all

  • Uri Alon
    Google Scholar Profile of Uri Alon
    (3000)
  • 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.

  • Yuval Hart, Avraham E Mayo, Ruth Mayo, Liron Rozenkrantz, Avichai Tendler, Uri Alon, Lior Noy
    Creative Foraging: an Experimental Paradigm For Studying Exploration and Discovery
    PLoS ONE , (2017)
  • Karin, O; Alon, U
    Biphasic Response as a Mechanism Against Mutant Takeover in Tissue Homeostasis Circuits
    Molecular Systems Biology , 13:933 (2017)
  • Hart, Y; Mayo, AE; Mayo, R; Rozenkrantz, L; Tendler, A; Alon, U; Noy, L
    Creative Foraging: an Experimental Paradigm For Studying Exploration and Discovery
    PLoS ONE , 12:e0182133 (2017)
  • Rozenkrantz, L; Mayo, AE; Ilan, T; Hart, Y; Noy, L; Alon, U
    Placebo Can Enhance Creativity
    PLoS ONE , 12:e0182466 (2017)
  • Hausser, J; Szekely, P; Bar, N; Tzimmer, A; Caldas, C; Alon, U
    Evolutionary Trade-Offs in Tumor Development
    Febs Journal , (2017)
  • Alon, U
    Evolutionary Tradeoffs and the Geometry of Phenotype Space
    Febs Journal , (2017)
  • Towbin, BD; Korem, Y; Bren, A; Doron, S; Sorek, R; Alon, U
    Optimality and Sub-Optimality in a Bacterial Growth Law
    Nature Communications , 8:14123 (2017)
  • Gaziv, G; Noy, L; Liron, Y; Alon, U
    A Reduced-Dimensionality Approach to Uncovering Dyadic Modes of Body Motion in Conversations
    PLoS ONE , 12:e0170786 (2017)
  • Adler, M; Szekely, P; Mayo, A; Alon, U
    Optimal Regulatory Circuit Topologies For Fold-Change Detection
    Cell Systems , (2017)
  • Zimmer, A; Amar-Farkash, S; Danon, T; Alon, U
    Dynamic Proteomics Reveals Bimodal Protein Dynamics of Cancer Cells in Response to Hsp90 Inhibitor
    Bmc Systems Biology , 11:33 (2017)
  • 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

  • Hart Y., Czerniak E., Karnieli-Miller O., Mayo A., Ziv A., Biegon A., Citron A., Alon U.
    Automated Video Analysis of Non-Verbal Communication in a Medical Setting
    Frontiers in Psychology , (2016) [PDF]

     Doctor patient body language associated with good placebo shows more synchrony and balanced leadership

  • Keren, L; Hausser, J; Lotan-Pompan, M; Vainberg S, I; Alisar, H; Kaminski, S; Weinberger, A; Alon, U; Milo, R; Segal, E
    Massively Parallel Interrogation of the Effects of Gene Expression Levels on Fitness
    Cell , (2016)
  • Zimmer, A; Katzir, I; Dekel, E; Mayo, AE; Alon, U
    Prediction of Multidimensional Drug Dose Responses Based on Measurements of Drug Pairs
    Proceedings of the National Academy of Sciences of the United States of America , (2016) [PDF]
  • Dahan, A; Noy, L; Hart, Y; Mayo, A; Alon, U
    Exit From Synchrony in Joint Improvised Motion
    PLoS ONE , 11:e0160747 (2016)
  • Yaroshevich, A; Bar-Yosef, O; Boaretto, E; Caracuta, V; Greenbaum, N; Porat, N; Roskin, J
    A Unique Assemblage of Engraved Plaquettes From Ein Qashish South, Jezreel Valley, Israel: Figurative and Non-Figurative Symbols of Late Pleistocene Hunters-Gatherers in the Levant
    PLoS ONE , 11:e0160687 (2016)
  • Hart, Y; Czerniak, E; Karnieli-Miller, O; Mayo, AE; Ziv, A; Biegon, A; Citron, A; Alon, U
    Automated Video Analysis of Non-Verbal Communication in a Medical Setting
    Frontiers in Psychology , 7:1130 (2016)
  • Alon, U
    Evolutionary Tradeoffs and the Geometry of Gene Expression Space
    Febs Journal , (2016)
  • Bren, A; Park, JO; Towbin, BD; Dekel, E; Rabinowitz, JD; Alon, U
    Glucose Becomes One of the Worst Carbon Sources For e-Coli on Poor Nitrogen Sources Due to Suboptimal Levels of CAMP
    Scientific Reports , 6:24834 (2016)
  • Czerniak, E; Biegon, A; Ziv, A; Karnieli-Miller, O; Weiser, M; Alon, U; Citron, A
    Manipulating the Placebo Response in Experimental Pain by Altering Doctor's Performance Style
    Frontiers in Psychology , 7:874 (2016)
  • Hart Y, Sheftel H, Hausser J, Szekely P, Ben-Moshe NB, Korem Y, Tendler A, Mayo AE, Alon U,
    Inferring Biological Tasks Using Pareto Analysis of High-Dimensional Data
    Nature Methods , (2015) [PDF]

