Publications of Year 2011  
Article (Journal)
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Shlomo Moran, Sagi Snir and Wing-Kin Sung. Partial Convex Recolorings of Trees and Galled Networks: Tight Upper and Lower bounds. In ACM Transactions on Algorithms, Vol. 7(4), 2011.  
Keywords: evaluation, galled tree, phylogenetic network.
Note: http://www.cs.technion.ac.il/~moran/r/PS/gnets-TOA-7Feb2007.pdf.
       
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Dan Levy and Lior Pachter. The Neighbor-Net Algorithm. In Advances in Applied Mathematics, Vol. 47(2):240-258, 2011.  
Keywords: abstract network, circular split system, evaluation, from distances, NeighborNet, phylogenetic network, phylogeny, split network.
Note: http://arxiv.org/abs/math/0702515.
       
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3

Miro Ferreri, Weijie Qu and Bo Han. Phylogenetic networks: A tool to display character conflict and demographic history. In African Journal of Biotechnology , Vol. 10(60):12799-12803, 2011.  
Keywords: phylogenetic network, phylogeny, survey, visualization.
       

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Leo van Iersel and Steven Kelk. Constructing the Simplest Possible Phylogenetic Network from Triplets. In ALG, Vol. 60(2):207-235, 2011.  
Keywords: explicit network, from triplets, galled tree, level k phylogenetic network, minimum number, phylogenetic network, phylogeny, polynomial, Program Marlon, Program Simplistic.
Note: http://dx.doi.org/10.1007/s00453-009-9333-0.
       
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Klaus Schliep. Phangorn: Phylogenetic analysis in R. In Bioinformatics, Vol. 27(4):592-593, 2011.  
Keywords: abstract network, from distances, phylogenetic network, Program Phangorn, software, split, split network.
Note: http://dx.doi.org/10.1093/bioinformatics/btq706.
       
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Stephen J. Willson. Restricted trees: simplifying networks with bottlenecks. In BMB, Vol. 73(10):2322-2338, 2011.  
Keywords: from network, phylogenetic network.
Note: http://arxiv.org/abs/1005.4956.
       
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Jean-Philippe Doyon, Vincent Ranwez, Vincent Daubin and Vincent Berry. Models, algorithms and programs for phylogeny reconciliation. In Briefings in Bioinformatics, Vol. 12(5):392-400, 2011.  
Keywords: explicit network, lateral gene transfer, phylogenetic network, phylogeny, reconstruction, survey.
       
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Daniel H. Huson and Celine Scornavacca. A survey of combinatorial methods for phylogenetic networks. In Genome Biology and Evolution, Vol. 3:23-35, 2011.  
Keywords: phylogenetic network, survey.
Note: http://dx.doi.org/10.1093/gbe/evq077.
       
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Marc Thuillard and Vincent Moulton. Identifying and reconstructing lateral transfers from distance matrices by combining the Minimum Contradiction Method and Neighbor-Net. In JBCB, Vol. 9(4):453-470, 2011.  
Keywords: from distances, lateral gene transfer, minimum contradiction, NeighborNet, phylogenetic network, phylogeny, reconstruction.
Note: http://dx.doi.org/10.1142/S0219720011005409, slides available at http://www.newton.ac.uk/programmes/PLG/seminars/062015501.html.
       
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10
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Josh Voorkamp né Collins, Simone Linz and Charles Semple. Quantifying hybridization in realistic time. In JCB, Vol. 18(10):1305-1318, 2011.  
Keywords: explicit network, FPT, from rooted trees, hybridization, minimum number, phylogenetic network, phylogeny, Program HybridInterleave, reconstruction, software.
Note: http://wwwcsif.cs.ucdavis.edu/~linzs/CLS10_interleave.pdf, software available at http://www.math.canterbury.ac.nz/~c.semple/software.shtml.
       
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11
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Lavanya Kannan, Hua Li and Arcady Mushegian. A Polynomial-Time Algorithm Computing Lower and Upper Bounds of the Rooted Subtree Prune and Regraft Distance. In JCB, Vol. 18(5):743-757, 2011.  
Keywords: bound, minimum number, polynomial, SPR distance.
Note: http://dx.doi.org/10.1089/cmb.2010.0045.
       
