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- Alexander Yu. Mitrophanov, Mark Borodovsky
- Briefings in Bioinformatics
- 2006

One of the major goals of computational sequence analysis is to find sequence similarities, which could serve as evidence of structural and functional conservation, as well as of evolutionary relations among the sequences. Since the degree of similarity is usually assessed by the sequence alignment score, it is necessary to know if a score is high enough to… (More)

- Alexander Y Mitrophanov, Gordon Churchward, Mark Borodovsky
- Journal of theoretical biology
- 2007

The CovR/S system in Streptococcus pyogenes (Group A Streptococcus, or GAS), a two-component signal transduction/transcription regulation system, controls the expression of major virulence factors. The presence of a negative feedback loop distinguishes the CovR/S system from the majority of bacterial two-component systems. We developed a deterministic model… (More)

For the distribution of a finite, homogeneous, continuous-time Markov chain, we derive perturbation bounds in terms of the ergodicity coefficient of the transition probability matrix. Our perturbation bounds improve upon the known results. We give sensitivity bounds for the coefficient of ergodicity, providing a sufficient condition for the uniqueness of… (More)

- Alexander Y Mitrophanov, Mark Borodovsky
- Mathematical biosciences
- 2007

The TKF91 model of biological sequence evolution describes changes in the sequence length via an infinite state-space birth-death process, which we term the TKF91-BD process. The TKF91 model assumes that, for any pair of modern sequences, the ancestral sequence has equilibrium length distribution, an assumption whose validity has not been rigorously… (More)

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