    For accessing the package:  click here

  • Tendler, A; Mayo, A; Alon, U
    Evolutionary Tradeoffs, Pareto Optimality and the Morphology of Ammonite Shells
    Bmc Systems Biology , 9:12 (2015) [PDF]

    Editors Pick BMC Systems Biology:

    "Optimizing ammonite forms

    Across ammonite genera, trade-offs between different shape phenotypes resulted in a small range of successful forms, that could be represented by a pyramid in the diagram of possible shape parameters, with each point representing an optimized archetype.

    BMC Systems Biology 2015, 9:12"

  • Friedlander T, Mayo AE, Tlusty T, Alon U,
    Evolution of Bow-Tie Architectures in Biology
    Plos Computational Biology , 11:UNSP e1004 (2015) [PDF]
  • Korem Y, Szekely P, Hart Y, Sheftel H, Hausser J,Mayo A, Rothenberg ME, Kalisky T, Alon U
    Geometry of the Gene Expression Space of Individual Cells
    Plos Computational Biology , (2015) [PDF] [SOM]
  • Szekely, Pablo; Korem, Yael; Moran, Uri; Mayo, Avi; Alon, Uri
    The Mass-Longevity Triangle: Pareto Optimality and the Geometry of Life-History Trait Space
    Plos Computational Biology , 11:26465336 (2015) [PDF]
  • Noy L, Alon U, Friedman J
    Corrective Jitter Motion Shows Similar Individual Frequencies For the Arm and the Finger
    Experimental Brain Research , (2015) [PDF]
  • Noy L, Levit-Binun N, Golland Y,
    Being in the Zone: Physiological Markers of Togetherness in Joint Improvisation
    Frontiers in Human Neuroscience , 9:187 (2015) [PDF]
  • Feniger-Schaal, R; Noy, L; Hart, Y; Koren-Karie, N; Mayo, A E; Alon, U
    Would You Like to Play Together? Adults' Attachment and the Mirror Game
    Attachment &Amp; Human Development , (2015) [PDF]
  • Noy, L; Alon, U; Friedman, J
    Corrective Jitter Motion Shows Similar Individual Frequencies For the Arm and the Finger
    Experimental Brain Research , (2015)
  • Hart, Y; Sheftel, H; Hausser, J; Szekely, P; Ben-Moshe, NB; Korem, Y; Tendler, A; Mayo, AE; Alon, U
    Inferring Biological Tasks Using Pareto Analysis of High-Dimensional Data
    Nature Methods , (2015)
  • 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]
  • 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]
  • Farkash-Amar, S; Zimmer, A; Eden, E; Cohen, A; Geva-Zatorsky, N; Cohen, L; Milo, R; Sigal, A; Danon, T; Alon, U
    Noise Genetics: Inferring Protein Function by Correlating Phenotype With Protein Levels and Localization in Individual Human Cells
    Plos Genetics , 10:e1004176 (2014) [PDF]
  • Noy L
    The Mirror Game: a Natural Science Study of Togetherness
    In: Citron, Atay, Sharon Aronson-Lehavi, and David Zerbib, Eds. Performance Studies in Motion: International Perspectives and Practices in the Twenty-First Century , (2014) [PDF] [SOM]
  • Hart Y, Noy L, Feniger-Schaal R, Mayo AE, Alon U,
    Individuality and Togetherness in Joint Improvised Motion
    PLoS ONE , 9:e87213 (2014) [PDF]
  • Rozenkrantz, L; Noy, L; Hart, Y; Mayo, A; Alon, U
    Increasing Creativity Using the Placebo Effect
    Journal of Molecular Neuroscience , (2014)
  • Hart, Y; Reich-Zeliger, S; Antebi, YE; Zaretsky, I; Mayo, AE; Alon, U; Friedman, N
    Paradoxical Signaling by a Secreted Molecule Leads to Homeostasis of Cell Levels
    Cell , (2014)
  • Dasgupta, T; Croll, DH; Owen, JA; Vander Heiden, MG; Locasale, JW; Alon, U; Cantley, LC; Gunawardena, J
    A Fundamental Trade-Off in Covalent Switching and Its Circumvention by Enzyme Bifunctionality in Glucose Homeostasis
    Journal of Biological Chemistry , (2014)
  • Hart, Y; Noy, L; Feniger-Schaal, R; Mayo, AE; Alon, U
    Individuality and Togetherness in Joint Improvised Motion
    PLoS ONE , 9:e87213 (2014)
  • 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)
  • 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

