Publications of Year 2010  
Article (Journal)
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Gabriel Cardona, Mercè Llabrés and Francesc Rosselló. Two Results on Distances for Phylogenetic Networks. In Advances in Intelligent and Soft Computing, Vol. 74:93-100, 2010.  
Keywords: distance between networks, explicit network, phylogenetic network, phylogeny, tree sibling network.
Note: http://www.merilibrary.com/books/bioinformatics/advances%20in%20bioinformatics.pdf#page=103.
       

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Zhi-Zhong Chen and Lusheng Wang. HybridNET: a tool for constructing hybridization networks. In BIO, Vol. 26(22):2912-2913, 2010.  
Keywords: agreement forest, FPT, from rooted trees, hybridization, phylogenetic network, phylogeny, Program HybridNET, software.
Note: http://rnc.r.dendai.ac.jp/~chen/papers/note2.pdf.
       
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Robert G. Beiko. Gene sharing and genome evolution: networks in trees and trees in networks. In Biology and Philosophy, Vol. 25(4):659-673, 2010.  
Keywords: abstract network, explicit network, from rooted trees, galled network, phylogenetic network, phylogeny, Program Dendroscope, Program SplitsTree, reconstruction, split network, survey.
Note: http://dx.doi.org/10.1007/s10539-010-9217-3.
       
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Joel Velasco and Elliott Sober. Testing for Treeness: Lateral Gene Transfer, Phylogenetic Inference, and Model Selection. In Biology and Philosophy, Vol. 25(4):675-687, 2010.  
Keywords: explicit network, model selection, phylogenetic network, phylogeny, reconstruction, statistical model.
Note: http://joelvelasco.net/Papers/velascosober-testingfortreeness.pdf.
       
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Leo van Iersel, Charles Semple and Mike Steel. Quantifying the Extent of Lateral Gene Transfer Required to Avert a 'Genome of Eden'. In BMB, Vol. 72:1783–1798, 2010.  
Note: http://www.win.tue.nl/~liersel/LGT.pdf.
       
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Stephen J. Willson. Properties of normal phylogenetic networks. In BMB, Vol. 72(2):340-358, 2010.  
Keywords: normal network, phylogenetic network, phylogeny, regular network.
Note: http://www.public.iastate.edu/~swillson/RestrictionsOnNetworkspap9.pdf, slides available at http://www.newton.cam.ac.uk/webseminars/pg+ws/2007/plg/plgw01/0904/willson/.
       
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7
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Miguel Arenas, Mateus Patricio, David Posada and Gabriel Valiente. Characterization of Phylogenetic Networks with NetTest. In BMCB, Vol. 11:268, 2010.  
Keywords: explicit network, galled tree, phylogenetic network, Program NetTest, software, time consistent network, tree child network, tree sibling network, visualization.
Note: http://dx.doi.org/10.1186/1471-2105-11-268, software available at http://darwin.uvigo.es/software/nettest/.
       
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8
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Sophie Abby, Eric Tannier, Manolo Gouy and Vincent Daubin. Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests. In BMCB, Vol. 11:324, 2010.  
Keywords: explicit network, from rooted trees, from species tree, heuristic, lateral gene transfer, phylogenetic network, phylogeny, Program EEEP, Program PhyloNet, Program Prunier, reconstruction, software.
Note: http://www.biomedcentral.com/1471-2105/11/324.
       
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9
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Hyun Jung Park, Guohua Jin and Luay Nakhleh. Bootstrap-based Support of HGT Inferred by Maximum Parsimony. In BMCEB, Vol. 10:131, 2010.  
Keywords: bootstrap, explicit network, from sequences, lateral gene transfer, parsimony, phylogenetic network, phylogeny, Program Nepal, reconstruction.
Note: http://dx.doi.org/10.1186/1471-2148-10-131.
       
