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% GENERATED FROM http://phylnet.univ-mlv.fr
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% IP : ec2-54-158-219-248.compute-1.amazonaws.com
% at : Mon, 21 May 2018 10:53:35 +0000 UTC
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% Selection : Keyword(s) = DistanceBetweenNetworks
%
% Complete Journal Names and Abbreviations (but to use them you have to delete the { and } around the abbreviations,
% and before that you may want to research/replace "" by "\url{" and "" by "}", it
% will be made automatically in a next update of the Who's Who...):
@String{UM = {Unpublished manuscript}}
@String{springer = {Springer Verlag}}
@String{LNCS = {Lecture Notes in Computer Science}}
@String{CABIOS = {Comput. Appl. Biosci.}}
@String{ABIO = {Applied Bioinformatics}}
@String{AHB = {Annals of Human Biology}}
@String{AMB = {Algorithms for Molecular Biology}}
@String{ARG = {Annual Review of Genetics}}
@String{BMB = {Bulletin of Mathematical Biology}}
@String{BMCEB = {BMC Evolutionary Biology}}
@String{BMCB = {BMC Bioinformatics}}
@String{CC = {Computers and Chemistry}}
@String{G = {Genomics}}
@String{GEN = {Genetics}}
@String{BIO = {Bioinformatics}}
@String{EBIO = {Evolutionary Bioinformatics}}
@String{GR = {Genome Research}}
@String{INCOMP = {INFORMS Journal on Computing}}
@String{IJP = {International Journal for Parasitology}}
@String{IJBRA = {The International Journal of Bioinformatics Research and Applications}}
@String{JBCB = {Journal of Bioinformatics and Computational Biology}}
@String{JCB = {Journal of Computational Biology}}
@String{JMB = {Journal of Molecular Biology}}
@String{JOMB = {Journal of Mathematical Biology}}
@String{JME = {Journal of Molecular Evolution}}
@String{MBIO = {Mathematical Biosciences}}
@String{MBE = {Molecular Biology and Evolution}}
@String{MOLE = {Molecular Ecology}}
@String{MPE = {Molecular Phylogenetics and Evolution}}
@String{NAR = {Nucleic Acids Research}}
@String{NG = {Nature Genetics}}
@String{PLONE = {PLoS ONE}}
@String{PSE = {Plant Systematics and Evolution}}
@String{SB = {Systematic Biology}}
@String{TCBB = {IEEE/ACM Transactions in Computational Biology and Bioinformatics}}
@String{TCSB2 = {Transactions on Computational Systems Biology II}}
@String{TEE = {TRENDS in Ecology and Evolution}}
@String{TPP = {Theoretical Population Biology}}
@String{PNAS = {Proceedings of the National Academy of Sciences}}
@String{BIBE05 = {Proceedings of the Fifth IEEE Symposium on Bioinformatics and Bioengineering (BIBE'05)}}
@String{PLGw01 = {EMBO Workshop on Current Challenges and Problems in Phylogenetics (Isaac Newton Institute for Mathematical Sciences)}}
@String{PSB03 = {Proceedings of the eigth Pacific Symposium on Biocomputing (PSB'03)}}
@String{PSB04 = {Proceedings of the ninth Pacific Symposium on Biocomputing (PSB'04)}}
@String{PSB05 = {Proceedings of the tenth Pacific Symposium on Biocomputing (PSB'05)}}
@String{RECOMB97 = {Proceedings of the first Annual International Conference on Research in Computational Molecular Biology (RECOMB'97)}}
@String{RECOMB98 = {Proceedings of the second Annual International Conference on Research in Computational Molecular Biology (RECOMB'98)}}
@String{RECOMB99 = {Proceedings of the third Annual International Conference on Research in Computational Molecular Biology (RECOMB'99)}}
@String{RECOMB00 = {Proceedings of the fourth Annual International Conference on Research in Computational Molecular Biology (RECOMB'00)}}
@String{RECOMB01 = {Proceedings of the fifth Annual International Conference on Research in Computational Molecular Biology (RECOMB'01)}}
@String{RECOMB02 = {Proceedings of the sixth Annual International Conference on Research in Computational Molecular Biology (RECOMB'02)}}
