Associative learning in biochemical networksNikhil Gandhi
College of Computing, Georgia Institute of Technology, Atlanta, GA 30332, USA
J Theor Biol 249:58-66. 2007
..We also describe how such a mechanism could be involved in genomic evolution, and suggest relevant bioinformatics studies that could potentially resolve these issues...
- Extracting viability landscapes from mutagen-response experiments
Emmanuel Tannenbaum
Department of Chemistry, Ben Gurion University of the Negev, Be er Sheva 84105, Israel
J Theor Biol 245:37-43. 2007
..Thus, such methods could shed light on the evolutionary history of an organism...
- Selective advantage for multicellular replicative strategies: a two-cell example
Emmanuel Tannenbaum
Ben Gurion University of the Negev, Be er Sheva 84105, Israel
Phys Rev E Stat Nonlin Soft Matter Phys 73:010904. 2006
..Such a framework is therefore consistent with the concept that natural selection does not act on individuals, but rather on populations...
Diploidy and the selective advantage for sexual reproduction in unicellular organismsMaya Kleiman
Department of Chemistry, Ben Gurion University of the Negev, Be er Sheva, Israel
Theory Biosci 128:249-85. 2009
..Finally, and perhaps most importantly, the results of this article demonstrate a selective advantage for sexual reproduction with fewer and much less restrictive assumptions than those of previous studies...
- Semiconservative quasispecies equations for polysomic genomes: the general case
Eran Itan
Department of Chemistry, Ben Gurion University of the Negev, Be er Sheva, Israel
Phys Rev E Stat Nonlin Soft Matter Phys 81:061915. 2010
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- A quasispecies approach to the evolution of sexual replication in unicellular organisms
Emmanuel Tannenbaum
Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva 84105, Israel
Theory Biosci 127:53-65. 2008
..We critically evaluate a common approach, based on a group selection perspective, used to study the competition between populations and show its flaws in addressing the evolution of sex problem...
- Selective advantage for sexual reproduction with random haploid fusion
Emmanuel Tannenbaum
Department of Chemistry, Ben Gurion University of the Negev, Beersheba, Israel
Theory Biosci 128:85-96. 2009
..Furthermore, the results of this article provide a basis for understanding sex as a stress response in unicellular organisms such as Saccharomyces cerevisiae (Baker's yeast)...
Effect of the SOS response on the mean fitness of unicellular populations: a quasispecies approachAmit Kama
Department of Chemistry, Ben Gurion University of the Negev, Be er Sheva, Israel
PLoS ONE 5:e14113. 2010
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- Comparison of three replication strategies in complex multicellular organisms: asexual replication, sexual replication with identical gametes, and sexual replication with distinct sperm and egg gametes
Emmanuel Tannenbaum
Department of Chemistry, Ben Gurion University of the Negev, Be er Sheva, Israel
Phys Rev E Stat Nonlin Soft Matter Phys 77:011915. 2008
..We discuss the usefulness of this model in understanding the evolution and maintenance of sexual replication as the preferred replication strategy in complex, multicellular organisms...
- Selection advantage of metabolic over non-metabolic replicators: a kinetic analysis
Nathaniel Wagner
Department of Chemistry, Ben Gurion University of the Negev, Be er Sheva, Israel
Biosystems 99:126-9. 2010
..The study reaffirms our view that the roots of Darwinian theory may be found within standard chemical kinetic theory...
- Effect of chromosomal instability on the mutation-selection balance in unicellular populations
Eran Itan
Department of Chemistry, Ben Gurion University of the Negev, Be er Sheva, Israel
PLoS ONE 7:e26513. 2012
..The results of this paper provide a useful baseline that can inform both future theoretial and experimental studies of chromosomal instability...
- Semiconservative quasispecies equations for polysomic genomes: the haploid case
Emmanuel Tannenbaum
Department of Chemistry, Ben Gurion University of the Negev, Be er Sheva 84105, Israel
J Theor Biol 241:791-805. 2006
..Based on this result, we conjecture that certain classes of tumor cells exhibit immortal strand co-segregation...
- A comparison of sexual and asexual replication strategies in a simplified model based on the yeast life cycle
Emmanuel Tannenbaum
Department of Chemistry, Ben Gurion University of the Negev, Beersheba, Israel
Theory Biosci 127:323-33. 2008
..That being said, our model does not contradict theories for the evolution of sex that argue that sex evolved because it allows a population to more easily adapt to changing conditions...
