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# Publications

# Preprints

[1] | C. Kirisits. Total variation denoising on hexagonal grids. Preprint on ArXiv arXiv:1204.3855, University of Vienna, Austria, 2012. [preprint] |

[2] | G. Bal, W. Naetar, O. Scherzer, and J. Schotland. The Levenberg-Marquardt Iteration for Numerical Inversion of the Power Density Operator. J. Inverse Ill-Posed Probl., feb 2013. [http | preprint] |

[3] | C. Kirisits, L. F. Lang, and O. Scherzer. Optical Flow on Evolving Surfaces with an Application to the Analysis of 4D Microscopy Data. In A. Kuijper, editor, SSVM'13: Proceedings of the fourth International Conference on Scale Space and Variational Methods in Computer Vision, volume 7893 of Lecture Notes in Computer Science, pages 246-257, Berlin, Heidelberg, 2013. Springer-Verlag. [http | preprint] |

[4] | Wolfgang Dvořák, Monika Henzinger, and David P. Williamson. Maximizing a Submodular Function with Viability Constraints. In ESA 2013: Proceedings of the 21st European Symposium on Algorithms, Lecture Notes in Computer Science, pages 409-420. Springer Berlin Heidelberg. [http | eprint] |

[5] | C. Kirisits, L. F. Lang, and O. Scherzer. Optical Flow on Evolving Surfaces with Space and Time Regularisation. J. Math. Imaging Vision, 52(1):55--70, 2015. [http | preprint] |

[6] | C. Kirisits, L. F. Lang, and O. Scherzer. Decomposition of optical flow on the sphere. GEM - International Journal on Geomathematics, volume 5, issue 1, pages 117-141, 2014. [http | preprint] |

[7] | M. Kucharík, I. L. Hofacker, P. F. Stadler, and J. Qin. Basin Hopping Graph: A computational framework to characterize RNA folding landscapes, Bioinformatics, 2014. [http] |

[8] | O. Chernomor, B.Q. Minh, F. Forest, S. Klaere, T. Ingram, M. Henzinger, and A. von Haeseler. Split Diversity in Constrained Conservation Prioritization using Integer Programming, 2014, accepted for publication in Methods in Ecology and Evolution. |

[9] | O. Chernomor, A. von Haeseler, and B.Q. Minh, Terrace Aware Phylogenomic Inference from Supermatrices, 2014, submitted. |

[10] | O. Chernomor, S. Klaere, A. von Haeseler, and B.Q. Minh, Split diversity: measuring and optimizing biodiversity using phylogenetic split networks. Biodiversity Conservation and Phylogenetic Systematics (eds R. Pellens & P. Grandcolas). Springer, 2014, in press. |

[11] | M. Bauer, M. Grasmair, and C. Kirisits. Optical flow on moving manifolds. SIAM J. Imaging Sciences, 8(1):484--512, 2015. [http | preprint] |

[12] | C. Kirisits, C. Pöschl, E. Resmerita, and O. Scherzer. Finite dimensional approximation of convex regularization via hexagonal pixel grids. Technical report, University of Vienna, Austria, 2014. Accepted in Appl. Anal. |

[13] | O. Scherzer and C. Kirisits. Convex variational regularization methods for inverse problems. In P. Bühlmann, T. Cai, A. Munk, and B. Yu, editors, Frontiers in Nonparametric Statistics, volume 14 of Oberwolfach reports, pages 43–45. EMS Publishing House, 2012. |

[14] | M. Mann, M. Kucharík, C. Flamm, and M.T. Wolfinger. Memory-efficient RNA energy landscape exploration. Bioinformatics, 2014. [http] |

[15] | C. Leitold and C. Dellago. Folding mechanism of a polymer chain with short-range attractions. Journal of Chemical Physics 141, 134901, 2014. [http] |

[16] | W. Naetar and O. Scherzer. Quantitative Photoacoustic Tomography with Piecewise Constant Material Parameters, SIAM J. Imaging Sci., 7(3), 1755–1774, 2014. [http | preprint] |

[17] | T. Flouri, F. Izquierdo-Carrasco, D. Darriba, A.J. Aberer, L-T. Nguyen, B.Q. Minh, A. von Haeseler, and A. Stamatakis. The phylogenetic likelihood library. Syst. Biol., 2014, in press. |

[18] | L.-T. Nguyen, H.A. Schmidt, A. von Haeseler, and B.Q. Minh. IQ-TREE: A fast and effective stochastic algorithm for estimating maximum likelihood phylogenies. Mol. Biol. Evol., 2014, in press. |

[19] | C. Leitold, W. Lechner, and C. Dellago. A string reaction coordinate for the folding of a polymer chain. J. Phys. Condens. Matter 27, 194126, 2015. [http] |

[20] | L. F. Lang, and O. Scherzer. Optical Flow on Evolving Sphere-Like Surfaces. Preprint on ArXiv arXiv:1506.03358, University of Vienna, Austria, 2015. [preprint] |