Selected publications:

See also Full list of publications

Network Motifs:

• Daniel Madar, Erez Dekel, Anat Bren and Uri Alon
  Negative auto-regulation increases the input dynamic-range of the arabinose system of Escherichia coli
  BMC System Biology, 5:111 (2011). [PDF] [SOM]
  
  
• Shai Kaplan, Anat Bren, Erez Dekel & Uri Alon,
  The incoherent feed-forward loop can generate non-monotonic input functions for genes
  Mol. Systems Biology 2008 July, 4:203 [PDF]
  


• Shai Kaplan, Anat Bren, Alon Zaslaver, Erez Dekel & Uri Alon,
  Diverse two-dimensional input functions control bacterial sugar genes
  Mol Cell. 2008 Mar 28;29(6):786-92 [PDF]
  


• Uri Alon,
  Network motifs: theory and experimental approaches
  Nature Reviews Genetics 8, 450-461 (June 2007) [PDF]
  


• R Milo, S Itzkovitz, N Kashtan, R Levitt, S Shen-Orr, I Ayzenshtat, M Sheffer & U Alon,
  Superfamilies of designed and evolved networks
  Science, 303:1538-42 (2004) [PDF]
  


• R Milo, S Shen-Orr, S Itzkovitz, N Kashtan, D Chklovskii & U Alon,
  Network Motifs: Simple Building Blocks of Complex Networks
  Science, 298:824-827 (2002). [PDF]
  


• S Shen-Orr, R Milo, S Mangan & U Alon,
  Network motifs in the transcriptional regulation network of Escherichia coli.
  Nature Genetics, 31:64-68 (2002). [PDF]
  


• S. Mangan, S. Itzkovitz, A. Zaslaver and U. Alon,
  The Incoherent Feed-forward Loop Accelerates the Response-time of the gal System of Escherichia coli.
  JMB, Vol 356 pp 1073-81 (2006). [PDF]
  


• S Mangan & U Alon,
  Structure and function of the feed-forward loop network motif.
  PNAS, 100:11980-11985 (2003). [PDF]
  


• S. Mangan, A. Zaslaver and U. Alon,
  The Coherent Feedforward Loop Serves as a Sign-sensitive Delay Element in Transcription Networks.
  JMB, Vol 334/2 pp 197-204 (2003). [PDF]
  


• more

Design principles of bio networks:

• Vered Sasson, Irit Shachrai, Anat Bren, Erez Dekel, and Uri Alon
  Mode of Regulation and the Insulation of Bacterial Gene Expression
  Molecular Cell, 46, 399–407 (2012). [PDF] [SOM]
  


• Yuval Hart, Yaron Antebi, Avraham Mayo, Nir Friedman, and Uri Alon
  Design principles of cell circuits with paradoxical components
  PNAS, 109, 8346-8351 May (2012). [PDF] [SOM]
  


• Yuval Hart, Avi Mayo, Ron Milo, and Uri Alon
  Robust Control of PEP Formation Rate in the Carbon Fixation Pathway of C4 Plants by a Bi-functional Enzyme.
  BMC System Biology, 5:171 (2011). [PDF]
  
  
• Daniel Madar, Erez Dekel, Anat Bren and Uri Alon
  Negative auto-regulation increases the input dynamic-range of the arabinose system of Escherichia coli
  BMC System Biology, 5:111 (2011). [PDF] [SOM]
  
  
• Yuval Hart, Daniel Madar, Jie Yuan, Anat Bren, Avraham E. Mayo, Joshua D. Rabinowitz, and Uri Alon
  Robust Control of Nitrogen Assimilation by a Bifunctional Enzyme in E. coli
  Molecular Cell, 41, 117-127 Jan (2010). [PDF] [SOM]
  [Preview by Allison and Collins]
  


• Elad Noor, Eran Eden, Ron Milo, and Uri Alon
  Central Carbon Metabolism as a Minimal Biochemical Walk between Precursors for Biomass and Energy
  Molecular Cell, 39, 809-820 Sep (2010). [PDF]


• Oren Shoval, Lea Goentoro, Yuval Hart, Avi Mayo, Eduardo Sontag, and Uri Alon
  Fold-change detection and scalar symmetry of sensory input fields
  PNAS, 36, Sep (2010). [PDF]


• Guy Shinar and Martin Feinberg
  Structural Sources of Robustness in Biochemical Reaction Networks
  Science, Vol. 327, pp. 1238-1291 Mar (2010) [PDF]
  


• Irit Shachrai, Alon Zaslaver, Uri Alon and Erez Dekel.,
  Cost of Unneeded Proteins in E. coli Is Reduced after Several Generations in Exponential Growth
  Molecular Cell, 38, May 28 (2010). [PDF]


• Goentoro, L., Shoval, O., Kirschner, M.W., and Alon, U.,
  The incoherent feedforward loop can provide fold change detection in gene regulation
  Molecular Cell, 36, Dec 08 (2009). [PDF]


• Shinar G, Rabinowitz JD, Alon U
  Robustness in Glyoxylate Bypass Regulation.
  PLoS Comput Biol 5(3): e1000297 (2009) [PDF]
  


• Guy Shinar, Uri Alon & Martin Feinberg
  Sensitivity and robustness in chemical reaction networks.
  SIAM J. Appl. Math., Vol. 69, No. 4, pp. 977–998 (2009) [PDF]
  


