Evolution

  • Hila Sheftel, Pablo Szekely, Avi Mayo, Guy Sella, Uri Alon
    Evolutionary Tradeoffs and the Structure of Allelic Polymorphisms
    Biorxiv , (2018) [PDF]

    Effects of common genetic variations are predicted to push phenotypes along optimal tradeoffs.

  • 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]
  • 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]
  • Hila Sheftel; Oren Shoval; Avi Mayo; Uri Alon
    The Geometry of the Pareto Front in Biological Phenotype Space
    Ecology and Evolution , 3:000035756 (2013) [PDF]
  • Tamar Friedlander; Avraham E. Mayo; Tsvi Tlusty; Uri Alon
    Mutation Rules and the Evolution of Sparseness and Modularity in Biological Systems
    PLoS ONE , 8:000013903 (2013) [PDF]
  • Pablo Szekely; Hila Sheftel; Avi Mayo; Uri Alon
    Evolutionary Tradeoffs Between Economy and Effectiveness in Biological Homeostasis Systems
    Plos Computational Biology , 9:000037920 (2013) [PDF]
  • Kathryn D. Kavanagh; Oren Shoval; Benjamin B. Winslow; Uri Alon; Brian P. Leary; Akinori Kan; Clifford J. Tabin
    Developmental Bias in the Evolution of Phalanges
    Proceedings of the National Academy of Sciences of the United States of America , 110:000021171 (2013) [PDF]
  • Oren Shoval; Hila Sheftel; Guy Shinar; Yuval Hart; Omer Ramote; Avi Mayo; Erez Dekel; K. Kavanagh; Uri Alon
    Evolutionary Trade-Offs, Pareto Optimality, and the Geometry of Phenotype Space
    Science , 336:000036281 (2012) [PDF] [SOM]
    • See also Science Perspective: [PDF]
  • Jay A. Rosenheim; Uri Alon; Guy Shinar
    Evolutionary Balancing of Fitness-Limiting Factors
    American Naturalist , 175:000032823 (2010)
  • Nadav Kashtan; Avi E. Mayo; Tomer Kalisky; Uri Alon
    An Analytically Solvable Model For Rapid Evolution of Modular Structure
    Plos Computational Biology , 5:000020859 (2009) [PDF]
  • Nadav Kashtan; Merav Parter; Erez Dekel; Avi E. Mayo; Uri Alon
    Extinctions in Heterogeneous Environments and the Evolution of Modularity
    Evolution , 63:000020861 (2009) [PDF]
  • Merav Parter; Nadav Kashtan; Uri Alon
    Facilitated Variation
    Plos Computational Biology , 4:000029751 (2008) [PDF] [SOM]
  • Oxman E., Dekel E., Alon U.
    Defined Order of Evolutionary Adaptations: Experimental Evidence.
    Evolution , (2008) [PDF]
  • Merav Parter; Nadav Kashtan; Uri Alon
    Environmental Variability and Modularity of Bacterial Metabolic Networks
    Bmc Evolutionary Biology , 7:000029750 (2007) [PDF]
  • Tomer Kalisky; Erez Dekel; Uri Alon
    Cost-Benefit theory and Optimal Design of Gene Regulation Functions
    Physical Biology , 4:000020406 (2007) [PDF]
  • Shalev Itzkovitz; Uri Alon
    The Genetic Code is Nearly Optimal For Allowing Additional Information Within Protein-Coding Sequences
    Genome Research , 17:000019706 (2007) [PDF]
    • Genome Research: [PDF]
    • Nature Reviews Genetics: [PDF]
  • Nadav Kashtan; Elad Noor; Uri Alon
    Varying Environments Can Speed up Evolution
    Proceedings of the National Academy of Sciences of the United States of America , 104:000020860 (2007) [PDF]
  • AE Mayo; Yaakov Setty; Shlomo Shavit; A Zaslaver; Uri Alon
    Plasticity of the Cis-Regulatory Input Function of a Gene
    PLoS Biology , 4:000026523 (2006) [PDF]
  • Shalev Itzkovitz; Tsvi Tlusty; Uri Alon
    Coding Limits on the Number of Transcription Factors
    Bmc Genomics , 7:000019714 (2006) [PDF]
  • Erez Dekel; Uri Alon
    Optimality and Evolutionary Tuning of the Expression Level of a Protein
    Nature , 436:000010549 (2005) [PDF]
  • Dekel, E; Alon, U
    Optimality and Evolutionary Tuning of the Expression Level of a Protein
    Nature , (2005) [PDF]
  • N Kashtan; Uri Alon
    Spontaneous Evolution of Modularity and Network Motifs
    Proceedings of the National Academy of Sciences of the United States of America , 102:000020856 (2005) [PDF]
  • Erez Dekel; S Mangan; Uri Alon
    Environmental Selection of the Feed-Forward Loop Circuit in Gene-Regulation Networks
    Physical Biology , 2:000010550 (2005) [PDF]