  • Bren, A; Hart, Y; Dekel, E; Koster, D; Alon, U
    The Last Generation of Bacterial Growth in Limiting Nutrient
    Bmc Systems Biology , (2013) [PDF]
  • Sheftel, H; Shoval, O; Mayo, A; Alon, U
    The Geometry of the Pareto Front in Biological Phenotype Space
    Ecology and Evolution , (2013) [PDF]
  • Friedlander, T; Mayo, AE; Tlusty, T; Alon, U
    Mutation Rules and the Evolution of Sparseness and Modularity in Biological Systems
    PLoS ONE , (2013) [PDF]
  • Szekely, P; Sheftel, H; Mayo, A; Alon, U
    Evolutionary Tradeoffs Between Economy and Effectiveness in Biological Homeostasis Systems
    Plos Computational Biology , (2013) [PDF]
  • Kavanagh, KD; Shoval, O; Winslow, BB; Alon, U; Leary, BP; Kan, A; Tabin, CJ
    Developmental Bias in the Evolution of Phalanges
    Proceedings of the National Academy of Sciences of the United States of America , (2013) [PDF]
  • Mitarai, N; Alon, U; Jensen, MH
    Entrainment of Noise-Induced and Limit Cycle Oscillators Under Weak Noise
    Chaos , (2013)
  • Hart, Y; Alon, U
    The Utility of Paradoxical Components in Biological Circuits
    Molecular Cell , (2013)
  • Shoval, O; Sheftel, H; Shinar, G; Hart, Y; Ramote, O; Mayo, A; Dekel, E; Kavanagh, K; Alon, U
    Response to Comment on Evolutionary Trade-Offs
    Science , (2013)
  • 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]
  • 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]
  • Farkash-Amar, S; Eden, E; Cohen, A; Geva-Zatorsky, N; Cohen, L; Milo, R; Sigal, A; Danon, T; Alon, U
    Dynamic Proteomics of Human Protein Level and Localization Across the Cell Cycle
    PLoS ONE , (2012) [PDF]
  • Geva-Zatorsky, N; Issaeva, I; Mayo, A; Cohen, A; Dekel, E; Danon, T; Cohen, L; Liron, Y; Alon, U; Eden, E
    Using Bleach-Chase to Measure Protein Half-Lives in Living Cells
    Nature Protocols , (2012) [PDF]
  • Shoval, O; Sheftel, H; Shinar, G; Hart, Y; Ramote, O; Mayo, A; Dekel, E; Kavanagh, K; Alon, U
    Evolutionary Trade-Offs, Pareto Optimality, and the Geometry of Phenotype Space
    Science , (2012) [PDF] [SOM]
    • See also Science Perspective: [PDF]
  • Noy L, Hart Y, Andrew N, Ramote O, Mayo A, Alon U
    A Quantitative Study of Creative Leaps
    International Conference on Computational Creativity , (2012) [PDF]
  • Alon, U
    Design Principles of Biological Circuits
    Febs Journal , (2012)
  • Koster, DA; Mayo, A; Bren, A; Alon, U
    Surface Growth of a Motile Bacterial Population Resembles Growth in a Chemostat
    Journal of Molecular Biology , (2012) [PDF]
  • Madar, D; Dekel, E; Bren, A; Alon, U
    Negative Auto-Regulation Increases the Input Dynamic-Range of the Arabinose System of Escherichia Coli
    Bmc Systems Biology , 5:111 (2011) [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]
  • Eden, E; Geva-Zatorsky, N; Issaeva, I; Cohen, A; Dekel, E; Danon, T; Cohen, L; Mayo, A; Alon, U
    Proteome Half-Life Dynamics in Living Human Cells
    Science , (2011) [PDF] [SOM]
  • Noy, L; Dekel, E; Alon, U
    The Mirror Game as a Paradigm For Studying the Dynamics of Two People Improvising Motion Together
    PNAS , (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
    Input Symmetry Invariance, and Applications to Biological Systems
    2011 50th Ieee Conference on Decision and Control and European Control Conference (Cdc-Ecc) , (2011)
  • Moran, GS; Alon, U
    Playback theatre and Recovery in Mental Health: Preliminary Evidence
    Arts in Psychotherapy , (2011) [PDF]
  • Shoval, O; Alon, U
    Snapshot: Network Motifs
    Cell , (2010)
  • 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]
  • 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]
  • Issaeva, I; Cohen, AA; Eden, E; Cohen-Saidon, C; Danon, T; Cohen, L; Alon, U
    Generation of Double-Labeled Reporter Cell Lines For Studying co-Dynamics of Endogenous Proteins in Individual Human Cells
    PLoS ONE , 5:e13524 (2010) [PDF]
  • Geva-Zatorsky, N; Dekel, E; Cohen, AA; Danon, T; Cohen, L; Alon, U
    Protein Dynamics in Drug Combinations: a Linear Superposition of Individual-Drug Responses
    Cell , (2010) [PDF]

