Zobrazeno 1 - 10
of 81
pro vyhledávání: '"Marc Hellmuth"'
Autor:
David Schaller, Tom Hartmann, Manuel Lafond, Peter F. Stadler, Nicolas Wieseke, Marc Hellmuth
Publikováno v:
Algorithms for Molecular Biology, Vol 18, Iss 1, Pp 1-43 (2023)
Abstract Background Evolutionary scenarios describing the evolution of a family of genes within a collection of species comprise the mapping of the vertices of a gene tree T to vertices and edges of a species tree S. The relative timing of the last c
Externí odkaz:
https://doaj.org/article/fc59eef7fb02402f8207917ae7fe7ca0
Publikováno v:
Algorithms for Molecular Biology, Vol 16, Iss 1, Pp 1-11 (2021)
Abstract Background The supertree problem, i.e., the task of finding a common refinement of a set of rooted trees is an important topic in mathematical phylogenetics. The special case of a common leaf set L is known to be solvable in linear time. Exi
Externí odkaz:
https://doaj.org/article/5692243f534442f0bfa8da57f643a766
Publikováno v:
Algorithms for Molecular Biology, Vol 16, Iss 1, Pp 1-32 (2021)
Abstract Background Best match graphs (BMGs) are a class of colored digraphs that naturally appear in mathematical phylogenetics as a representation of the pairwise most closely related genes among multiple species. An arc connects a gene x with a ge
Externí odkaz:
https://doaj.org/article/0691ed3cc2fd411eb070e18cd3e69ee2
Autor:
Manuel Lafond, Marc Hellmuth
Publikováno v:
Algorithms for Molecular Biology, Vol 15, Iss 1, Pp 1-27 (2020)
Abstract Background The history of gene families—which are equivalent to event-labeled gene trees—can to some extent be reconstructed from empirically estimated evolutionary event-relations containing pairs of orthologous, paralogous or xenologou
Externí odkaz:
https://doaj.org/article/9ee33f831f9a47c6b8acb6d7964ccd01
Autor:
Peter F. Stadler, Manuela Geiß, David Schaller, Alitzel López Sánchez, Marcos González Laffitte, Dulce I. Valdivia, Marc Hellmuth, Maribel Hernández Rosales
Publikováno v:
Algorithms for Molecular Biology, Vol 15, Iss 1, Pp 1-20 (2020)
Abstract Background Many of the commonly used methods for orthology detection start from mutually most similar pairs of genes (reciprocal best hits) as an approximation for evolutionary most closely related pairs of genes (reciprocal best matches). T
Externí odkaz:
https://doaj.org/article/b2d7a667623a4363a60d45f12cc82c93
Publikováno v:
Discrete Mathematics & Theoretical Computer Science, Vol vol. 23 no. 1, Iss Graph Theory (2021)
Binary relations derived from labeled rooted trees play an import role in mathematical biology as formal models of evolutionary relationships. The (symmetrized) Fitch relation formalizes xenology as the pairs of genes separated by at least one horizo
Externí odkaz:
https://doaj.org/article/8f8235d4f4704389950d40c3474fde25
Autor:
Nikolai Nøjgaard, Manuela Geiß, Daniel Merkle, Peter F. Stadler, Nicolas Wieseke, Marc Hellmuth
Publikováno v:
Algorithms for Molecular Biology, Vol 13, Iss 1, Pp 1-17 (2018)
Abstract Background In the absence of horizontal gene transfer it is possible to reconstruct the history of gene families from empirically determined orthology relations, which are equivalent to event-labeled gene trees. Knowledge of the event labels
Externí odkaz:
https://doaj.org/article/4d253f1ee17e4042964f8fae543eaa7b
Autor:
Marc Hellmuth
Publikováno v:
Algorithms for Molecular Biology, Vol 12, Iss 1, Pp 1-16 (2017)
Abstract Background The history of gene families—which are equivalent to event-labeled gene trees—can be reconstructed from empirically estimated evolutionary event-relations containing pairs of orthologous, paralogous or xenologous genes. The qu
Externí odkaz:
https://doaj.org/article/1b18b024f9d94e7ba6ad36ed6b3eff02
Autor:
Richa Batra, Nicolas Alcaraz, Kevin Gitzhofer, Josch Pauling, Henrik J. Ditzel, Marc Hellmuth, Jan Baumbach, Markus List
Publikováno v:
npj Systems Biology and Applications, Vol 3, Iss 1, Pp 1-8 (2017)
Computational biology: Evaluation of network-based pathway enrichment tools De novo pathway enrichment methods are essential to understand disease complexity. They can uncover disease-specific functional modules by integrating molecular interaction n
Externí odkaz:
https://doaj.org/article/d4aeb2316347474c8564b07783489ae1
Publikováno v:
Algorithms, Vol 14, Iss 4, p 110 (2021)
Best match graphs (BMGs) are vertex-colored digraphs that naturally arise in mathematical phylogenetics to formalize the notion of evolutionary closest genes w.r.t. an a priori unknown phylogenetic tree. BMGs are explained by unique least resolved tr
Externí odkaz:
https://doaj.org/article/fc5d03c86c154bbb99a6c45abe1b163e