• Zaslaver Alon, Kaplan Shai, Bren Anat, Jinich Adrian, Mayo Avi, Dekel Erez, Alon Uri and Itzkovitz Shalev,
  Invariant distribution of promoter activities in Escherichia coli
  PLoS Comput Biol 5, 5(10) (2009). [PDF]
  


• Guy Shinar, Ron Milo, Martinez MR, Uri Alon
  Input output robustness in simple bacterial signaling systems.
  Proc Natl Acad Sci U S A. 104(50):19931-5. (2007) [PDF]
  


• Guy Shinar, Erez Dekel, Tsvi Tlusty & Uri Alon,
  Rules for biological regulation based on error minimization
  Proc Natl Acad Sci U S A. 103(11), 3999-4004 (2006). [PDF]
  


• Alon Zaslaver, Avi E Mayo, Revital Rosenberg, Pnina Bashkin, Hila Sberro, Miri Tsalyuk, Michael G Surette & Uri Alon,
  Just-in-time transcription program in metabolic pathways
  Nature Genetics 36, 486 - 491 (2004). [PDF]
  
See features in:

• Nature Reviews Genetics : [PDF]
• Journal of Cell Biology : [PDF]



• U. Alon, M.G. Surette, N. Barkai, S. Leibler,
  Robustness in Bacterial Chemotaxis
  Nature 397,168-171 (1999). [PDF]
  


• M Ronen, R Rosenberg, B Shraiman & U Alon,
  Assigning numbers to the arrows: Parameterizing a gene regulation network by using accurate expression kinetics.
  PNAS, 99:10555–10560 (2002). [PDF]
• See also JCB news: [PDF]




• N Rosenfeld, M Elowitz & U Alon,
  Negative Autoregulation Speeds the Response Times of Transcription Networks
  JMB, 323:785-793 (2002). [PDF]
  


• N Rosenfeld & U Alon,
  Response Delays and the Structure of Transcription Networks
  JMB, 329:645–654 (2003). [PDF]
  


• S. Kalir, J. McClure, K. Pabbaraju, C. Southward, M. Ronen, S. Leibler, M.G. Surette, U. Alon,
  Ordering genes in a flagella pathway by analysis of expression kinetics from living bacteria.
  Science, 292:2080-2083 (2001). [PDF]
• See also at Ambion: URL.




• Y. Setty, A. E. Mayo, M. G. Surette, and U. Alon,
  Detailed map of a cis-regulatory input function
  PNAS, 100:7702-7707 (2003). [PDF]
  


• Shiraz Kalir and Uri Alon,
  Using a Quantitative Blueprint to Reprogram the Dynamics of the Flagella Gene Network
  Cell, 117:713–720, (2004). [PDF]
• See also cover page: URL.
• See also Preview article: [PDF]

Evolution:

• Shoval O, Sheftel H, Shinar G, Hart Y, Ramote O, Mayo A, Dekel E, Kavanagh K, and Alon U,
  Evolutionary Trade-Offs, Pareto Optimality, and the Geometry of Phenotype Space
  Science, 336:1157–1160 (2012). [PDF] [SOM]
• See also Science perspective: [PDF]


• Nadav Kashtan, Merav Parter, Erez Dekel, Avi Mayo, Uri Alon
  Extinctions in heterogeneous environments and the evolution of modularity
  Evolution 1558-5646.2009.00684 (2009) [PDF]



• Nadav Kashtan, Avi Mayo, Tomer Kalisky, Uri Alon
  An Analytically Solvable Model for Rapid Evolution of Modular Structure
  PLoS Comput Biol 5(4): e1000355 (2009) [PDF]



• Merav Parter, Nadav Kashtan and Uri Alon,
  Facilitated Variation: How evolution learns from past environments to generalize to new environments
  PLoS Comput Biol 4(11): e1000206 (2008). [PDF], SI [DOC]



• Erez Oxman, Erez Dekel and Uri Alon,
  Defined order of evolutionary adaptations: experimental evidence
  Evolution. Apr 11. (2008) [PDF]



• Merav Parter, Nadav Kashtan and Uri Alon,
  Environmental variability and modularity of bacterial metabolic networks
  BMC Evol Biol. 7 (1):169 (2007). [PDF]



• Tomer Kalisky, Erez Dekel and Uri Alon,
  Cost-benefit theory and optimal design of gene regulation functions
  Phys. Biol. 4 229-245 (2007). [PDF]



• Nadav Kashtan, Elad Noor and Uri Alon,
  Varying environments can speed up evolution
  PNAS, 104: 13711-13716 (2007). [PDF]



• Nadav Kashtan and Uri Alon,
  From the Cover: Spontaneous evolution of modularity and network motifs
  PNAS, 102: 13773-13778 (2005). [PDF]



• Erez Dekel and Uri Alon,
  Optimality and evolutionary tuning of the expression level of a protein
  Nature, 436, 7050, 588-922 (2005). [PDF]



• Erez Dekel, Shmoolik Mangan and Uri Alon,
  Environmental selection of the feed-forward loop circuit in gene-regulation networks
  Physical biology, 2, 2, 81-88 (2005). [PDF]



• Mayo AE, Setty Y, Shavit S, Zaslaver A, Alon U,
  Plasticity of the cis-regulatory input function of a gene
  PLoS Biol. Apr;4(4):e45. (2006). [PDF]

