Publications of Year 2004  
Article (Journal)
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Katharina Huber, Michael Langton, David Penny, Vincent Moulton and Mike Hendy. Spectronet: A package for computing spectra and median networks. In ABIO, Vol. 1(3):159-161, 2004.  
Keywords: from splits, median network, phylogenetic network, phylogeny, Program Spectronet, software, split, visualization.
Note: http://citeseer.ist.psu.edu/631776.html.
       
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Mihaela Baroni, Charles Semple and Mike Steel. A framework for representing reticulate evolution. In ACOM, Vol. 8:398-401, 2004.  
Keywords: explicit network, from clusters, hybridization, minimum number, phylogenetic network, phylogeny, reconstruction, regular network, SPR distance.
Note: http://www.math.canterbury.ac.nz/~c.semple/papers/BSS04.pdf.
       
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David Bryant. The Splits in the Neighborhood of a Tree. In ACOM, Vol. 8(1):1-11, 2004.  
Note: http://citeseer.ist.psu.edu/668699.html.
       

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C. Randal Linder and Loren H. Rieseberg. Reconstructing patterns of reticulate evolution in plants. In American Journal of Botany, Vol. 91(10):1700-1708, 2004.  
Keywords: distance between networks, hybridization, phylogenetic network, phylogeny, reconstruction, survey, tripartition distance.
Note: http://www.amjbot.org/cgi/reprint/91/10/1700.pdf.
       

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Mohd Abdul Hai Zahid, Ankush Mittal and Ramesh C. Joshi. Use of Phylogenetic network and its reconstruction Algorithms. In Bioinformatics India, Vol. 2:47-58, 2004.  
Keywords: evaluation, from distances, NeighborNet, Program SplitsTree, Program T REX, split decomposition.
Note: http://www.isical.ac.in/~zahid_t/publications/papers/1.pdf.
       

6
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Katharina Huber, Vincent Moulton and Charles Semple. Replacing cliques by stars in quasi-median graphs. In DAM, Vol. 143(1-3), 2004.  
Note: http://dx.doi.org/10.1016/j.dam.2004.03.002.
       
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Dan Gusfield, Satish Eddhu and Charles Langley. The fine structure of galls in phylogenetic networks. In INCOMP, Vol. 16(4):459-469, 2004.  
Keywords: explicit network, from sequences, galled tree, phylogenetic network, phylogeny, reconstruction.
Note: http://wwwcsif.cs.ucdavis.edu/~gusfield/informs.pdf.
       
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Dan Gusfield, Satish Eddhu and Charles Langley. Optimal, Efficient Reconstruction of Phylogenetic Networks with Constrained Recombination. In JBCB, Vol. 2(1):173-213, 2004.  
Keywords: explicit network, from sequences, galled tree, phylogenetic network, phylogeny, recombination, reconstruction.
Note: http://wwwcsif.cs.ucdavis.edu/~gusfield/exfinalrec.pdf.
       
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Vladimir Makarenkov and Pierre Legendre. From a phylogenetic tree to a reticulated network. In JCB, Vol. 11(1):195-212, 2004.  
Keywords: abstract network, from distances, phylogenetic network, phylogeny, Program T REX, reticulogram.
Note: http://www.labunix.uqam.ca/~makarenv/makarenv/article_JCB2004.pdf.
       

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Yun S. Song and Jotun Hein. On the Minimum Number of Recombination Events in the Evolutionary History of DNA Sequences. In JOMB, Vol. 48(2):160-186, 2004.  
Keywords: minimum number, recombination.
Note: http://dx.doi.org/10.1007/s00285-003-0227-5.
       
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David Bryant and Vincent Moulton. NeighborNet: An Agglomerative Method for the Construction of Phylogenetic Networks. In MBE, Vol. 21(2):255-265, 2004.  
Keywords: phylogenetic network, phylogeny, Program SplitsTree, reconstruction, split network.
Note: http://www.math.auckland.ac.nz/~bryant/Papers/04NeighborNet.pdf.
       
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Barbara R. Holland, Katharina Huber, Vincent Moulton and Peter J. Lockhart. Using consensus networks to visualize contradictory evidence for species phylogeny. In MBE, Vol. 21(7):1459-1461, 2004.  
Keywords: consensus, from trees, phylogenetic network, phylogeny, split, visualization.
Note: http://dx.doi.org/10.1093/molbev/msh145.
       
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13
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Bernard M. E. Moret, Luay Nakhleh, Tandy Warnow, C. Randal Linder, Anna Tholse, Anneke Padolina, Jerry Sun and Ruth Timme. Phylogenetic Networks: Modeling, Reconstructibility, and Accuracy. In TCBB, Vol. 1(1):13-23, 2004.  
Keywords: distance between networks, evaluation, phylogenetic network, phylogeny, time consistent network, tripartition distance.
Note: http://www.cs.rice.edu/~nakhleh/Papers/tcbb04.pdf.
       

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Vineet Bafna and Vikas Bansal. The Number of Recombination Events in a Sample History: Conflict Graph and Lower Bounds. In TCBB, Vol. 1(2):78-90, 2004.  
Keywords: ARG, bound, minimum number, phylogeny, recombination.
Note: http://www-cse.ucsd.edu/users/vbafna/pub/tcbb04.pdf.
       