- Temporal differentiation and the optimization of system output
Emmanuel Tannenbaum
Department of Chemistry, Ben Gurion University of the Negev, Be er Sheva, Israel
Phys Rev E Stat Nonlin Soft Matter Phys 77:011922. 2008
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- Selective advantage for sexual reproduction
Emmanuel Tannenbaum
Department of Chemistry, Ben Gurion University of the Negev, Be er Sheva 84105, Israel
Phys Rev E Stat Nonlin Soft Matter Phys 73:061925. 2006
..In fact, at a given replication rate and for a fixed environment volume, sexual reproduction is selected for in high populations because of the reduced time spent finding a reproductive partner...
- The influence of horizontal gene transfer on the mean fitness of unicellular populations in static environments
Yoav Raz
Department of Chemistry, Ben Gurion University of the Negev, Be er Sheva, Israel
Genetics 185:327-37. 2010
..Rather, its advantage must lie in its ability to promote faster adaptation in dynamic environments, an interpretation that is consistent with the observation that HGT can be promoted by environmental stresses on a population...
- Second order catalytic quasispecies yields discontinuous mean fitness at error threshold
Nathaniel Wagner
Department of Chemistry, Ben Gurion University of the Negev, Be er Sheva, Israel
Phys Rev Lett 104:188101. 2010
..We discuss potential implications for understanding replication in the RNA world and in virology...
- Speculations on the emergence of self-awareness in big-brained organisms: the roles of associative memory and learning, existential and religious questions, and the emergence of tautologies
Emmanuel Tannenbaum
Department of Chemistry, Ben Gurion University of the Negev, Sderot Ben Gurion, Be er Sheva, Israel
Conscious Cogn 18:414-27. 2009
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- An RNA-centered view of eukaryotic cells
Emmanuel Tannenbaum
Department of Chemistry, Ben Gurion University of the Negev, Be er Sheva 84105, Israel
Biosystems 84:217-24. 2006
..We conclude this paper by arguing that a sufficient amount of biological knowledge has been accumulated to initiate a systematic program of experimental and computational studies of the origins and macroevolution of terrestrial life...
- Equilibrium distribution of mutators in the single fitness peak model
Emmanuel Tannenbaum
Harvard University, Cambridge, Massachusetts 02138, USA
Phys Rev Lett 91:138105. 2003
..The repair catastrophe therefore occurs when the repair error probability exceeds the fraction of deleterious mutations. Our model also gives a quantitative estimate for the equilibrium fraction of mutators in Escherichia coli...
- Solution of the quasispecies model for an arbitrary gene network
Emmanuel Tannenbaum
Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
Phys Rev E Stat Nonlin Soft Matter Phys 70:021903. 2004
..The results in this paper also have implications for mutational robustness and what C.O. Wilke termed "survival of the flattest."..
- When does division of labor lead to increased system output?
Emmanuel Tannenbaum
School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA
J Theor Biol 247:413-25. 2007
..Finally, the results of this paper may be useful for understanding how, in an economic context, firm productivity is maximized at intermediate firm sizes...
- Evolutionary dynamics of adult stem cells: comparison of random and immortal-strand segregation mechanisms
Emmanuel Tannenbaum
Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
Phys Rev E Stat Nonlin Soft Matter Phys 71:041914. 2005
..For human stem cells, we obtain that mispaired bases still present after replication and cell division should be left untouched, to avoid potentially fixing a mutation in both DNA strands...
- Imperfect DNA lesion repair in the semiconservative quasispecies model: derivation of the Hamming class equations and solution of the single-fitness peak landscape
Emmanuel Tannenbaum
Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
Phys Rev E Stat Nonlin Soft Matter Phys 70:061915. 2004
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- Semiconservative replication in the quasispecies model
Emmanuel Tannenbaum
Harvard University, Cambridge, Massachusetts 02138, USA
Phys Rev E Stat Nonlin Soft Matter Phys 69:061916. 2004
..Thus, in contrast to Eigen's original model, the semiconservative quasispecies equations are able to provide a mathematical basis for explaining the efficacy of mutagens as chemotherapeutic agents...
- Error and repair catastrophes: A two-dimensional phase diagram in the quasispecies model
Emmanuel Tannenbaum
Harvard University, Cambridge, Massachusetts 02138, USA
Phys Rev E Stat Nonlin Soft Matter Phys 69:011902. 2004
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- Asexual and sexual replication in sporulating organisms
Bohyun Lee
School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
Phys Rev E Stat Nonlin Soft Matter Phys 76:021909. 2007
..Therefore, the results of this model suggest that, for complex multicellular organisms, sexual replication is favored at high population densities and low growth and sporulation rates...