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Mukul S. Bansal, Guy Banay, J. Peter Gogarten and Ron Shamir. Detecting Highways of Horizontal Gene Transfer. In JCB, Vol. 18(9):1087-1114, 2011.  
Keywords: explicit network, from rooted trees, from species tree, lateral gene transfer, phylogenetic network, phylogeny, polynomial, reconstruction.
Note: http://people.csail.mit.edu/mukul/HighwayFull_preprint.pdf.
       
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13
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Leo van Iersel and Steven Kelk. When two trees go to war. In JTB, Vol. 269(1):245-255, 2011.  
Keywords: APX hard, explicit network, from clusters, from rooted trees, from sequences, from triplets, level k phylogenetic network, minimum number, NP complete, phylogenetic network, phylogeny, polynomial, reconstruction.
Note: http://arxiv.org/abs/1004.5332.
       
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14
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Gergely J. Szöllösi and Vincent Daubin. Modeling Gene Family Evolution and Reconciling Phylogenetic Discord. In Evolutionary Genomics, Statistical and Computational Methods, Volume 2, Methods in Molecular Biology, Vol. 856:29-51, Chapter 2, springer, 2011.  
Keywords: duplication, from multilabeled tree, lateral gene transfer, likelihood, phylogeny, reconstruction, statistical model.
Note: ArXiv version entitled The pattern and process of gene family evolution.
       
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Alix Boc and Vladimir Makarenkov. Towards an accurate identification of mosaic genes and partial horizontal gene transfers. In NAR, Vol. 39(21):e144, 2011.  
Keywords: explicit network, from sequences, lateral gene transfer, phylogenetic network, phylogeny, Program T REX, reconstruction.
Note: http://dx.doi.org/10.1093/nar/gkr735.
       
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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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Yun Yu, Cuong Than, James H. Degnan and Luay Nakhleh. Coalescent Histories on Phylogenetic Networks and Detection of Hybridization Despite Incomplete Lineage Sorting. In Systematic Biology, Vol. 60(2):138-149, 2011.  
Keywords: coalescent, hybridization, lineage sorting, reconstruction, statistical model.
Note: http://www.cs.rice.edu/~nakhleh/Papers/YuEtAl-SB11.pdf.
       
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18
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Gabriel Cardona, Mercè Llabrés, Francesc Rosselló and Gabriel Valiente. Comparison of Galled Trees. In TCBB, Vol. 8(2):410-427, 2011.  
Note: http://arxiv.org/abs/0906.1166.
       
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Ali Tofigh, Mike Hallett and Jens Lagergren. Simultaneous Identification of Duplications and Lateral Gene Transfers. In TCBB, Vol. 8(2):517-535, 2011.  
Keywords: duplication, explicit network, FPT, from rooted trees, from species tree, lateral gene transfer, loss, NP complete, phylogenetic network, phylogeny, reconstruction.
Note: http://dx.doi.org/10.1109/TCBB.2010.14.
       
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20
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Katharina Huber, Leo van Iersel, Steven Kelk and Radoslaw Suchecki. A Practical Algorithm for Reconstructing Level-1 Phylogenetic Networks. In TCBB, Vol. 8(3):607-620, 2011.  
Keywords: explicit network, from triplets, galled tree, generation, heuristic, phylogenetic network, phylogeny, Program LEV1ATHAN, Program Lev1Generator, reconstruction, software.
Note: http://arxiv.org/abs/0910.4067.
       
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InProceedings
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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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Celine Scornavacca, Franziska Zickmann and Daniel H. Huson. Tanglegrams for Rooted Phylogenetic Trees and Networks. In ISMB11, Vol. 27(13):i248-i256 of BIO, 2011.  
Keywords: from network, heuristic, phylogenetic network, phylogeny, Program Dendroscope, tanglegram, visualization.
Note: http://dx.doi.org/10.1093/bioinformatics/btr210.
       
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Changiz Eslahchi and Reza Hassanzadeh. New Algorithm for Constructing Supernetworks from Partial Trees. In MCCMB11, Pages 106-107, 2011.  
Keywords: abstract network, from unrooted trees, heuristic, phylogenetic network, phylogeny, Program SNSA, reconstruction, simulated annealing, split network.
Note: http://mccmb.belozersky.msu.ru/2011/mccmb11.pdf#page=106.
       