    BioWorld: [PDF]

  • Frenkel-Morgenstern, M; Cohen, AA; Geva-Zatorsky, N; Eden, E; Prilusky, J; Issaeva, I; Sigal, A; Cohen-Saidon, C; Liron, Y; Cohen, L; Danon, T; Perzov, N; Alon, U
    Dynamic Proteomics: a Database For Dynamics and Localizations of Endogenous Fluorescently-Tagged Proteins in Living Human Cells
    Nucleic Acids Research , (2010) [PDF]
  • Geva-Zatorsky, N; Dekel, E; Batchelor, E; Lahav, G; Alon, U
    Fourier Analysis and Systems Identification of the P53 Feedback Loop
    Proceedings of the National Academy of Sciences of the United States of America , (2010) [PDF]
  • Geva-Zatorsky, N; Cohen, AA; Eden, E; Dekel, E; Frenkel-Morgenstern, M; Issaeva, I; Danon, T; Cohen, L; Perzov, N; Milo, R; Sigal, A; Alon, U
    Dynamics Proteomics of Individual Cancer Cells in Response to Drugs
    Febs Journal , (2010)
  • Rosenheim, JA; Alon, U; Shinar, G
    Evolutionary Balancing of Fitness-Limiting Factors
    American Naturalist , (2010)
  • Alon, U
    How to Build a Motivated Research Group
    Molecular Cell , (2010) [PDF]
  • Alon, U
    Design Principles of Biological Circuits
    Febs Journal , (2010)
  • Rahat, O; Alon, U; Levy, Y; Schreiber, G
    Understanding Hydrogen-Bond Patterns in Proteins Using Network Motifs
    Bioinformatics , (2009)
  • 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; 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]
  • Cohen, AA; Kalisky, T; Mayo, A; Geva-Zatorsky, N; Danon, T; Issaeva, I; Kopito, RB; Perzov, N; Milo, R; Sigal, A; Alon, U
    Protein Dynamics in Individual Human Cells: Experiment and theory
    PLoS ONE , (2009) [PDF]
  • Cohen-Saidon, C; Cohen, AA; Sigal, A; Liron, Y; Alon, U
    Dynamics and Variability of Erk2 Response to Egf in Individual Living Cells
    Molecular Cell , (2009) [PDF]
  • Oved, K; Eden, E; Akerman, M; Noy, R; Wolchinsky, R; Izhaki, O; Schallmach, E; Kubi, A; Zabari, N; Schachter, J; Alon, U; Mandel-Gutfreund, Y; Besser, MJ; Reiter, Y
    Predicting and Controlling the Reactivity of Immune Cell Populations Against Cancer
    Molecular Systems Biology , (2009)
  • Cohen-Saidon, C; Cohen, AA; Sigal, A; Alon, U
    Dynamics of Erk2 in Individual Living Human Cells
    Febs Journal , (2009)
  • Kashtan, N; Mayo, AE; Kalisky, T; Alon, U
    An Analytically Solvable Model For Rapid Evolution of Modular Structure
    Plos Computational Biology , (2009) [PDF]
  • Kashtan, N; Parter, M; Dekel, E; Mayo, AE; Alon, U
    Extinctions in Heterogeneous Environments and the Evolution of Modularity
    Evolution , (2009) [PDF]
  • Alon, U
    How to Give a Good Talk
    Molecular Cell , (2009)
  • Alon, U
    How to Choose a Good Scientific Problem
    Molecular Cell , (2009)
  • Kaplan, S; Bren, A; Zaslaver, A; Dekel, E; Alon, U
    Diverse Two-Dimensional Input Functions Control Bacterial Sugar Genes
    Molecular Cell , (2008) [PDF]
  • Kaplan, S; Bren, A; Dekel, E; Alon, U
    The Incoherent Feed-Forward Loop Can Generate Non-Monotonic Input Functions For Genes
    Molecular Systems Biology , (2008) [PDF]
  • Cohen, AA; Geva-Zatorsky, N; Eden, E; Frenkel-Morgenstern, M; Issaeva, I; Sigal, A; Milo, R; Cohen-Saidon, C; Liron, Y; Kam, Z; Cohen, L; Danon, T; Perzov, N; Alon, U
    Dynamic Proteomics of Individual Cancer Cells in Response to a Drug
    Science , (2008) [PDF] [SOM]