@String{RECOMB03 = {Proceedings of the seventh Annual International Conference on Research in Computational Molecular Biology (RECOMB'03)}}
@String{RECOMB04 = {Proceedings of the eighth Annual International Conference on Research in Computational Molecular Biology (RECOMB'04)}}
@String{RECOMB05 = {Proceedings of the ninth Annual International Conference on Research in Computational Molecular Biology (RECOMB'05)}}
@String{RECOMB06 = {Proceedings of the tenth Annual International Conference on Research in Computational Molecular Biology (RECOMB'06)}}
@String{RECOMB07 = {Proceedings of the eleventh Annual International Conference on Research in Computational Molecular Biology (RECOMB'07)}}
@String{RECOMB08 = {Proceedings of the twelfth Annual International Conference on Research in Computational Molecular Biology (RECOMB'08)}}
@String{RECOMB09 = {Proceedings of the 13$^{th}$ Annual International Conference on Research in Computational Molecular Biology (RECOMB'09)}}
@String{ISBRA05 = {Proceedings of the first International Symposium on Bioinformatics Research and Applications (ISBRA'05)}}
@String{ISBRA06 = {Proceedings of the second International Symposium on Bioinformatics Research and Applications (ISBRA'06)}}
@String{ISBRA07 = {Proceedings of the third International Symposium on Bioinformatics Research and Applications (ISBRA'07)}}
@String{ECCB01 = {Proceedings of the first European Conference on Computational Biology (ECCB'01)}}
@String{ECCB02 = {Proceedings of the second European Conference on Computational Biology (ECCB'02)}}
@String{ECCB03 = {Proceedings of the third European Conference on Computational Biology (ECCB'03)}}
@String{ECCB04 = {Proceedings of the fourth European Conference on Computational Biology (ECCB'04)}}
@String{ECCB05 = {Proceedings of the fifth European Conference on Computational Biology (ECCB'05)}}
@String{ECCB06 = {Proceedings of the sixth European Conference on Computational Biology (ECCB'06)}}
@String{ECCB07 = {Proceedings of the seventh European Conference on Computational Biology (ECCB'07)}}
@String{ECCB08 = {Proceedings of the eighth European Conference on Computational Biology (ECCB'08)}}
@String{APBC05 = {Proceedings of the Third Asia-Pacific Bioinformatics Conference (APBC'05)}}
@String{APBC06 = {Proceedings of the Fourth Asia-Pacific Bioinformatics Conference (APBC'06)}}
@String{APBC08 = {Proceedings of the Sixth Asia-Pacific Bioinformatics Conference (APBC'08)}}
@String{SAC01 = {Proceedings of the 16th ACM Symposium on Applied Computing (SAC'01)}}
@String{CSB03 = {Proceedings of the 2003 IEEE Computational Systems Bioinformatics Conference (CSB2003)}}
@String{CSB05 = {Proceedings of the 2005 IEEE Computational Systems Bioinformatics Conference (CSB2005)}}
@String{CSB06 = {Proceedings of the 2006 IEEE Computational Systems Bioinformatics Conference (CSB2006)}}
@String{WABI01 = {Proceedings of the first Workshop on Algorithms in Bioinformatics (WABI'01)}}
@String{WABI02 = {Proceedings of the second Workshop on Algorithms in Bioinformatics (WABI'02)}}
@String{WABI03 = {Proceedings of the third Workshop on Algorithms in Bioinformatics (WABI'03)}}
@String{WABI04 = {Proceedings of the fourth Workshop on Algorithms in Bioinformatics (WABI'04)}}
@String{WABI05 = {Proceedings of the fifth Workshop on Algorithms in Bioinformatics (WABI'05)}}
@String{WABI06 = {Proceedings of the sixth Workshop on Algorithms in Bioinformatics (WABI'06)}}
@String{WABI07 = {Proceedings of the seventh Workshop on Algorithms in Bioinformatics (WABI'07)}}
@String{WABI08 = {Proceedings of the eighth Workshop on Algorithms in Bioinformatics (WABI'08)}}
@String{ISMB05 = {Proceedings of the $13^{th}$ International Conference on Intelligent Systems in Molecular Biology (ISMB'05)}}
@String{ISMB11 = {Proceedings of the $19^{th}$ International Conference on Intelligent Systems in Molecular Biology (ISMB'05)}}