Mammalian systems:

• Eran Eden, Naama Geva-Zatorsky, Irina Issaeva, Ariel Cohen, Erez Dekel, Tamar Danon, Lydia Cohen, Avi Mayo and Uri Alon
  Proteome Half-Life Dynamics in Living Human Cells
  Science, Vol 331, Issue 764, Feb (2011). [PDF] [SOM]
  
  
• Irina Issaeva, Ariel A. Cohen., Eran Eden, Cellina Cohen-Saidon, Tamar Danon, Lydia Cohen, and Uri Alon
  Generation of Double-Labeled Reporter Cell Lines for Studying Co-Dynamics of Endogenous Proteins in Individual Human Cells
  PLOS One, Vol 5, Issue 10, Oct (2010). [PDF]
  
  
• Naama Geva-Zatorsky, Erez Dekel, Eric Batchelor, Galit Lahav, and Uri Alon,
  Fourier analysis and systems identification of the p53 feedback loop
  PNAS, 140, June (2010). [PDF]
  
  
• Naama Geva-Zatorsky, Erez Dekel, Ariel A. Cohen, Tamar Danon, Lydia Cohen and Uri Alon,
  Protein Dynamics in Drug Combinations: a Linear Superposition of Individual-Drug Responses
  Cell, 140, Mar (2010). [PDF+SOM]
  See also review:
  • BioWorld: [PDF]
  
  
• Cellina Cohen-Saidon, Ariel A. Cohen, Alex Sigal, Yuvalal Liron, and Uri Alon,
  Dynamics and Variability of ERK2 Response to EGF in Individual Living Cells
  Molecular Cell, 36, Dec 08 (2009). [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, October 9, 2009. Vol 38(Database issue 2010):D508-D512. [PDF]


• Ariel Cohen, Tomer Kalisky, Avi Mayo, Naama Geva-Zatorsky, Tamar Danon, Irina Issaeva, Ronen Benjamine Kopito, Natalie Perzov, Ron Milo, Alex Sigal & Uri Alon,
  Protein Dynamics in Individual Human Cells: Experiment and Theory
  PLoS ONE April 4(4) (2009). [PDF]


• A. A. Cohen, N. Geva-Zatorsky, E. Eden, M. Frenkel-Morgenstern, I. Issaeva, A. Sigal, Ron Milo, C. Cohen-Saidon, Y. Liron, Z. Kam, L. Cohen, T. Danon, N. Perzov, U. Alon
  Dynamic Proteomics of Individual Cancer Cells in Response to a Drug
  Science. 2008 Nov 20, [PDF], SOM [PDF]
  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]


• Alex Sigal, Tamar Danon, Ariel Cohen, Ron Milo, Naama Geva-Zatorsky, Gila Lustig, Yuvalal Liron, Uri Alon & Natalie Perzov,
  Generation of a fluorescently labeled endogenous protein library in living human cells
  Nature Protocols 2(6) (2007). [PDF]


• Alex Sigal, Ron Milo, Ariel Cohen, Naama Geva-Zatorsky, Yael Klein, Yuvalal Liron, Nitzan Rosenfeld, Tami Danon, Natalie Perzov &Uri Alon,
  Variability and memory of protein levels in human cells
  Nature. Nov 19 (2006). [PDF]
• See also News & Views: [PDF]

• Alex Sigal, Ron Milo, Ariel Cohen, Naama Geva-Zatorsky, Yael Klein, Inbal Alaluf, Naamah Swerdlin, Natalie Perzov, Tamar Danon, Yuvalal Liron, Tal Raveh, Anne E Carpenter, Galit Lahav & Uri Alon,
  Dynamic proteomics in individual human cells uncovers widespread cell-cycle dependence of nuclear proteins.
  Nature Methods 3, 525 - 531 (2006). [PDF]
  
• See also in 'currents' in Journal of Proteome Research: [PDF]


• Naama Geva-Zatorsky, Nitzan Rosenfeld, Shalev Itzkovitz, Ron Milo, Alex Sigal, Erez Dekel, Talia Yarnitzky, Yuvalal Liron, Paz Polak, Galit Lahav and Uri Alon,
  Oscillations and variability in the p53 system.
  Molecular Systems Biology 2, E1 - E13 (2006). [PDF]
  
• See also News & Views: [PDF]


• Galit Lahav, Nitzan Rosenfeld, Alex Sigal, Naama Geva-Zatorsky, Arnold J Levine, Michael B Elowitz & Uri Alon,
  Dynamics of the p53-Mdm2 feedback loop in individual cells.
  Nat. Gen., 36:147-150 (2004). [PDF]
  (See also Nature Reviews Genetics [PDF].)
  