    See also reviews:

    • Science: [PDF]
    • Nature: [PDF]
    • Nature Reviews Cancer: [PDF]
    • Nature Chemical Biology: [PDF]
    • Nature Biotechnology: [PDF]
    • Chemical Research in Toxicology: [PDF]
    • Journal of Proteome Research: [Link]
    • Chemical & Engineering News: [Link]
  • Oxman E., Dekel E., Alon U.
    Defined Order of Evolutionary Adaptations: Experimental Evidence.
    Evolution , (2008) [PDF]
  • Parter, M; Kashtan, N; Alon, U
    Facilitated Variation: How Evolution Learns From Past Environments to Generalize to New Environments
    Plos Computational Biology , (2008) [PDF] [SOM]
  • Uri Alon
    (Essay) a Biophysicist Learns the Art of Hugging.
    Nature , (2008) [PDF]
  • Rosenfeld, N; Young, JW; Alon, U; Swain, PS; Elowitz, MB
    Accurate Prediction of Gene Feedback Circuit Behavior From Component Properties
    Molecular Systems Biology , (2007)
  • Alon, U
    Network Motifs: theory and Experimental Approaches
    Nature Reviews Genetics , (2007) [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]
  • Sigal, A; Danon, T; Cohen, A; Milo, R; Geva-Zatorsky, N; Lustig, G; Liron, Y; Alon, U; Perzov, N
    Generation of a Fluorescently Labeled Endogenous Protein Library in Living Human Cells
    Nature Protocols , (2007) [PDF]
  • Parter, M; Kashtan, N; Alon, U
    Environmental Variability and Modularity of Bacterial Metabolic Networks
    Bmc Evolutionary Biology , (2007) [PDF]
  • Kalisky, T; Dekel, E; Alon, U
    Cost-Benefit theory and Optimal Design of Gene Regulation Functions
    Physical Biology , (2007) [PDF]
  • Itzkovitz, S; Alon, U
    The Genetic Code is Nearly Optimal For Allowing Additional Information Within Protein-Coding Sequences
    Genome Research , (2007) [PDF]
    • Genome Research: [PDF]
    • Nature Reviews Genetics: [PDF]
  • Kashtan, N; Noor, E; Alon, U
    Varying Environments Can Speed up Evolution
    Proceedings of the National Academy of Sciences of the United States of America , (2007) [PDF]
  • Alon, U
    Simplicity in Biology
    Nature , (2007) [PDF]
  • Amit, I; Citri, A; Shay, T; Lu, YL; Katz, M; Zhang, F; Tarcic, G; Siwak, D; Lahad, J; Jacob-Hirsch, J; Amariglio, N; Vaisman, N; Segal, E; Rechavi, G; Alon, U; Mills, GB; Domany, E; Yarden, Y
    A Module of Negative Feedback Regulators Defines Growth Factor Signaling
    Nature Genetics , (2007) [PDF]
  • Itzkovitz, S; Milo, R; Kashtan, N; Levitt, R; Lahav, A; Alon, U
    Recurring Harmonic Walks and Network Motifs in Western Music
    Advances in Complex Systems , (2006) [PDF]
  • Frankenstein, Z; Alon, U; Cohen, IR
    The Immune-Body Cytokine Network Defines a Social Architecture of Cell Interactions
    Biology Direct , (2006) [PDF]
  • Mangan, S; Itzkovitz, S; Zaslaver, A; Alon, U
    The Incoherent Feed-Forward Loop Accelerates the Response-Time of the Gal System of Escherichia Coli
    Journal of Molecular Biology , (2006) [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]
  • Sigal, A; Milo, R; Cohen, A; Geva-Zatorsky, N; Klein, Y; Alaluf, I; Swerdlin, N; Perzov, N; Danon, T; Liron, Y; Raveh, T; Carpenter, AE; Lahav, G; Alon, U
    Dynamic Proteomics in Individual Human Cells Uncovers Widespread Cell-Cycle Dependence of Nuclear Proteins
    Nature Methods , (2006) [PDF]
  • Rosenfeld, N; Perkins, TJ; Alon, U; Elowitz, MB; Swain, PS
    A Fluctuation Method to Quantify in Vivo Fluorescence Data
    Biophysical Journal , (2006) [PDF]
  • Geva-Zatorsky, N; Rosenfeld, N; Itzkovitz, S; Milo, R; Sigal, A; Dekel, E; Yarnitzky, T; Liron, Y; Polak, P; Lahav, G; Alon, U
    Oscillations and Variability in the P53 System