@String{ISAAC04 = {Proceedings of the $15^{th}$ International Symposium on Algorithms and Computation (ISAAC'04)}}
@String{ISAAC05 = {Proceedings of the $16^{th}$ International Symposium on Algorithms and Computation (ISAAC'05)}}
@String{MFCS05 = {Proceedings of the $30^{th}$ International Symposium on Mathematical Foundations of Computer Science (MFCS'05)}}
@String{MCCMB11 = {Proceedings of the fifth Moscow Conference on Computational Molecular Biology (MCCMB11'11)}}
@String{IWBRA05 = {Proceedings of the 2005 International Workshop on Bioinformatics Research and Applications (IWBRA'05)}}
@String{IFCS00 = {Data Analysis, Classification, and Related Methods, Proceedings of the seventh Conference on the International Federation of Classification Societies (IFCS'00)}}
@String{IFCS02 = {Proceedings of the eighth Conference of the International Federation of Classification Societies (IFCS'02)}}
@String{IFCS04 = {Proceedings of the ninth Conference of the International Federation of Classification Societies (IFCS'04)}}
@String{CPM98 = {Proceedings of the ninth Annual Symposium on Combinatorial Pattern Matching (CPM'98)}}
@String{CPM07 = {Proceedings of the $18^{th}$ Annual Symposium on Combinatorial Pattern Matching (CPM'07)}}
@String{CPM07 = {Proceedings of the $18^{th}$ Annual Symposium on Combinatorial Pattern Matching (CPM'07)}}
@String{COCOON04 = {Proceedings of the tenth Annual International Computing and Combinatorics Conference (COCOON'04)}}
@String{COCOON05 = {Proceedings of the $11^{th}$ Annual International Computing and Combinatorics Conference (COCOON'06)}}
@String{COCOON06 = {Proceedings of the $12^{th}$ Annual International Computing and Combinatorics Conference (COCOON'06)}}
@String{COCOON07 = {Proceedings of the $13^{th}$ Annual International Computing and Combinatorics Conference (COCOON'07)}}
@String{COCOA07 = {Proceedings of the first International Conference on Combinatorial Optimization and Applications (COCOA'07)}}
@String{COCOA08 = {Proceedings of the second International Conference on Combinatorial Optimization and Applications (COCOA'08)}}
@String{PADL03 = {Proceedings of the fifth International Symposium on Practical Aspects of Declarative Languages (PADL'03)}}
@String{SODA94 = {Proceedings of the fifth Annual ACM-SIAM Symposium on Discrete Algorithms (SODA'94)}}
@String{SODA05 = {Proceedings of the $16^{th}$ Annual ACM-SIAM Symposium on Discrete Algorithms (SODA'05)}}
@String{SEA10 = {Proceedings of the ninth International Symposium on Experimental Algorithms (SEA'10)}}
@String{ADM = {Annals of Discrete Mathematics}}
@String{ACOM = {Annals of Combinatorics}}
@String{ALG = {Algorithmica}}
@String{C = {Combinatorica}}
@String{CN = {Congressus Numerantium}}
@String{CSQ = {Computational Statistics Quarterly}}
@String{DCG = {Discrete and Computational Geometry}}
@String{DM = {Discrete Mathematics}}
@String{DAM = {Discrete Applied Mathematics}}
@String{EJC = {European Journal of Combinatorics}}
@String{IPL = {Information Processing Letters}}
@String{JADM = {SIAM Journal on Algebraic and Discrete Methods}}
@String{JCLA = {Journal of Classification}}
@String{JCO = {Journal of Combinatorial Optimization}}
@String{JDM = {SIAM Journal on Discrete Mathematics}}
@String{JAM = {SIAM Journal on Applied Mathematics}}
@String{JMAA = {SIAM Journal on Matrix Analysis and Applications}}
@String{JOC = {SIAM Journal on Computing}}
@String{JCTB = {Journal of Combinatorial Theory Series B}}
@String{JGT = {Journal of Graph Theory}}
@String{TCS = {Theoretical Computer Science}}
@String{JACM = {Journal of the ACM (JACM)}}
@String{JOA = {Journal of Algorithms}}
@String{DMTCS = {Discrete Mathematics and Theoretical Computer Science}}
@string{ICOMP = {Information and Computation}}
%
% 35 out of 41 publication(s) listed below is/are indexed by Scopus. Use the URL below to access it/them.