• U. Alon, N. Barkai, D.A. Notterman, K. Gish, S. Ybarra, D. Mack, A. J. Levine,
  Broad Patterns of Gene Expression Revealed by Clustering Analysis of Tumor and Normal Colon Tissues Probed by Oligonucleotide Arrays
  Proc. Natl. Acad. Sci., USA , 96,6745-50 (1999). [PDF]
  

Improvisation:

• Lior Noy, Erez Dekel, and Uri Alon
  The mirror game as a paradigm for studying the dynamics of two people improvising motion together
  Proceedings of the National Academies of Sciences, USA, (2011). [PDF] [SOM]
  
  • See also: Inter-Brain Synchronization during Social Interaction.
  • See also Nature news: [PDF]
  • See also Weizmann news (Hebrew): [PDF]
  
  

Misc.:

• Uri Alon,
  (Viewpoint) How To Choose a Good Scientific Problem
  Molecular Cell 35, September 25, (2009) [PDF]
  


• Uri Alon,
  (Essay) A biophysicist learns the art of hugging
  Nature. 2008 Jun 5;453(7196):701. *2: * [PDF]
  


• Uri Alon,
  (Essay) Simplicity in biology
  Nature. 2007 Mar 29;446(7135):497 [PDF]
  


• Uri Alon,
  (Viewpoint) Biological Networks: The Tinkerer as an Engineer.
  Science, 301:1866-1867 (2003). [PDF]
  

Full list of publications:

• Shoval O, Sheftel H, Shinar G, Hart Y, Ramote O, Mayo A, Dekel E, Kavanagh K, and Alon U,
  Evolutionary Trade-Offs, Pareto Optimality, and the Geometry of Phenotype Space
  Science, 336:1157–1160 (2012). [PDF] [SOM]
• See also Science perspective: [PDF]


• Vered Sasson, Irit Shachrai, Anat Bren, Erez Dekel, and Uri Alon
  Mode of Regulation and the Insulation of Bacterial Gene Expression
  Molecular Cell, 46, 399–407 (2012). [PDF] [SOM]
  


• Yuval Hart, Yaron Antebi, Avraham Mayo, Nir Friedman, and Uri Alon
  Design principles of cell circuits with paradoxical components
  PNAS, 109, 8346-8351 May (2012). [PDF] [SOM]
  


• Lior Noy, Erez Dekel, and Uri Alon
  The mirror game as a paradigm for studying the dynamics of two people improvising motion together
  Proceedings of the National Academies of Sciences, USA, (2011). [PDF] [SOM]
  
  • See also: Inter-Brain Synchronization during Social Interaction.
  • See also Nature news: [PDF]
  • See also Weizmann news (Hebrew): [PDF]
  
  
• Galya Moran and Uri Alon
  Playback theatre and recovery in mental health: Preliminary evidence
  The Arts in Psychotherapy (2011) [PDF]
  
  
• Yuval Hart, Avi Mayo, Ron Milo, and Uri Alon
  Robust Control of PEP Formation Rate in the Carbon Fixation Pathway of C4 Plants by a Bi-functional Enzyme.
  BMC System Biology, 5:171 (2011). [PDF]
  
  
• Daniel Madar, Erez Dekel, Anat Bren and Uri Alon
  Negative auto-regulation increases the input dynamic-range of the arabinose system of Escherichia coli
  BMC System Biology, 5:111 (2011). [PDF] [SOM]
  
  
• Eran Eden, Naama Geva-Zatorsky, Irina Issaeva, Ariel Cohen, Erez Dekel, Tamar Danon, Lydia Cohen, Avi Mayo and Uri Alon
  Proteome Half-Life Dynamics in Living Human Cells
  Science, Vol 331, Issue 764, Feb (2011). [PDF] [SOM]
  
  
• Yuval Hart, Daniel Madar, Jie Yuan, Anat Bren, Avraham E. Mayo, Joshua D. Rabinowitz, and Uri Alon
  Robust Control of Nitrogen Assimilation by a Bifunctional Enzyme in E. coli
  Molecular Cell, 41, 117-127 Jan (2010). [PDF] [SOM]
  [Preview by Allison and Collins]
  


• Irina Issaeva, Ariel A. Cohen., Eran Eden, Cellina Cohen-Saidon, Tamar Danon, Lydia Cohen, and Uri Alon
  Generation of Double-Labeled Reporter Cell Lines for Studying Co-Dynamics of Endogenous Proteins in Individual Human Cells
  PLOS One, Vol 5, Issue 10, Oct (2010). [PDF]
  
  
• Elad Noor, Eran Eden, Ron Milo, and Uri Alon
  Central Carbon Metabolism as a Minimal Biochemical Walk between Precursors for Biomass and Energy
  Molecular Cell, 39, 809-820 Sep (2010). [PDF]


• Oren Shoval, Lea Goentoro, Yuval Hart, Avi Mayo, Eduardo Sontag, and Uri Alon
  Fold-change detection and scalar symmetry of sensory input fields
  PNAS, 36, Sep (2010). [PDF]


• Naama Geva-Zatorsky, Erez Dekel, Eric Batchelor, Galit Lahav, and Uri Alon,
  Fourier analysis and systems identification of the p53 feedback loop
  PNAS, 140, June (2010). [PDF]
  
  
• Guy Shinar and Martin Feinberg
  Structural Sources of Robustness in Biochemical Reaction Networks
  Science, Vol. 327, pp. 1238-1291 Mar (2010) [PDF]
  


• Irit Shachrai, Alon Zaslaver, Uri Alon and Erez Dekel.,
  Cost of Unneeded Proteins in E. coli Is Reduced after Several Generations in Exponential Growth
  Molecular Cell, 38, May 28 (2010). [PDF]