    Molecular Systems Biology , (2006) [PDF]
  • Sigal, A; Milo, R; Cohen, A; Geva-Zatorsky, N; Klein, Y; Liron, Y; Rosenfeld, N; Danon, T; Perzov, N; Alon, U
    Variability and Memory of Protein Levels in Human Cells
    Nature , (2006) [PDF]
  • Mayo, AE; Setty, Y; Shavit, S; Zaslaver, A; Alon, U
    Plasticity of the Cis-Regulatory Input Function of a Gene
    PLoS Biology , (2006) [PDF]
  • Itzkovitz, S; Tlusty, T; Alon, U
    Coding Limits on the Number of Transcription Factors
    Bmc Genomics , (2006) [PDF]
  • Zaslaver, A; Mayo, A; Ronen, M; Alon, U
    Optimal Gene Partition Into Operons Correlates With Gene Functional Order
    Physical Biology , (2006) [PDF]
  • Itzkovitz, S; Alon, U
    Subgraphs and Network Motifs in Geometric Networks
    Physical Review E , (2005) [PDF]
  • Kalir, S; Mangan, S; Alon, U
    A Coherent Feed-Forward Loop With a Sum Input Function Prolongs Flagella Expression in Escherichia Coli
    Molecular Systems Biology , (2005) [PDF]
  • Itzkovitz, S; Levitt, R; Kashtan, N; Milo, R; Itzkovitz, M; Alon, U
    Coarse-Graining and Self-Dissimilarity of Complex Networks
    Physical Review E , (2005) [PDF]
  • Dekel E, Alon U
    Optimality and Evolutionary Tuning of the Expression Level of a Protein
    Nature , (2005) [PDF]
  • Dekel, E; Alon, U
    Optimality and Evolutionary Tuning of the Expression Level of a Protein
    Nature , (2005) [PDF]
  • Kashtan, N; Alon, U
    Spontaneous Evolution of Modularity and Network Motifs
    Proceedings of the National Academy of Sciences of the United States of America , (2005) [PDF]
  • Dekel, E; Mangan, S; Alon, U
    Environmental Selection of the Feed-Forward Loop Circuit in Gene-Regulation Networks
    Physical Biology , (2005) [PDF]
  • Rosenfeld, N; Young, JW; Alon, U; Swain, PS; Elowitz, MB
    Gene Regulation at the Single-Cell Level
    Science , (2005) [PDF]
  • Friedman, N; Vardi, S; Ronen, M; Alon, U; Stavans, J
    Precise Temporal Modulation in the Response of the Sos Dna Repair Network in Individual Bacteria
    PLoS Biology , (2005)
  • Kashtan, N; Itzkovitz, S; Milo, R; Alon, U
    Topological Generalizations of Network Motifs
    Physical Review E , (2004) [PDF]
  • Milo, R; Itzkovitz, S; Kashtan, N; Levitt, R; Alon, U
    Response to Comment on &Quot;Network Motifs: Simple Building Blocks of Complex Networks&Quot; and &Quot;Superfamilies of Evolved and Designed Networks&Quot;
    Science , (2004)
  • Kashtan, N; Itzkovitz, S; Milo, R; Alon, U
    Efficient Sampling Algorithm For Estimating Subgraph Concentrations and Detecting Network Motifs
    Bioinformatics , (2004) [PDF]
  • Yeger-Lotem, E; Sattath, S; Kashtan, N; Itzkovitz, S; Milo, R; Pinter, RY; Alon, U; Margalit, H
    Network Motifs in Integrated Cellular Networks of Transcription-Regulation and Protein-Protein Interaction
    Proceedings of the National Academy of Sciences of the United States of America , (2004)
  • Itzkovitz, S; Milo, R; Kashtan, N; Newman, MEJ; Alon, U
    Reply to &Quot;Comment on 'Subgraphs in Random Networks' &Quot;
    Physical Review E , (2004)
  • Milo, R; Itzkovitz, S; Kashtan, N; Levitt, R; Shen-Orr, S; Ayzenshtat, I; Sheffer, M; Alon, U
    Superfamilies of Evolved and Designed Networks
    Science , (2004) [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]
  • Lahav, G; Rosenfeld, N; Sigal, A; Geva-Zatorsky, N; Levine, AJ; Elowitz, MB; Alon, U
    Dynamics of the P53-Mdm2 Feedback Loop in Individual Cells
    Nature Genetics , (2004) [PDF]
  • Friedman, N; Vardi, S; Ronen, M; Alon, U; Stavans, J
    Precise Modulations in the Sos Dna Repair System Observed in Individual Escherichia Coli Cells.
