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Jager S, Schiller B, Babel P, et al. StreAM-[Formula: see text]: algorithms for analyzing coarse grained RNA dynamics based on Markov models of connectivity-graphs. Algorithms Mol Biol. 2017;12:15doi: 10.1186/s13015-017-0105-0.
Jager, S., Schiller, B., Babel, P., Blumenroth, M., Strufe, T., & Hamacher, K. (2017). StreAM-[Formula: see text]: algorithms for analyzing coarse grained RNA dynamics based on Markov models of connectivity-graphs. Algorithms for molecular biology : AMB, 1215. https://doi.org/10.1186/s13015-017-0105-0
Jager, Sven, et al. "StreAM-[Formula: see text]: algorithms for analyzing coarse grained RNA dynamics based on Markov models of connectivity-graphs." Algorithms for molecular biology : AMB vol. 12 (2017): 15. doi: https://doi.org/10.1186/s13015-017-0105-0
Jager S, Schiller B, Babel P, Blumenroth M, Strufe T, Hamacher K. StreAM-[Formula: see text]: algorithms for analyzing coarse grained RNA dynamics based on Markov models of connectivity-graphs. Algorithms Mol Biol. 2017 May 30;12:15. doi: 10.1186/s13015-017-0105-0. eCollection 2017. PMID: 28572834; PMCID: PMC5450175.
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Algorithms Mol Biol. 2017 May 30;12:15. doi: 10.1186/s13015-017-0105-0. eCollection 2017.

StreAM-[Formula: see text]: algorithms for analyzing coarse grained RNA dynamics based on Markov models of connectivity-graphs.

Algorithms for molecular biology : AMB

Sven Jager, Benjamin Schiller, Philipp Babel, Malte Blumenroth, Thorsten Strufe, Kay Hamacher

Affiliations

  1. Department of Biology, TU Darmstadt, Schnittspahnstr. 2, 64283 Darmstadt, Germany.
  2. Department of Computer Science, TU Dresden, Nöthnitzer Str. 46, 01187 Dresden, Germany.
  3. Department of Biology, Department of Computer Science, Department of Physics, TU Darmstadt, Schnittspahnstr. 2, 64283 Darmstadt, Germany.

PMID: 28572834 PMCID: PMC5450175 DOI: 10.1186/s13015-017-0105-0

Abstract

BACKGROUND: In this work, we present a new coarse grained representation of RNA dynamics. It is based on adjacency matrices and their interactions patterns obtained from molecular dynamics simulations. RNA molecules are well-suited for this representation due to their composition which is mainly modular and assessable by the secondary structure alone. These interactions can be represented as adjacency matrices of

RESULTS: We benchmark

CONCLUSIONS: The proposed algorithm performs well on large simulated as well as real world dynamic graphs. Additionally,

Keywords: Coarse graining; Dynamic graphs; Markovian dynamics; Molecular dynamics; RNA; Synthetic biology

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