• Naama Geva-Zatorsky, Erez Dekel, Ariel A. Cohen, Tamar Danon, Lydia Cohen and Uri Alon,
  Protein Dynamics in Drug Combinations: a Linear Superposition of Individual-Drug Responses
  Cell, 140, Mar (2010). [PDF]


• Goentoro, L., Shoval, O., Kirschner, M.W., and Alon, U.,
  The incoherent feedforward loop can provide fold change detection in gene regulation
  Molecular Cell, 36, Dec 08 (2009). [PDF]


• Cellina Cohen-Saidon, Ariel A. Cohen, Alex Sigal, Yuvalal Liron, and Uri Alon,
  Dynamics and Variability of ERK2 Response to EGF in Individual Living Cells
  Molecular Cell, 36, Dec 08 (2009). [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, October 9, 2009. Vol 38(Database issue 2010):D508-D512. [PDF]


• Zaslaver Alon, Kaplan Shai, Bren Anat, Jinich Adrian, Mayo Avi, Dekel Erez, Alon Uri and Itzkovitz Shalev,
  Invariant distribution of promoter activities in Escherichia coli
  PLoS Comput Biol 5, 5(10) (2009). [PDF]
  


• Ariel Cohen, Tomer Kalisky, Avi Mayo, Naama Geva-Zatorsky, Tamar Danon, Irina Issaeva, Ronen Benjamine Kopito, Natalie Perzov, Ron Milo, Alex Sigal & Uri Alon,
  Protein Dynamics in Individual Human Cells: Experiment and Theory
  PLoS ONE April 4(4) (2009). [PDF]


• Nadav Kashtan, Merav Parter, Erez Dekel, Avi Mayo, Uri Alon
  Extinctions in heterogeneous environments and the evolution of modularity
  Evolution 1558-5646.2009.00684 (2009) [PDF]



• Nadav Kashtan, Avi Mayo, Tomer Kalisky, Uri Alon
  An Analytically Solvable Model for Rapid Evolution of Modular Structure
  PLoS Comput Biol 5(4): e1000355 (2009) [PDF]



• Shinar G, Rabinowitz JD, Alon U
  Robustness in Glyoxylate Bypass Regulation.
  PLoS Comput Biol 5(3): e1000297 (2009) [PDF]
  


• Guy Shinar, Uri Alon & Martin Feinberg
  Sensitivity and robustness in chemical reaction networks.
  SIAM J. Appl. Math., Vol. 69, No. 4, pp. 977–998 (2009) [PDF]
  


• A. A. Cohen, N. Geva-Zatorsky, E. Eden, M. Frenkel-Morgenstern, I. Issaeva, A. Sigal, Ron Milo, C. Cohen-Saidon, Y. Liron, Z. Kam, L. Cohen, T. Danon, N. Perzov, U. Alon
  Dynamic Proteomics of Individual Cancer Cells in Response to a Drug
  Science. 2008 Nov 20, [PDF], SOM [PDF]
  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]
  
  
  
• Merav Parter, Nadav Kashtan and Uri Alon,
  Facilitated Variation: How evolution learns from past environments to generalize to new environments
  PLoS Comput Biol 4(11): e1000206 (2008). [PDF], SI [DOC]



• Shai Kaplan, Anat Bren, Erez Dekel & Uri Alon,
  The incoherent feed-forward loop can generate non-monotonic input functions for genes
  Mol. Systems Biology 2008 July, 4:203 [PDF]
  


• Uri Alon,
  (Essay) A biophysicist learns the art of hugging
  Nature. Jun 5;453(7196):701. *2: * (2008) [PDF]
  


• Erez Oxman, Erez Dekel and Uri Alon,
  Defined order of evolutionary adaptations: experimental evidence
  Evolution. Apr 11. (2008) [PDF]


• Shai Kaplan, Anat Bren, Alon Zaslaver, Erez Dekel & Uri Alon,
  Diverse two-dimensional input functions control bacterial sugar genes
  Mol Cell. Mar 28;29(6):786-92 (2008)[PDF]
  


• Merav Parter, Nadav Kashtan and Uri Alon,
  Environmental variability and modularity of bacterial metabolic networks
  BMC Evol Biol. 7 (1):169 (2007). [PDF]
  


• Guy Shinar, Ron Milo, Martinez MR, Uri Alon
  Input output robustness in simple bacterial signaling systems.
  Proc Natl Acad Sci U S A. 104(50):19931-5. (2007) [PDF]
  


• Tomer Kalisky, Erez Dekel & Uri Alon,
  Cost-benefit theory and optimal design of gene regulation functions
  Phys. Biol. 4 229-245 (2007). [PDF]
  


• Alex Sigal, Tamar Danon, Ariel Cohen, Ron Milo, Naama Geva-Zatorsky, Gila Lustig, Yuvalal Liron, Uri Alon & Natalie Perzov,
  Generation of a fluorescently labeled endogenous protein library in living human cells
  Nature Protocols 2(6) (2007). [PDF]


• Nadav Kashtan, Elad Noor and Uri Alon,
  Varying environments can speed up evolution
  PNAS, 104: 13711-13716 (2007). [PDF]
  


• Sigal Alex, Danon Tamar, Cohen Ariel, Milo Ron, Geva-Zatorsky Naama, Lustig Gil, Liron Yuvalal, Alon Uri & Perzov Natalie
  Generation of a fluorescently labeled endogenous protein library in living human cells
  Nature Protocols 2(6):1515-27. (2007) [PDF]
  


