Publications related to 'dynamic programming'
 
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Article (Journal)
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Charles Choy, Jesper Jansson, Kunihiko Sadakane and Wing-Kin Sung. Computing the maximum agreement of phylogenetic networks. In TCS, Vol. 335(1):93-107, 2005.  
Keywords: dynamic programming, FPT, level k phylogenetic network, MASN, NP complete, phylogenetic network, phylogeny.
Note: http://www.df.lth.se/~jj/Publications/masn8_TCS2005.pdf.
       
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Lawrence A. David and Eric J. Alm. Rapid evolutionary innovation during an Archaean genetic expansion. In Nature, Vol. 469:93-96, 2011.  
Keywords: duplication, dynamic programming, from multilabeled tree, from rooted trees, from species tree, parsimony, phylogenetic network, phylogeny, Program Angst.
Note: http://dx.doi.org/10.1038/nature09649, Program Angst described here.
       

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Bui Quang Minh, Fabio Pardi, Steffen Klaere and Arndt von Haeseler. Budgeted Phylogenetic Diversity on Circular Split Systems. In TCBB, Vol. 6(1):22-29, 2009.  
Keywords: abstract network, circular split system, dynamic programming, from network, phylogenetic network, polynomial, split, split network.
Note: http://dx.doi.org/10.1109/TCBB.2008.54.
       
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Lavanya Kannan and Ward C Wheeler. Maximum Parsimony on Phylogenetic Networks. In ALMOB, Vol. 7:9, 2012.  
Keywords: dynamic programming, explicit network, from sequences, heuristic, parsimony, phylogenetic network, phylogeny.
Note: http://dx.doi.org/10.1186/1748-7188-7-9.
       
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InProceedings
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Charles Choy, Jesper Jansson, Kunihiko Sadakane and Wing-Kin Sung. Computing the maximum agreement of phylogenetic networks. In Proceedings of Computing: the Tenth Australasian Theory Symposium (CATS'04), Vol. 91:134-147 of Electronic Notes in Theoretical Computer Science, 2004.  
Keywords: dynamic programming, FPT, level k phylogenetic network, MASN, NP complete, phylogenetic network, phylogeny.
Note: http://www.df.lth.se/~jj/Publications/masn6_CATS2004.pdf.
       
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Jesper Jansson and Wing-Kin Sung. The Maximum Agreement of Two Nested Phylogenetic Networks. In ISAAC04, Vol. 3341:581-593 of LNCS, springer, 2005.  
Keywords: dynamic programming, MASN, nested network, NP complete, phylogenetic network, phylogeny, polynomial.
Note: http://www.df.lth.se/~jj/Publications/nested7_ISAAC2004.pdf.
       

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Jean-Philippe Doyon, Celine Scornavacca, Konstantin Yu Gorbunov, Gergely J. Szöllösi, Vincent Ranwez and Vincent Berry. An efficient algorithm for gene/species trees parsimonious reconciliation with losses, duplications, and transfers. In Proceedings of the Eighth RECOMB Comparative Genomics Satellite Workshop (RECOMB-CG'10), Vol. 6398:93-108 of LNCS, springer, 2011.  
Keywords: branch length, duplication, dynamic programming, explicit network, from multilabeled tree, from species tree, from unrooted trees, lateral gene transfer, loss, phylogenetic network, phylogeny, polynomial, Program Mowgli, reconstruction.
Note: http://www.lirmm.fr/~vberry/Publis/MPR-DoyonEtAl.pdf, software available at http://www.atgc-montpellier.fr/MPR/.
       
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Louxin Zhang, Yen Kaow Ng, Taoyang Wu and Yu Zheng. Network model and efficient method for detecting relative duplications or horizontal gene transfers. In ICCABS11, Pages 214-219, 2011.  
Keywords: dynamic programming, explicit network, from network, from rooted trees, from species tree, phylogenetic network, phylogeny, polynomial, reconstruction.
       
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Jittat Fakcharoenphol, Tanee Kumpijit and Attakorn Putwattana. A Faster Algorithm for the Tree Containment Problem for Binary Nearly Stable Phylogenetic Networks. In Proceedings of the The 12th International Joint Conference on Computer Science and Software Engineering (JCSSE'15), Pages 337-342, IEEE, 2015.  
Keywords: dynamic programming, explicit network, from network, from rooted trees, nearly-stable network, phylogenetic network, phylogeny, polynomial, tree containment.
       

InBook
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Jesper Jansson and Wing-Kin Sung. The Maximum Agreement of Two Nested Phylogenetic Networks. In Oleg N. Terikhovsky and William N. Burton editors, New Topics in Theoretical Computer Science, Pages 119-141, Nova Publishers, 2008.  
Keywords: dynamic programming, MASN, nested network, phylogenetic network, phylogeny, polynomial.
Note: http://www.df.lth.se/~jj/Publications/nested12_NTTCS2008_corrected.pdf.
       

MastersThesis
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Julia Matsieva. A Static Formulation of the History Bound Problem. Master's thesis, UC Davis, 2014.  
Keywords: bound, dynamic programming, explicit network, from binary characters, from clusters, phylogenetic network, phylogeny, polynomial.
Note: https://escholarship.org/uc/item/3741t064.
       

PhdThesis
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Ali Tofigh. Using Trees to Capture Reticulate Evolution, Lateral Gene Transfers and Cancer Progression. PhD thesis, KTH Royal Institute of Technology, Sweden, 2009.  
Keywords: duplication, dynamic programming, from multilabeled tree, from rooted trees, from species tree, lateral gene transfer, loss, NP complete, phylogenetic network, phylogeny, reconstruction.
Note: http://kth.diva-portal.org/smash/record.jsf?pid=diva2:220830&searchId=1.