Evolution

  • 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]
  • 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]
  • Sheftel, H; Shoval, O; Mayo, A; Alon, U
    The Geometry of the Pareto Front in Biological Phenotype Space
    Ecology and Evolution , (2013) [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]
  • Rosenheim, JA; Alon, U; Shinar, G
    Evolutionary Balancing of Fitness-Limiting Factors
    American Naturalist , (2010)
  • 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]
  • 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]
  • Oxman E., Dekel E., Alon U.
    Defined Order of Evolutionary Adaptations: Experimental Evidence.
    Evolution , (2008) [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]
  • 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]
  • 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]
  • 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]
  • Dekel E, Alon U
    Optimality and Evolutionary Tuning of the Expression Level of a Protein
    Nature , (2005) [PDF]