• Uri Alon,
  Network motifs: theory and experimental approaches
  Nature Reviews Genetics 8, 450-461 (June 2007). [PDF]


• Uri Alon,
  (Essay) Simplicity in biology
  Nature. Mar 29;446(7135):497 (2007)[PDF]


• Shalev Itzkovitz & Uri Alon,
  The genetic code is nearly optimal for allowing additional information within protein-coding sequences
  Genome Res. Apr;17(4):405-12 (2007) [PDF]
  See reviews in:
  • Genome Research: [PDF]
  • Nature Reviews Genetics: [PDF]


• Amit I, Citri A, Shay T, Lu Y, 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.
  Nat Genet. Apr;39(4):503-12 (2007). [PDF]


• Alon Zaslaver , Avi Mayo, Michal Ronen & Uri Alon,
  Optimal gene partition into operons correlates with gene functional order
  Phys Biol. Sep 18;3(3):183-9 (2006)[PDF]
  


• Alex Sigal, Ron Milo, Ariel Cohen, Naama Geva-Zatorsky, Yael Klein, Yuvalal Liron, Nitzan Rosenfeld, Tami Danon, Natalie Perzov &Uri Alon,
  Variability and memory of protein levels in human cells
  Nature. Nov 19 (2006). [PDF]
  


• Shalev Itzkovitz, Zvi Tlusty & Uri ALon,
  Coding limits on the number of transcription factors
  BMC Genomics. Sep 19;7:239 (2006). [PDF]
  


• Shalev Itzkovitz, Ron Milo, Nadav Kashtan, Reuven Levitt, Amir Lahav & Uri ALon,
  Recurring Harmonic Walks and Network Motifs in Western Music
  Advances in Complex Systems, Vol. 9, Nos. 1&2 121–132 (2006). [PDF]
  


• Alon Zaslaver, Avi Mayo, Michal Ronen & Uri Alon,
  Optimal gene partition into operons correlates with gene functional order
  Phys Biol. Sep 18;3(3):183-9 (2006). [PDF]
  


• Alon Zaslaver, Anat Bren, Michal Ronen, Shalev Itzkovitz, Ilya Kikoin, Seagull Shavit, Wolfram Liebermeister, Michael G Surette & Uri Alon,
  A comprehensive library of fluorescent transcriptional reporters for Escherichia coli
  Nature Methods 3, 623 - 628 (2006). [PDF]
  


• Alex Sigal, Ron Milo, Ariel Cohen, Naama Geva-Zatorsky, Yael Klein, Inbal Alaluf, Naamah Swerdlin, Natalie Perzov, Tamar Danon, Yuvalal Liron, Tal Raveh, Anne E Carpenter, Galit Lahav & Uri Alon,
  Dynamic proteomics in individual human cells uncovers widespread cell-cycle dependence of nuclear proteins.
  Nature Methods 3, 525 - 531 (2006). [PDF]
  


• Naama Geva-Zatorsky, Nitzan Rosenfeld, Shalev Itzkovitz, Ron Milo, Alex Sigal, Erez Dekel, Talia Yarnitzky, Yuvalal Liron, Paz Polak, Galit Lahav and Uri Alon,
  Oscillations and variability in the p53 system.
  Molecular Systems Biology 2, E1 - E13 (2006). [PDF]
  


• Rosenfeld N, Perkins TJ, Alon U, Elowitz MB, Swain PS,
  A fluctuation method to quantify in vivo fluorescence data
  Biophys J. Apr 28(2006). [PDF]
  


• Mayo AE, Setty Y, Shavit S, Zaslaver A, Alon U,
  Plasticity of the cis-regulatory input function of a gene
  PLoS Biol. Apr;4(4):e45. (2006). [PDF]
  


• Guy Shinar, Erez Dekel, Tsvi Tlusty & Uri Alon,
  Rules for biological regulation based on error minimization
  Proc Natl Acad Sci U S A. 103(11), 3999-4004 (2006). [PDF]
  


• S. Mangan, S. Itzkovitz, A. Zaslaver and U. Alon,
  The Incoherent Feed-forward Loop Accelerates the Response-time of the gal System of Escherichia coli.
  JMB, Vol 356 pp 1073-81 (2006). [PDF]
  


• Frankenstein Z, Alon U and Cohen IR.,
  The immune-body cytokine network defines a social architecture of cell interactions.
  Biol Direct. 2006 Oct 24;1:32 (2006). [PDF]
  


• Nadav Kashtan and Uri Alon,
  From the Cover: Spontaneous evolution of modularity and network motifs
  PNAS, 102: 13773-13778 (2005). [PDF]
  


• Erez Dekel and Uri Alon,
  Optimality and evolutionary tuning of the expression level of a protein
  Nature, 436, 7050, 588-922 (2005). [PDF]
  


• Erez Dekel, Shmoolik Mangan and Uri Alon,
  Environmental selection of the feed-forward loop circuit in gene-regulation networks
  Physical biology, 2, 2, 81-88 (2005). [PDF]
  


• Shiraz Kalir, Shmoolik Mangan and Uri Alon,
  A coherent feed-forward loop with a SUM input function prolongs flagella expression in Escherichia coli
  Mol Syst Biol, msb4100010-E1-msb4100010-E6, (2005). [PDF]
  


