Reconstructing gene trees from Fitch’s xenology relation

[1]  Marc Hellmuth,et al.  Generalized Fitch Graphs: Edge-labeled Graphs that are explained by Edge-labeled Trees , 2018, Discret. Appl. Math..

[2]  Peter F. Stadler,et al.  A Short Note on Undirected Fitch Graphs , 2017, Art Discret. Appl. Math..

[3]  Daniel Merkle,et al.  Partial Homology Relations - Satisfiability in Terms of Di-Cographs , 2017, COCOON.

[4]  Marc Hellmuth,et al.  The matroid structure of representative triple sets and triple-closure computation , 2017, Eur. J. Comb..

[5]  Nicolas Wieseke,et al.  On tree representations of relations and graphs: symbolic ultrametrics and cograph edge decompositions , 2015, J. Comb. Optim..

[6]  Jeroniza Nunes Marchaukoski,et al.  New Tools in Orthology Analysis: A Brief Review of Promising Perspectives , 2017, Front. Genet..

[7]  E. Danchin,et al.  Alienness: Rapid Detection of Candidate Horizontal Gene Transfers across the Tree of Life , 2017, Genes.

[8]  Marc Hellmuth,et al.  Biologically feasible gene trees, reconciliation maps and informative triples , 2017, Algorithms for Molecular Biology.

[9]  Daniel Merkle,et al.  Forbidden Time Travel: Characterization of Time-Consistent Tree Reconciliation Maps , 2017, WABI.

[10]  Peter F. Stadler,et al.  The mathematics of xenology: di-cographs, symbolic ultrametrics, 2-structures and tree-representable systems of binary relations , 2016, Journal of Mathematical Biology.

[11]  David Fernández-Baca,et al.  Fast Compatibility Testing for Rooted Phylogenetic Trees , 2015, Algorithmica.

[12]  Riccardo Dondi,et al.  Orthology Correction for Gene Tree Reconstruction: Theoretical and Experimental Results , 2017, ICCS.

[13]  Mike A. Steel,et al.  Phylogeny - discrete and random processes in evolution , 2016, CBMS-NSF regional conference series in applied mathematics.

[14]  Riccardo Dondi,et al.  Correction of Weighted Orthology and Paralogy Relations - Complexity and Algorithmic Results , 2016, WABI.

[15]  Riccardo Dondi,et al.  The link between orthology relations and gene trees: a correction perspective , 2016, Algorithms for Molecular Biology.

[16]  Adrian M. Altenhoff,et al.  Standardized benchmarking in the quest for orthologs , 2016, Nature Methods.

[17]  Nicolas Wieseke,et al.  From Sequence Data Including Orthologs, Paralogs, and Xenologs to Gene and Species Trees , 2016 .

[18]  Nadia El-Mabrouk,et al.  Orthology Relation and Gene Tree Correction: Complexity Results , 2015, WABI.

[19]  Christophe Dessimoz,et al.  Inferring Horizontal Gene Transfer , 2015, PLoS Comput. Biol..

[20]  Martin Middendorf,et al.  Phylogenomics with paralogs , 2015, Proceedings of the National Academy of Sciences.

[21]  Nadia El-Mabrouk,et al.  Orthology and paralogy constraints: satisfiability and consistency , 2014, BMC Genomics.

[22]  Krister M. Swenson,et al.  Gene tree correction guided by orthology , 2013, BMC Bioinformatics.

[23]  E. Koonin,et al.  Functional and evolutionary implications of gene orthology , 2013, Nature Reviews Genetics.

[24]  Katharina T. Huber,et al.  Orthology relations, symbolic ultrametrics, and cographs , 2013, Journal of mathematical biology.

[25]  Katharina T. Huber,et al.  From event-labeled gene trees to species trees , 2012, BMC Bioinformatics.

[26]  Mike Steel,et al.  Closure operations in phylogenetics. , 2007, Mathematical biosciences.

[27]  Ross M. McConnell,et al.  Linear-time modular decomposition of directed graphs , 2005, Discret. Appl. Math..

[28]  E. Koonin.  Orthologs, paralogs, and evolutionary genomics. , 2005, Annual review of genetics.

[29]  Mikhail S. Gelfand,et al.  Genome-Wide Molecular Clock and Horizontal Gene Transfer in Bacterial Evolution , 2004, Journal of bacteriology.

[30]  Kunihiko Sadakane,et al.  Rooted Maximum Agreement Supertrees , 2004, Algorithmica.

[31]  Christophe Paul,et al.  Fully dynamic recognition algorithm and certificate for directed cographs , 2004, Graph-Theoretic Concepts in Computer Science.

[32]  R. Jensen.  Orthologs and paralogs - we need to get it right , 2001, Genome Biology.

[33]  Mikkel Thorup,et al.  Poly-logarithmic deterministic fully-dynamic algorithms for connectivity, minimum spanning tree, 2-edge, and biconnectivity , 2001, JACM.

[34]  W. Fitch.  Homology a personal view on some of the problems. , 2000, Trends in genetics : TIG.

[35]  Andreas W. M. Dress,et al.  Recovering Symbolically Dated, Rooted Trees from Symbolic Ultrametrics , 1998 .

[36]  D. Bryant.  Building trees, hunting for trees, and comparing trees : theory and methods in phylogenetic analysis , 1997 .

[37]  Leizhen Cai,et al.  Fixed-Parameter Tractability of Graph Modification Problems for Hereditary Properties , 1996, Inf. Process. Lett..

[38]  Tandy J. Warnow,et al.  Constructing a Tree from Homeomorphic Subtrees, with Applications to Computational Evolutionary Biology , 1996, SODA '96.

[39]  M. Steel,et al.  Extension Operations on Sets of Leaf-Labeled Trees , 1995 .

[40]  Andrzej Ehrenfeucht,et al.  Primitivity is Hereditary for 2-Structures , 1990, Theor. Comput. Sci..

[41]  F. Radermacher,et al.  Substitution Decomposition for Discrete Structures and Connections with Combinatorial Optimization , 1984 .

[42]  Alfred V. Aho,et al.  Inferring a Tree from Lowest Common Ancestors with an Application to the Optimization of Relational Expressions , 1981, SIAM J. Comput..

[43]  John M. Lewis,et al.  The Node-Deletion Problem for Hereditary Properties is NP-Complete , 1980, J. Comput. Syst. Sci..

[44]  Mihalis Yannakakis,et al.  Node-and edge-deletion NP-complete problems , 1978, STOC.

[45]  W. Fitch.  Distinguishing homologous from analogous proteins. , 1970, Systematic zoology.