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Mukul S. Bansal, J. Peter Gogarten and Ron Shamir. Detecting Highways of Horizontal Gene Transfer. In Proceedings of the Eighth RECOMB Comparative Genomics Satellite Workshop (RECOMB-CG'10), Vol. 6398:109-120 of LNCS, springer, 2011.  
Keywords: explicit network, from rooted trees, from species tree, lateral gene transfer, phylogenetic network, phylogeny, polynomial, reconstruction.
Note: http://www.cs.iastate.edu/~bansal/Highways_RCG10.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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MastersThesis
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Puspal Bhabak. Improving the approximation ratio of the maximum agreement forest (MAF) on k trees and estimating the approximation ratio of the acyclic-MAF on k trees. Master's thesis, University of Windsor, Canada, 2011.  
Keywords: agreement forest, approximation, explicit network, from rooted trees, phylogenetic network, phylogeny, reconstruction.
Note: http://scholar.uwindsor.ca/cgi/viewcontent.cgi?article=1315&context=etd.
       

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Benjamin Albrecht. Fast Computation of Hybridization Networks. Master's thesis, University of Tübingen, Germany, 2011.  
Keywords: explicit network, from rooted trees, minimum number, phylogenetic network, phylogeny, reconstruction.
       

PhdThesis
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Paul Phipps. Planar phylogenetic network optimization. PhD thesis, University of Texas at Dallas, U.S.A., 2011.  
Keywords: abstract network, from distances, phylogenetic network, Program PhippsNetwork, split, split network.
Note: http://proquest.umi.com/pqdlink?did=2337197411&Fmt=7&clientId=176295&RQT=309&VName=PQD.
       

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Thu-Hien To. On some graph problems in phylogenetics. PhD thesis, Université Paris Diderot - Paris 7, France, 2011.  
Keywords: explicit network, from triplets, level k phylogenetic network, phylogenetic network, phylogeny, polynomial, reconstruction.
Note: http://www.liafa.jussieu.fr/~toth/thesis.pdf.
       

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Alethea Rea. Statistical approaches to phylogenetic networks, recombination and testing of incongruence. PhD thesis, The University of Auckland, New Zealand, 2011.  
Keywords: abstract network, AIC, BIC, phylogenetic network, phylogeny, split, split network, statistical model.
Note: https://researchspace.auckland.ac.nz/handle/2292/67624.
       

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Rosalba Radice. A Bayesian Approach to Phylogenetic Networks. PhD thesis, University of Bath, U.K., 2011.  
Keywords: bayesian, explicit network, from sequences, phylogenetic network, phylogeny, reconstruction, statistical model.
Note: http://opus.bath.ac.uk/25521/.
       

Misc
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Ruzbeh Tusserkani, Changiz Eslahchi, Hadi Poormohammadi and Azin Azadi. TripNet: A Method for Constructing Phylogenetic Networks from Triplets. 2011.  
Keywords: explicit network, heuristic, level k phylogenetic network, phylogenetic network, phylogeny, Program TripNet, reconstruction, software.
Note: http://arxiv.org/abs/1104.4720.
       

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Sha Zhu, James H. Degnan and Mike Steel. Probabilistic modeling of gene trees given species networks. 2011.  
Keywords: from network, generation, phylogenetic network, phylogeny, statistical model.
Note: Poster, http://www.newton.ac.uk/programmes/PLG/Zhu.pdf.
       

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Steven Kelk. A note on efficient computation of hybridization number via softwired clusters. 2011.  
Keywords: explicit network, FPT, from clusters, phylogenetic network, phylogeny, reconstruction.
Note: http://arxiv.org/abs/1108.4642.
       

Book
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Daniel H. Huson, Regula Rupp and Celine Scornavacca. Phylogenetic Networks: Concepts, Algorithms and Applications. Cambridge University Press, 2011.  
Keywords: phylogenetic network, phylogeny, survey.
Note: http://www.phylogenetic-networks.org/, buy at Amazon.com. Reviews here and there.
       

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David A. Morrison. Introduction to Phylogenetic Networks. RJR Productions, 2011.  
Keywords: phylogenetic network, phylogeny, reconstruction, survey.
Note: http://www.rjr-productions.org/Networks/Download.html.