• Nitzan Rosenfeld, Jonathan W. Young, Uri Alon, Peter S. Swain, Michael B. Elowitz ,
  Gene Regulation at the Single-Cell Level
  Science, Vol 307:1962-1965 , (2005). [PDF]
  


• Shiraz Kalir and Uri Alon,
  Using a Quantitative Blueprint to Reprogram the Dynamics of the Flagella Gene Network
  Cell, 117:713–720, (2004). [PDF]
• See also cover page: URL.
• See also Preview article: [PDF]




• Alon Zaslaver, Avi E Mayo, Revital Rosenberg, Pnina Bashkin, Hila Sberro, Miri Tsalyuk, Michael G Surette & Uri Alon,
  Just-in-time transcription program in metabolic pathways
  Nature Genetics 36, 486 - 491 (2004). [PDF]
  
See features in:

• Nature Reviews Genetics : [PDF]
• Journal of Cell Biology : [PDF]


• Ron Milo, Shalev Itzkovitz, Nadav Kashtan, Reuven Levitt, Shai Shen-Orr, Inbal Ayzenshtat, Michal Sheffer, Uri Alon,
  Superfamilies of Evolved and Designed Networks.
  Science, Vol 303, Issue 5663, 1538-1542,(2004). [PDF]
  


• N. Kashtan, S. Itzkovitz, R. Milo, U. Alon,
  Efficient sampling algorithm for estimating subgraph concentrations and detecting network motifs.
  Bioinformatics. 2004 Jul 22;20(11):1746-58. [PDF].
  


• N. Kashtan, S. Itzkovitz, R. Milo, U. Alon,
  Topological Generalizations of network motifs.
  Phys Rev E 70, 031909 (2004). [PDF].
  


• Shalev Itzkovitz, Reuven Levitt, Nadav Kashtan, Ron Milo, Michael Itzkovitz, Uri Alon,
  Coarse-Graining and Self-Dissimilarity of Complex Networks.
  Phys Rev E 71, 016127 (2005). [PDF]
  


• Shalev Itzkovitz and Uri Alon,
  Subgraphs and network motifs in geometric networks.
  Phys Rev E 71, 026117 (2005). [PDF]
  


• Galit Lahav, Nitzan Rosenfeld, Alex Sigal, Naama Geva-Zatorsky, Arnold J Levine, Michael B Elowitz & Uri Alon,
  Dynamics of the p53-Mdm2 feedback loop in individual cells.
  Nat. Gen., 36:147-150 (2004). [PDF]
  


• S. Mangan, A. Zaslaver and U. Alon,
  The Coherent Feedforward Loop Serves as a Sign-sensitive Delay Element in Transcription Networks.
  JMB, Vol 334/2 pp 197-204 (2003). [PDF]
  


• S Mangan & U Alon,
  Structure and function of the feed-forward loop network motif.
  PNAS, 100:11980-11985 (2003). [PDF]
  


• U Alon,
  (Viewpoint) Biological Networks: The Tinkerer as an Engineer.
  Science, 301:1866-1867 (2003). [PDF]
  


• Y. Setty, A. E. Mayo, M. G. Surette, and U. Alon,
  Detailed map of a cis-regulatory input function
  PNAS, 100:7702-7707 (2003). [PDF]
  


• N Rosenfeld & U Alon,
  Response Delays and the Structure of Transcription Networks
  JMB, 329:645–654 (2003). [PDF]
  


• S Itzkovitz, R Milo, N Kashtan, G Ziv & U Alon,
  Subgraphs in random networks
  Phys Rev E 68, 026127 (2003). [PDF]
  


• N Rosenfeld, M Elowitz & U Alon,
  Negative Autoregulation Speeds the Response Times of Transcription Networks
  JMB, 323:785-793 (2002). [PDF]
  


• R Milo, S Shen-Orr, S Itzkovitz, N Kashtan, D Chklovskii & U Alon,
  Network Motifs: Simple Building Blocks of Complex Networks
  Science, 298:824-827 (2002). [PDF]
  


• M Ronen, R Rosenberg, B Shraiman & U Alon,
  Assigning numbers to the arrows: Parameterizing a gene regulation network by using accurate expression kinetics.
  PNAS, 99:10555–10560 (2002). [PDF]
• See also JCB news: [PDF]




• S Shen-Orr, R Milo, S Mangan & U Alon,
  Network motifs in the transcriptional regulation network of Escherichia coli.
  Nature Genetics, 31:64-68 (2002). [PDF]
  


• S. Kalir, J. McClure, K. Pabbaraju, C. Southward, M. Ronen, S. Leibler, M.G. Surette, U. Alon,
  Ordering genes in a flagella pathway by analysis of expression kinetics from living bacteria.
  Science, 292:2080-2083 (2001). [PDF]
  


• 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. 61:3124-30. (2001).
  


• N. Barkai, U. Alon, S. Leibler,
  Robust Amplification in adaptive signal transduction networks.
  C. R. Acad. Sci. Paris, 2:1-7 (2001) [PDF]
  


• R. Lev Bar-Or, R. Maya, L.A. Segel, U. Alon, A.J. Levine, M. Oren
  Generation of oscillations in the p53-Mdm2 feedback loop: A theoretical and experimental study
  Proc. Natl. Acad. Sci., USA , 97,11256-11261 (2000).
  


