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- Richard Münch, Karsten Hiller, +4 authors Dieter Jahn
- Nucleic Acids Research
- 2003

The database PRODORIC aims to systematically organize information on prokaryotic gene expression, and to integrate this information into regulatory networks. The present version focuses on pathogenic bacteria such as Pseudomonas aeruginosa. PRODORIC links data on environmental stimuli with trans-acting transcription factors, cis-acting promoter elements and… (More)

- Simone Linz, Charles Semple
- IEEE/ACM Transactions on Computational Biology…
- 2009

Reticulate evolution—the umbrella term for processes like hybridization, horizontal gene transfer, and recombination—plays an important role in the history of life of many species. Although the occurrence of such events is widely accepted, approaches to calculate the extent to which reticulation has influenced evolution are relatively rare. In… (More)

- Magnus Bordewich, Simone Linz, Katherine St. John, Charles Semple
- Evolutionary bioinformatics online
- 2007

Hybridization is an important evolutionary process for many groups of species. Thus, conflicting signals in a data set may not be the result of sampling or modeling errors, but due to the fact that hybridization has played a significant role in the evolutionary history of the species under consideration. Assuming that the initial set of gene trees is… (More)

- SIMONE LINZ
- 2009

Calculating the rooted subtree prune and regraft (rSPR) distance between two rooted binary phylogenetic trees is a frequently applied process in various areas of molecular evolution. However, computing this distance is an NP-hard problem and practical algorithms for computing it exactly are rare. In this paper, a divide-and-conquer approach to calculating… (More)

- Joshua Collins, Simone Linz, Charles Semple
- Journal of Computational Biology
- 2011

Recently, numerous practical and theoretical studies in evolutionary biology aim at calculating the extent to which reticulation-for example, horizontal gene transfer, hybridization, or recombination-has influenced the evolution for a set of present-day species. It has been shown that inferring the minimum number of hybridization events that is needed to… (More)

- Simone Linz, Achim Radtke, Arndt von Haeseler
- Molecular biology and evolution
- 2007

We suggest a likelihood-based approach to estimate an overall rate of horizontal gene transfer (HGT) in a simplified setting. To this end, we assume that the number of occurring HGT events within a given time interval follows a Poisson process. To obtain estimates for the rate of HGT, we simulate the distribution of tree topologies for different numbers of… (More)

- Steven Kelk, Leo van Iersel, Nela Lekic, Simone Linz, Céline Scornavacca, Leen Stougie
- SIAM J. Discrete Math.
- 2012

We show that the problem of computing the hybridization number of two rooted binary phylogenetic trees on the same set of taxa X has a constant factor polynomial-time approximation if and only if the problem of computing a minimum-size feedback vertex set in a directed graph (DFVS) has a constant factor polynomial-time approximation. The latter problem,… (More)

- Leo van Iersel, Simone Linz
- Inf. Process. Lett.
- 2013

It has recently been shown that the NP-hard problem of calculating the minimum number of hybridization events that is needed to explain a set of rooted binary phylogenetic trees by means of a hybridization network is fixed-parameter tractable if an instance of the problem consists of precisely two such trees. In this paper, we show that this problem remains… (More)

- Simone Linz, Charles Semple, Tanja Stadler
- Journal of mathematical biology
- 2010

Reticulation networks are now frequently used to model the history of life for various groups of species whose evolutionary past is likely to include reticulation events such as horizontal gene transfer or hybridization. However, the reconstructed networks are rarely guaranteed to be temporal. If a reticulation network is temporal, then it satisfies the two… (More)

- Simone Linz, Katherine St. John, Charles Semple
- SIAM J. Comput.
- 2013

Answering a problem posed by Nakhleh, we prove that counting the number of phylogenetic trees inferred by a (binary) phylogenetic network is #P-complete. An immediate consequence of this result is that counting the number of phylogenetic trees commonly inferred by two (binary) phylogenetic networks is also #P-complete. 1. Introduction. A fundamental problem… (More)