    Abstracts of Papers of the American Chemical Society , (2004)
  • Milo, R; Itzkovitz, S; Kashtan, N; Levitt, R; Alon, U
    Response to Comment on &Quot;Network Motifs: Simple Building Blocks of Complex Networks&Quot; and &Quot;Superfamilies of Evolved and Designed Networks&Quot;
    Science , (2004)
  • Itzkovitz S, Milo R, Kashtan N, Ziv G, Alon U.
    Subgraphs in Random Networks.
    Phys Rev e Stat Nonlin Soft Matter Phys , (2003) [PDF]
  • Mangan, S; Alon, U
    Structure and Function of the Feed-Forward Loop Network Motif
    Proceedings of the National Academy of Sciences of the United States of America , (2003) [PDF]
  • Mangan, S; Zaslaver, A; Alon, U
    The Coherent Feedforward Loop Serves as a Sign-Sensitive Delay Element in Transcription Networks
    Journal of Molecular Biology , (2003)
  • 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]
  • Itzkovitz, S; Milo, R; Kashtan, N; Ziv, G; Alon, U
    Subgraphs in Random Networks
    Physical Review E , (2003)
  • Alon, U
    Biological Networks: the Tinkerer as an Engineer
    Science , (2003) [PDF]
  • Rikanati, A; Alon, U; Shvarts, D
    Vortex-Merger Statistical-Mechanics Model For the Late Time Self-Similar Evolution of the Kelvin-Helmholtz Instability
    Physics of Fluids , (2003)
  • Milo, R; Shen-Orr, S; Itzkovitz, S; Kashtan, N; Chklovskii, D; Alon, U
    Network Motifs: Simple Building Blocks of Complex Networks
    Science , (2002) [PDF]
  • Shen-Orr, SS; Milo, R; Mangan, S; Alon, U
    Network Motifs in the Transcriptional Regulation Network of Escherichia Coli
    Nature Genetics , (2002)
  • Shen-Orr Shai S, Milo Ron, Mangan Shmoolik, Alon Uri
    Network Motifs in the Transcriptional Regulation Network of Escherichia Coli.
    Nature Genetics , (2002) [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]
  • Oron, D; Arazi, L; Kartoon, D; Rikanati, A; Alon, U; Shvarts, D
    Dimensionality Dependence of the Rayleigh-Taylor and Richtmyer-Meshkov Instability Late-Time Scaling Laws
    Physics of Plasmas , (2001)
  • Notterman DA, Alon U, Sierk AJ, Levine AJ.
    Transcriptional Gene Expression Profiles of Colorectal Adenoma, Adenocarcinoma, and Normal Tissue Examined by Oligonucleotide Arrays
    Cancer Res. , (2001)
  • Barkai N, Alon U, Leibler S
    Robust Amplification in Adaptive Signal Transduction Networks
    Comptes Rendus de l'AcadéMie Des Sciences - Series iv - Physics , (2001) [PDF]
  • Bar-Or, RL; Maya, R; Segel, LA; Alon, U; Levine, AJ; Oren, M
    Generation of Oscillations by the P53-Mdm2 Feedback Loop: a theoretical and Experimental Study
    Proceedings of the National Academy of Sciences of the United States of America , (2000)
  • Staropoli, JF; Alon, U
    Computerized Analysis of Chemotaxis at Different Stages of Bacterial Growth
    Biophysical Journal , (2000)
  • Rikanati, A.; Oron, D.; Alon, U.; Shvarts, D.
    Statistical Mechanics Merger Model For Hydrodynamic Instabilities
    The Astrophysical Journal Supplement Series , (2000)
  • Sadot O, Erez L, Oron D, Erez G, Ben-Dor G, Alon U, Levin LA, Shvarts D
    Studies on the Nonlinear Evolution of the Richtmyer-Meshkov Instability
    The Astrophysical Journal Supplement Series , (2000)
  • Alon U, Surette MG, Barkai N, Leibler S.
    Robustness in Bacterial Chemotaxis
    Nature , (1999) [PDF]
  • Alon U, Barkai N, Notterman DA, Gish K, Ybarra S, Mack D, Levine AJ.
    Broad Patterns of Gene Expression Revealed by Clustering Analysis of Tumor and Normal Colon Tissues Probed by Oligonucleotide Arrays.
    Proc Natl Acad Sci u s a , (1999) [PDF]