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10
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Changiz Eslahchi, Mahnaz Habibi, Reza Hassanzadeh and Ehsan Mottaghi. MC-Net: a method for the construction of phylogenetic networks based on the Monte-Carlo method. In BMCEB, Vol. 10:254, 2010.  
Keywords: abstract network, circular split system, from distances, heuristic, phylogenetic network, Program MC-Net, Program SplitsTree, software, split, split network.
Note: http://dx.doi.org/10.1186/1471-2148-10-254.
       
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Pawel Górecki. H-trees: a model of evolutionary scenario with horizontal gene transfer. In Fundamenta Informaticae, Vol. 103:105-128, 2010.  
Keywords: duplication, lateral gene transfer, loss, phylogenetic network, phylogeny, uniqueness.
       

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Gabriel Cardona, Mercè Llabrés, Francesc Rosselló and Gabriel Valiente. Path lengths in tree-child time consistent hybridization networks. In Information Sciences, Vol. 180(3):366-383, 2010.  
Keywords: distance between networks, phylogenetic network, phylogeny, time consistent network, tree child network.
Note: http://arxiv.org/abs/0807.0087?context=cs.CE.
       
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Leo van Iersel, Charles Semple and Mike Steel. Locating a tree in a phylogenetic network. In IPL, Vol. 110(23), 2010.  
Keywords: cluster containment, explicit network, from network, level k phylogenetic network, normal network, NP complete, phylogenetic network, polynomial, regular network, time consistent network, tree child network, tree containment, tree sibling network.
Note: http://arxiv.org/abs/1006.3122.
       
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Johannes Fischer and Daniel H. Huson. New Common Ancestor Problems in Trees and Directed Acyclic Graphs. In IPL, Vol. 110(8-9):331-335, 2010.  
Keywords: explicit network, phylogenetic network, polynomial.
Note: http://www-ab.informatik.uni-tuebingen.de/people/fischer/lsa.pdf.
       
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Sagi Snir and Edward Trifonov. A Novel Technique for Detecting Putative Horizontal Gene Transfer in the Sequence Space. In JCB, Vol. 17(11):1535-1548, 2010.  
Keywords: from sequences, phylogenetic network, phylogeny, reconstruction.
Note: http://research.haifa.ac.il/~ssagi/published%20papers/JCB-HGT.pdf.
       
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16
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Fumei Lam, Ryan Tarpine and Sorin Istrail. The Imperfect Ancestral Recombination Graph Reconstruction Problem: Upper Bounds for Recombination and Homoplasy. In JCB, Vol. 17(6), 2010.  
Keywords: explicit network, from sequences, heuristic, phylogenetic network, phylogeny, reconstruction.
Note: http://www.cs.brown.edu/~sorin/pdfs/Lam%20the%20imperfect.pdf.
       

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Frederick A. Matsen. ConstNJ: an algorithm to reconstruct sets of phylogenetic trees satisfying pairwise topological constraints. In JCB, Vol. 17(6):799-818, 2010.  
Keywords: from distances, Program constNJ, reconstruction.
Note: http://arxiv.org/abs/0901.1598v2.
       
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Simone Linz, Charles Semple and Tanja Stadler. Analyzing and reconstructing reticulation networks under timing constraints. In JOMB, Vol. 61(5):715-737, 2010.  
Keywords: explicit network, from rooted trees, hybridization, lateral gene transfer, NP complete, phylogenetic network, phylogeny, reconstruction, time consistent network.
Note: http://dx.doi.org/10.1007/s00285-009-0319-y..
       
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19
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Jaroslaw Byrka, Pawel Gawrychowski, Katharina Huber and Steven Kelk. Worst-case optimal approximation algorithms for maximizing triplet consistency within phylogenetic networks. In Journal of Discrete Algorithms, Vol. 8(1):65-75, 2010.  
Keywords: approximation, explicit network, from triplets, galled tree, level k phylogenetic network, phylogenetic network, phylogeny, reconstruction.
Note: http://arxiv.org/abs/0710.3258.
       
