprogram the Dynamics of the Flagella Gene Network
    Cell , (2004) [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]
  • N Rosenfeld; Uri Alon
    Response Delays and the Structure of Transcription Networks
    Journal of Molecular Biology , 329:000032802 (2003) [PDF]
  • Yaakov Setty; AE Mayo; MG Surette; Uri Alon
    Detailed Map of a Cis-Regulatory Input Function
    Proceedings of the National Academy of Sciences of the United States of America , 100:000034976 (2003) [PDF]
  • N Rosenfeld; MB Elowitz; Uri Alon
    Negative Autoregulation Speeds the Response Times of Transcription Networks
    Journal of Molecular Biology , 323:000032803 (2002) [PDF]
  • M Ronen; R Rosenberg; BI Shraiman; Uri Alon
    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 , 99:000032680 (2002) [PDF]

    See also JCB news:  [PDF]

  • Shiraz Kalir; J McClure; K Pabbaraju; C Southward; M Ronen; S Leibler; MG Surette; Uri Alon
    Ordering Genes in a Flagella Pathway by Analysis of Expression Kinetics From Living Bacteria
    Science , 292:000020396 (2001) [PDF]
  • Alon U, Surette MG, Barkai N, Leibler S.
    Robustness in Bacterial Chemotaxis
    Nature , (1999) [PDF]