  • Oron D, Sadot O, Srebro Y, Rikanati A, Yedvab Y, Alon U, Erez L, Erez G, Ben-Dor G, Levin LA, Ofer D, Shvarts D
    Studies in the Nonlinear Evolution of the Rayleigh–Taylor and Richtmyer–Meshkov Instabilities and their Role in Inertial Confinement Fusion
    Laser and Particle Beams , (1999)
  • Rikanati, A.; Alon, U.; Shvarts, D.
    Vortex Model For the Nonlinear Evolution of the Multimode Richtmyer-Meshkov Instability at Low Atwood Numbers
    Phys. Rev. e , (1998)
  • Sadot D, Alon U, Shvarts D
    Scaling Laws of the Rayleigh–Taylor Ablation Front Mixing Zone Evolution in Inertial Confinement Fusion
    Physics of Plasmas , (1998)
  • Sadot O, Erez L, Alon U, Oron O, Levin LA, Erez G, Ben-Dor G, Shvarts D
    Study of Nonlinear Evolution of Single-Mode and Two-Bubble Interaction Under Richtmyer-Meshkov Instability
    Phys. Rev. Lett. , (1998)
  • Alon, U; Evans, MR; Hinrichsen, H; Mukamel, D
    Smooth Phases, Roughening Transitions, and Novel Exponents in One-Dimensional Growth Models
    Physical Review E , (1998)
  • Alon U, Camarena L, Surette M G, Aguera y Arcas B, Liu Y, Leibler S, and Stock J B
    Response Regulator Output in Bacterial Chemotaxis.
    Embo j , (1998)
  • Alon, U; Mukamel, D
    Gel Electrophoresis and Diffusion of Ring-Shaped DNA
    Physical Review E , (1997)
  • Alon, U; Evans, MR; Hinrichsen, H; Mukamel, D
    Roughening Transition in a One-Dimensional Growth Process
    Physical Review Letters , (1996)
  • Ofer, D; Alon, U; Shvarts, D; McCrory, RL; Verdon, CP
    Modal Model For the Nonlinear Multimode Rayleigh-Taylor Instability
    Physics of Plasmas , (1996)
  • Hecht J, Ofer D, Alon U, Shvarts D, Orszag SA, McCrory RL
    Three-Dimensional Simulations and Analysis of the Nonlinear Stage of the Rayleigh-Taylor Instability
    Laser and Particle Beams , (1995)
  • Shvarts D, Alon U, Ofer D, McCrory RL, Verdon CP
    Nonlinear Evolution of Multimode Rayleigh–Taylor Instability in Two and Three Dimensions
    Physics of Plasmas , (1995)
  • Alon U, Hecht J, Ofer D, Shvarts D
    Power Laws and Similarity of Rayleigh-Taylor and Richtmyer-Meshkov Mixing Fronts at All Density Ratios
    Phys. Rev. Lett. , (1995)
  • SHVARTS, D; ALON, U; OFER, D; MCCRORY, RL; VERDON, CP
    Nonlinear Evolution of Multimode Rayleigh-Taylor Instability in 2 and 3 Dimensions
    Physics of Plasmas , (1995)
  • Jacob Hecht J, Alon U, Shvarts D
    Potential Flow Models of Rayleigh–Taylor and Richtmyer–Meshkov Bubble Fronts
    Physics of Fluids , (1994)
  • Alon U, Hecht J, Mukamel D, Shvarts D
    Scale Invariant Mixing Rates of Hydrodynamically Unstable Interfaces
    Physical Review Letters , (1994)
  • ALON, U; HECHT, J; MUKAMEL, D; SHVARTS, D
    Scale-Invariant Mixing Rates of Hydrodynamically Unstable Interfaces
    Physical Review Letters , (1994)
  • HECHT, J; ALON, U; SHVARTS, D
    Potential Flow Models of Rayleigh-Taylor and Richtmyer-Meshkov Bubble Fronts
    Physics of Fluids , (1994)
  • Alon U, Shvarts D, Mukamel D
    Scale Invariant Regime in Rayleigh-Taylor Bubble Front Dynamics
    Phys. Rev. e , (1993)
  • ALON, U; SHVARTS, D; MUKAMEL, D
    Scale-Invariant Regime in Rayleigh-Taylor Bubble-Front Dynamics
    Physical Review E , (1993)
  • Drory A, Balberg I, Alon U, Berkowitz B
    Analytic Derivation of Percolation Thresholds in Anisotropic Systems of Permeable Objects
    Physical Review A , (1991)
  • U Alon U, Balberg I, Drory A
    New, Heuristic, Percolation Criterion For Continuum Systems
    Phys. Rev. Lett. , (1991)
  • Alon U, Drory A, Balberg I
    Systematic Derivation of Percolation Thresholds in Continuum Systems
    Phys. Rev. a , (1990)