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Andreas W. M. Dress and Daniel H. Huson. Constructing splits graphs. In TCBB, Vol. 1(3):109-115, 2004.  
Keywords: abstract network, circular split system, from trees, phylogenetic network, phylogeny, Program SplitsTree, reconstruction, split network, visualization.
Note: http://scilib.kiev.ua/ieee/tcbb/2004/03/n3/n0109.pdf.
       
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Daniel H. Huson, Tobias Dezulian, Tobias Kloepper and Mike Steel. Phylogenetic Super-Networks from Partial Trees. In TCBB, Vol. 1(4):151-158, 2004.  
Keywords: abstract network, from unrooted trees, phylogenetic network, phylogeny, Program SplitsTree, reconstruction, supernetwork.
Note: http://hdl.handle.net/10092/3177.
       
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Vladimir Makarenkov, Pierre Legendre and Yves Desdevises. Modeling phylogenetic relationships using reticulated networks. In Zoologica Scripta, Vol. 33(1):89-96, 2004.  
Note: http://www.labunix.uqam.ca/~makarenv/articles/ZoologicaScripta.pdf.
       

InProceedings
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Jesper Jansson and Wing-Kin Sung. Inferring a level-1 phylogenetic network from a dense set of rooted triplets. In COCOON04, Vol. 3106:462-471 of LNCS, springer, 2004. 1 comment  
Keywords: explicit network, from triplets, galled tree, level k phylogenetic network, phylogenetic network, phylogeny, polynomial, reconstruction.
Note: http://www.df.lth.se/~jj/Publications/ipnrt6_COCOON2004.pdf.
       

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Tobias Dezulian and Mike Steel. Phylogenetic closure operations and homoplasy-free evolution. In IFCS04, Pages 395-416, springer, 2004.  
Note: http://www.math.canterbury.ac.nz/~m.steel/Non_UC/files/research/closure_ops.pdf.
       

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Alix Boc, Vladimir Makarenkov and Abdoulaye B. Diallo. Une nouvelle méthode pour la détection de transferts horizontaux de gène : la réconciliation topologique d'arbres de gène et d'espèces. In JOBIM04, 2004.  
Note: http://www.labunix.uqam.ca/~makarenv/makarenv/JOBIM_2004.pdf.
       

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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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C. Randal Linder, Bernard M. E. Moret, Luay Nakhleh and Tandy Warnow. Network (Reticulate) Evolution: Biology, Models, and Algorithms. In PSB04, 2004.  
Note: http://www.cs.rice.edu/~nakhleh/Papers/psb04.pdf.
       

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Pawel Górecki. Reconciliation problems for duplication, loss and horizontal gene transfer. In RECOMB04, Pages 316-325, 2004.  
Keywords: duplication, explicit network, from rooted trees, from species tree, lateral gene transfer, loss, NP complete, parsimony, phylogenetic network, phylogeny, polynomial, reconstruction.
Note: http://ai.stanford.edu/~serafim/CS374_2004/Papers/Gorecki_Reconciliation.pdf.
       

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Luay Nakhleh, Tandy Warnow and C. Randal Linder. Reconstructing reticulate evolution in species - theory and practice. In RECOMB04, Pages 337-346, 2004.  
Keywords: from rooted trees, galled tree, phylogenetic network, phylogeny, polynomial, Program SPNet, reconstruction, software.
Note: http://www.cs.rice.edu/~nakhleh/Papers/144-nakhleh.pdf.
       

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Mike Hallett, Jens Lagergren and Ali Tofigh. Simultaneous Identification of Duplications and Lateral Transfers. In RECOMB04, Pages 347-356, 2004.  
Keywords: duplication, explicit network, FPT, from rooted trees, from species tree, lateral gene transfer, loss, NP complete, parsimony, phylogenetic network, phylogeny, polynomial, reconstruction.
Note: http://www.nada.kth.se/~jensl/p164-hallett.pdf.
       

PhdThesis
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Luay Nakhleh. Phylogenetic Networks. PhD thesis, University of Texas at Austin, U.S.A., 2004.  
Keywords: distance between networks, evaluation, generation, phylogenetic network, phylogeny, Program SPNet, reconstruction, split, statistical model, tree sibling network.
Note: http://www.library.utexas.edu/etd/d/2004/nakhlehl042/nakhlehl042.pdf.
       

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Mihaela Baroni. Hybrid phylogenies : a graph-based approach to represent reticulate evolution. PhD thesis, University of Canterbury, New Zealand, 2004.  
Keywords: explicit network, from rooted trees, galled tree, hybridization, minimum number, phylogenetic network, phylogeny, reconstruction, regular network.
Note: http://ir.canterbury.ac.nz/bitstream/10092/4803/1/baroni_thesis.pdf.
       

Misc
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Dan Gusfield and Dean Hickerson. A Fundamental, Efficiently-Computed Lower Bound on the Number of Recombinations Needed in Phylogenetic Networks. 2004.  
Note: UC Davis Computer Science Technical Report.
       

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Mike Hallett and Jens Lagergren. Efficient algorithms for lateral gene transfers problems. 2004.  
Keywords: from rooted trees, lateral gene transfer, NP complete, phylogeny, polynomial, reconstruction.
Note: submitted to SIAM Journal on Computing, http://www.mcb.mcgill.ca/~hallett/Lateral.pdf.