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David A. Morrison. Using data-display networks for exploratory data analysis in phylogenetic studies. In MBE, Vol. 27(5):1044-1057, 2010.  
Keywords: abstract network, hybridization, NeighborNet, Program SplitsTree, recombination, split decomposition.
Note: http://dx.doi.org/10.1093/molbev/msp309.
       
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Gianluca Della Vedova, Riccardo Dondi, Tao Jiang, Giulio Pavesi, Yuri Pirola and Lusheng Wang. Beyond evolutionary trees. In Natural Computing, Vol. 9(2):421-435, 2010.  
Note: http://dx.doi.org/10.1007/s11047-009-9156-6.
       
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Marta Melé, Asif Javed, Marc Pybus, Francesc Calafell, Laxmi Parida, Jaume Bertranpetit and Genographic Consortium. A New Method to Reconstruct Recombination Events at a Genomic Scale. In PLoS Computational Biology, Vol. 6(11):e1001010, 2010.  
Keywords: explicit network, from sequences, phylogenetic network, phylogeny.
Note: http://dx.doi.org/10.1371/journal.pcbi.1001010.
       
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Erik W. Bloomquist and Marc A. Suchard. Unifying Vertical and Nonvertical Evolution: A Stochastic ARG-based Framework. In Systematic Biology, Vol. 59(1):27-41, 2010.  
Note: http://dx.doi.org/10.1093/sysbio/syp076.
       

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Alix Boc, Hervé Philippe and Vladimir Makarenkov. Inferring and Validating Horizontal Gene Transfer Events Using Bipartition Dissimilarity. In Systematic Biology, Vol. 59(2):195-211, 2010.  
Note: http://www.info2.uqam.ca/~makarenv/makarenv/Artcile_SB_2010.pdf.
       

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Luay Nakhleh. A Metric on the Space of Reduced Phylogenetic Networks. In TCBB, Vol. 7(2), 2010.  
Keywords: distance between networks, phylogenetic network, phylogeny.
Note: http://www.cs.rice.edu/~nakhleh/Papers/tcbb-Metric.pdf.
       
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Stephen J. Willson. Regular Networks Can Be Uniquely Constructed from Their Trees. In TCBB, Vol. 8(3):785-796, 2010.  
Keywords: explicit network, from rooted trees, phylogenetic network, phylogeny, reconstruction, regular network.
Note: http://www.public.iastate.edu/~swillson/RegularNetsFromTrees5.pdf.
       
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InProceedings
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Tetsuo Asano, Jesper Jansson, Kunihiko Sadakane, Ryuhei Uehara and Gabriel Valiente. Faster Computation of the Robinson-Foulds Distance between Phylogenetic Networks. In CPM10, Vol. 6129:190-201 of LNCS, springer, 2010.  
Keywords: distance between networks, explicit network, level k phylogenetic network, phylogenetic network, polynomial, spread.
Note: http://hdl.handle.net/10119/9859, slides available at http://cs.nyu.edu/parida/CPM2010/MainPage_files/18.pdf.
       
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28
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Hyun Jung Park, Guohua Jin and Luay Nakhleh. Algorithmic strategies for estimating the amount of reticulation from a collection of gene trees. In CSB10, 2010.  
Keywords: bound, from rooted trees, heuristic, phylogenetic network, phylogeny, reconstruction, SPR distance.
Note: http://www.cs.rice.edu/~nakhleh/Papers/ParkEtAl-CSB2010.pdf.
       

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Yufeng Wu and Jiayin Wang. Fast Computation of the Exact Hybridization Number of Two Phylogenetic Trees. In ISBRA10, Vol. 6053:203-214 of LNCS, springer, 2010.  
Keywords: agreement forest, explicit network, from rooted trees, hybridization, integer linear programming, minimum number, phylogenetic network, phylogeny, Program HybridNumber, Program SPRDist, SPR distance.
Note: http://www.engr.uconn.edu/~ywu/Papers/ISBRA10WuWang.pdf.
       
