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- Eli Hershkovitz, Emmanuel Tannenbaum, Shelley B Howerton, Ajay Sheth, Allen Tannenbaum, Loren Dean Williams
- Nucleic acids research
- 2003

We develop novel methods for recognizing and cataloging conformational states of RNA, and for discovering statistical rules governing those states. We focus on the conformation of the large ribosomal subunit from Haloarcula marismortui. The two approaches described here involve torsion matching and binning. Torsion matching is a pattern-recognition code… (More)

- Nathaniel Wagner, Addy Pross, Emmanuel Tannenbaum
- Biosystems
- 2010

A kinetic analysis and simulation of the replication reactions of two competing replicators-one non-metabolic (thermodynamic), the other metabolic, are presented. Our analysis indicates that in a rich resource environment the non-metabolic replicator is likely to be kinetically selected for over the metabolic replicator. However, in the more typical… (More)

- Emmanuel Tannenbaum, Eugene I Shakhnovich
- Physical review. E, Statistical, nonlinear, and…
- 2004

In this paper, we study the equilibrium behavior of Eigen's quasispecies equations for an arbitrary gene network. We consider a genome consisting of N genes, so that the full genome sequence sigma may be written as sigma= sigma1sigma2...sigmaN, where sigma(i) are sequences of individual genes. We assume a single fitness peak model for each gene, so that… (More)

- Emmanuel Tannenbaum, Eric J Deeds, Eugene I Shakhnovich
- Physical review letters
- 2003

This Letter develops an analytically tractable model for determining the equilibrium distribution of mismatch repair deficient strains in unicellular populations. The approach is based on the single fitness peak model, which has been used in Eigen's quasispecies equations in order to understand various aspects of evolutionary dynamics. As with the… (More)

- Emmanuel Tannenbaum, Eric J Deeds, Eugene I Shakhnovich
- Physical review. E, Statistical, nonlinear, and…
- 2004

This paper extends Eigen's quasispecies equations to account for the semiconservative nature of DNA replication. We solve the equations in the limit of infinite sequence length for the simplest case of a static, sharply peaked fitness landscape. We show that the error catastrophe occurs when micro, the product of sequence length and per base pair mismatch… (More)

- Emmanuel Tannenbaum, Eugene I Shakhnovich
- Physical review. E, Statistical, nonlinear, and…
- 2004

This paper develops a two-gene, single fitness peak model for determining the equilibrium distribution of genotypes in a unicellular population which is capable of genetic damage repair. The first gene, denoted by sigma(via), yields a viable organism with first-order growth rate constant k>1 if it is equal to some target "master" sequence sigma(via,0). The… (More)

- Nikhil Gandhi, Gonen Ashkenasy, Emmanuel Tannenbaum
- Journal of theoretical biology
- 2007

It has been recently suggested that there are likely generic features characterizing the emergence of systems constructed from the self-organization of self-replicating agents acting under one or more selection pressures. Therefore, structures and behaviors at one length scale may be used to infer analogous structures and behaviors at other length scales.… (More)

- Nathaniel Wagner, Emmanuel Tannenbaum, Gonen Ashkenasy
- Physical review letters
- 2010

The quasispecies model describes processes related to the origin of life and viral evolutionary dynamics. We discuss how the error catastrophe that reflects the transition from localized to delocalized quasispecies population is affected by catalytic replication of different reaction orders. Specifically, we find that second order mechanisms lead to a… (More)

- Emmanuel Tannenbaum
- Physical review. E, Statistical, nonlinear, and…
- 2006

This paper develops a quasispecies model where cells can adopt a two-cell survival strategy. Within this strategy, pairs of cells join together, at which point one of the cells sacrifices its own replicative ability for the sake of the other cell. We develop a simplified model for the evolutionary dynamics of this process, allowing us to solve for the… (More)