• J.F. Staropoli, U. Alon,
  Computerized analysis of chemotaxis at different stages of bacterial growth
  Biophys. J. 78, 513-519 (2000).
  


• U. Alon, N. Barkai, D.A. Notterman, K. Gish, S. Ybarra, D. Mack, A. J. Levine,
  Broad Patterns of Gene Expression Revealed by Clustering Analysis of Tumor and Normal Colon Tissues Probed by Oligonucleotide Arrays
  Proc. Natl. Acad. Sci., USA , 96,6745-50 (1999). [PDF]
  


• U. Alon, M.G. Surette, N. Barkai, S. Leibler,
  Robustness in Bacterial Chemotaxis
  Nature 397,168-171 (1999). [PDF]
  


• U. Alon, L. Camarena, M.G. Surette, B. Aguera y Arcas, Y. Liu, S. Leibler, J.B. Stock
  Response Regulator Output in Bacterial Chemotaxis,
  EMBO J., 17,4238-4248 (1998).
  


• Rikanati A, Oron D, Alon U, Shvarts D
  Statistical mechanics merger model for hydrodynamic instabilities
  Astrophysical Journal (supplement series)127: (2) 451-457 (2000)
  


• 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 8 (6): 2883-2889 (2001)
  


• 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
  Astrophysical Journal (supplement series) 127: (2) 469-473 (2000)
  


• 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 17,465-475 (1999)
  


• A. Rikanati, U. Alon and D. Shvarts,
  Vortex Model for the Nonlinear Evolution of the Multimode Richtmyer-Meshkov Instability at Low Atwood Numbers,
  Phys. Rev E. 58, 7410-7418 (1998).
  


• D. Oron, U. Alon and D. Shvarts,
  Scaling Laws of the Rayleigh-Taylor Ablation Front Mixing Evolution in Inertial Confinement Fusion,
  Phys. Plasmas 5,1467-1476 (1998).
  


• U. Alon, M.R. Evans, H. Hinrichson, D. Mukamel,
  Smooth Phases, Roughening Transitions, and Novel Exponents in One-Dimensional Growth Models,
  Phys. Rev. E, 57,4997-5012 (1998).
  


• O. Sadot, L. Erez, U. Alon, D. Oron, L. A. Levin, G. Erez, G. Ben-Dor, and D. Shvarts,
  Study of Nonlinear Evolution of Single-Mode and Two-Bubble Interaction Under the Richtmyer-Meshkov instability,
  Phys. Rev. Lett. 80,1654-1657 (1998).
  


• U. Alon, D. Mukamel,
  Gel-Electrophoresis and Diffusion of Ring Shaped DNA,
  Phys. Rev. E 55,1783-1793 (1997).
  


• U. Alon, M.R. Evans, H. Hinrichson, D. Mukamel,
  Roughening Transition in a One-Dimensional Growth Process,
  Phys. Rev. Lett. 76, 2746-2749 (1996).
  


• D. Ofer, U. Alon, D. Shvarts, R.L. McCrory and C.P. Verdon,
  Modal Model for the Nonlinear Multi-Mode Rayleigh-Taylor Instability,
  Physics of Plasmas 3, 3073-3090 (1996).
  


• J. Hecht, D. Ofer, U. Alon, D. Shvarts, S.A. Orszag, R.L. McCrory,
  3D Simulations and Analysis of the Nonlinear Stage of the Rayleigh-Taylor Instability
  Laser and Particle Beams 13, 423-450 (1995).
  


• D. Shvarts, U. Alon, D. Ofer, C.P. Verdon, R.L. McCrory,
  Nonlinear Multi-Mode Rayleigh-Taylor Instability in Two and Three Dimensions,
  Physics of Plasmas 2, 2465-2472 (1995).
  


• U. Alon, J. Hecht, D. Ofer, D. Shvarts,
  Power Laws and Similarity of Rayleigh-Taylor and Richtmyer-Meshkov Mixing Fronts at All Density Ratios,
  Phys. Rev. Lett. 74, 534-537 (1995).
  


• J. Hecht, U. Alon, D. Shvarts,
  Potential Flow Models of Rayleigh-Taylor and Richtmyer-Meshkov Bubble Fronts,
  Phys. of Fluids 6, 4019-4030 (1994).
  


• U. Alon, J. Hecht, D. Mukamel, D. Shvarts,
  Scale Invariant Growth of Hydrodynamically Unstable Interfaces,
  Phys. Rev. Lett. 72, 2867-2870 (1994).
  


• U. Alon, D. Shvarts, D. Mukamel,
  Scale Invariant Regime in Rayleigh-Taylor Bubble Front Dynamics,
  Phys. Rev. E 48, 1008-1014 (1993).
  


• A. Drory, I. Balberg, U. Alon, B. Berkowitz,
  Analytic Determination of Percolation Thresholds in Anisotropic Systems,
  Phys. Rev. A 43, 6604-6612 (1991).
  


• U. Alon, I. Balberg, A. Drory,
  New, Heuristic Percolation Criterion for Continuum Systems,
  Phys. Rev. Lett. 66, 2879-2882 (1991).
  


• U. Alon, A. Drory, I. Balberg,
  Systematic Derivation of Percolation thresholds in Continuum Systems,
  Phys. Rev. A 42, 4634-4638 (1990).