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Leo van Iersel, Steven Kelk, Regula Rupp and Daniel H. Huson. Phylogenetic Networks Do not Need to Be Complex: Using Fewer Reticulations to Represent Conflicting Clusters. In ISMB10, Vol. 26(12):i124-i131 of BIO, 2010.  
Keywords: from clusters, level k phylogenetic network, Program Dendroscope, Program HybridInterleave, Program HybridNumber, reconstruction.
Note: http://dx.doi.org/10.1093/bioinformatics/btq202, with proofs: http://arxiv.org/abs/0910.3082.
       
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Yufeng Wu. Close Lower and Upper Bounds for the Minimum Reticulate Network of Multiple Phylogenetic Trees. In ISMB10, Vol. 26(12):i140-i148 of BIO, 2010.  
Keywords: explicit network, from rooted trees, hybridization, minimum number, phylogenetic network, phylogeny, Program PIRN, software.
Note: http://dx.doi.org/10.1093/bioinformatics/btq198.
       
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Chris Whidden, Robert G. Beiko and Norbert Zeh. Fast FPT Algorithms for Computing Rooted Agreement Forests: Theory and Experiments. In Proceedings of the ninth International Symposium on Experimental Algorithms (SEA'10), Vol. 6049:141-153 of LNCS, springer, 2010.  
Keywords: agreement forest, explicit network, FPT, from rooted trees, hybridization, minimum number, phylogenetic network, phylogeny, Program HybridInterleave, reconstruction, SPR distance.
Note: https://www.cs.dal.ca/sites/default/files/technical_reports/CS-2010-03.pdf.
       
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InBook
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David A. Morrison. Phylogenetic networks in systematic biology (and elsewhere) In R.M. Mohan editor, Research Advances in Systematic Biology, Global Research Network, Trivandrum, India, 2010.  
Keywords: abstract network, explicit network, phylogenetic network, phylogeny, reconstruction, survey.
       

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Luay Nakhleh. Evolutionary phylogenetic networks: models and issues. In L. Heath and N. Ramakrishnan editors, The Problem Solving Handbook for Computational Biology and Bioinformatics, Springer, 2010.  
Keywords: phylogenetic network, phylogeny, survey.
Note: http://www.cs.rice.edu/~nakhleh/Papers/HeathRamakrishnanBookChapter.pdf.
       

PhdThesis
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Philippe Gambette. Méthodes combinatoires de reconstruction de réseaux phylogénétiques. PhD thesis, Université Montpellier 2, France, 2010.  
Keywords: abstract network, characterization, circular split system, explicit network, FPT, from clusters, from triplets, integer linear programming, level k phylogenetic network, NP complete, phylogenetic network, phylogeny, Program Dendroscope, pyramid, reconstruction, split network, weak hierarchy.
Note: http://tel.archives-ouvertes.fr/tel-00608342/en/.
       

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Cuong Than. Inference of parsimonious species phylogenies from multi-locus data. PhD thesis, Rice University, U.S.A., 2010.  
Keywords: explicit network, from sequences, parsimony, phylogenetic network, phylogeny, reconstruction.
Note: http://hdl.handle.net/1911/62177.
       

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Binh T. Nguyen. Novel Split-Based Approaches to Computing Phylogenetic Diversity and Planar Split Networks. PhD thesis, University of East Anglia, U.K., 2010.  
Keywords: abstract network, diversity, from splits, phylogenetic network, phylogeny, reconstruction, split, split network, visualization.
Note: https://ueaeprints.uea.ac.uk/id/eprint/34218.
       

Misc
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Gabriel Cardona, Mercè Llabrés and Francesc Rosselló. A metric for galled networks. 2010.  
Keywords: distance between networks, explicit network, from network, galled network, phylogenetic network, phylogeny.
Note: http://arxiv4.library.cornell.edu/abs/1009.0652.