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Start Over Descriptor "05C62" Publisher springer berlin heidelberg
17 results on '"05C62"'

5. On the Computational Complexity of Degenerate Unit Distance Representations of Graphs

Author

Horvat, Boris, Kratochvíl, Jan, Pisanski, Tomaž, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Sudan, Madhu, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Vardi, Moshe Y., Series editor, Weikum, Gerhard, Series editor, Iliopoulos, Costas S., editor, and Smyth, William F., editor

Published
2011
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6. Approximating the Crossing Number of Toroidal Graphs

Author

Hliněný, Petr, Salazar, Gelasio, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Doug, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, and Tokuyama, Takeshi, editor

Published
2007
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10. Best match graphs and reconciliation of gene trees with species trees

Author

Maribel Hernández Rosales, Peter F. Stadler, Manuela Geiß, Dulce I. Valdivia, Marcos González Laffitte, Alitzel López Sánchez, and Marc Hellmuth

Subjects
FOS: Computer and information sciences, Colored digraph, Theoretical computer science, Discrete Mathematics (cs.DM), Gene Transfer, Horizontal, Computer science, Genetic Speciation, 0206 medical engineering, Phylogenetic combinatorics, 02 engineering and technology, Article, Evolution, Molecular, 03 medical and health sciences, 05C05, Orthology, Gene Duplication, 92B10, Computer Graphics, Cograph, Computer Simulation, 05C62, Quantitative Biology - Populations and Evolution, Phylogeny, 030304 developmental biology, 0303 health sciences, Models, Genetic, Applied Mathematics, Populations and Evolution (q-bio.PE), Computational Biology, Horizontal gene transfer, Mathematical Concepts, Agricultural and Biological Sciences (miscellaneous), Graph, FOS: Biological sciences, Modeling and Simulation, 020602 bioinformatics, Reciprocal, Algorithms, Gene Deletion, Intuition, Computer Science - Discrete Mathematics
Abstract

A wide variety of problems in computational biology, most notably the assessment of orthology, are solved with the help of reciprocal best matches. Using an evolutionary definition of best matches that captures the intuition behind the concept we clarify rigorously the relationships between reciprocal best matches, orthology, and evolutionary events under the assumption of duplication/loss scenarios. We show that the orthology graph is a subgraph of the reciprocal best match graph (RBMG). We furthermore give conditions under which an RBMG that is a cograph identifies the correct orthlogy relation. Using computer simulations we find that most false positive orthology assignments can be identified as so-called good quartets—and thus corrected—in the absence of horizontal transfer. Horizontal transfer, however, may introduce also false-negative orthology assignments. Electronic supplementary material The online version of this article (10.1007/s00285-020-01469-y) contains supplementary material, which is available to authorized users.

Published
2020

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