% 1) Go to http://www.scopus.com/search/form.url?display=advanced&clear=t&origin=SearchAffiliationLookup
% 2) Type the following text in the search box:
% DOI(http://dx.doi.org/10.1016/j.mbs.2007.11.003) OR DOI(http://dx.doi.org/10.3732/ajb.91.10.1700) OR DOI(http://dx.doi.org/10.1109/tcbb.2004.10) OR DOI(http://dx.doi.org/10.1007/11602613_41) OR DOI(http://dx.doi.org/10.1007/s10878-006-9025-5) OR DOI(http://dx.doi.org/10.1142/9789812776303_0030) OR DOI(http://dx.doi.org/10.1186/1471-2105-9-175) OR DOI(http://dx.doi.org/10.1109/TCBB.2009.2) OR DOI(http://dx.doi.org/10.1371/journal.pone.0001913) OR DOI(http://dx.doi.org/10.1093/bioinformatics/btn231) OR DOI(http://dx.doi.org/10.1109/TCBB.2008.70) OR DOI(http://dx.doi.org/10.1109/TCBB.2008.127) OR DOI(http://dx.doi.org/10.1016/j.ins.2009.09.013) OR DOI(http://dx.doi.org/10.1109/TCBB.2009.33) OR DOI(http://dx.doi.org/10.1155/2014/254279) OR DOI(http://dx.doi.org/10.1201/9781420069747) OR DOI(http://dx.doi.org/10.1007/978-3-642-13509-5_18) OR DOI(http://dx.doi.org/10.1007/978-3-642-13214-8_12) OR DOI(http://dx.doi.org/10.1089/cmb.2011.0254) OR DOI(http://dx.doi.org/10.1007/978-3-642-31265-6_31) OR DOI(http://dx.doi.org/10.1016/j.ins.2012.01.038) OR DOI(http://gradworks.umi.com/35/11/3511361.html) OR DOI(http://arxiv.org/abs/1209.0871) OR DOI(http://arxiv.org/abs/1209.1040) OR DOI(http://dx.doi.org/10.1016/j.jda.2013.10.002) OR DOI(http://dx.doi.org/10.1007/s00285-015-0899-7) OR DOI(http://dx.doi.org/10.1016/j.jtbi.2016.05.030) OR DOI(http://dx.doi.org/10.1155/2016/7534258) OR DOI(https://dx.doi.org/10.1007/s00285-017-1171-0) OR DOI(http://dx.doi.org/10.1186/s12864-017-3500-5) OR DOI(https://doi.org/10.1016/j.ipl.2017.03.002) OR DOI(https://doi.org/10.1016/j.jtbi.2017.03.032) OR DOI(http://dx.doi.org/10.1007/978-3-319-58163-7_8) OR DOI(http://dx.doi.org/10.1371/journal.pcbi.1005611) OR DOI(https://dx.doi.org/10.1038/s41598-017-03363-y)
%
@Article{CRV2008,
AUTHOR = {Cardona, Gabriel and Rossell{\~A}³, Francesc and Valiente, Gabriel},
TITLE = {Tripartitions do not always discriminate phylogenetic networks.},
YEAR = {2008},
JOURNAL = {MBIO},
VOLUME = {211},
NUMBER = {2},
PAGES = {356-370},
URL = {http://dx.doi.org/10.1016/j.mbs.2007.11.003},
NOTE = {http://arxiv.org/abs/0707.2376, slides available at http://www.newton.cam.ac.uk/webseminars/pg+ws/2007/plg/plgw01/0904/valiente/},
ANNOTE = {BIBUPDATE : 20080516},
KEYWORDS = {distance between networks, phylogenetic network, phylogeny, Program Bio PhyloNetwork, tree child network, tripartition distance}
}
@Article{LinderRieseberg2004,
AUTHOR = {Linder, C. Randal and Rieseberg, Loren H.},
TITLE = {Reconstructing patterns of reticulate evolution in plants},
YEAR = {2004},
JOURNAL = {American Journal of Botany},
VOLUME = {91},
NUMBER = {10},
PAGES = {1700-1708},
URL = {http://dx.doi.org/10.3732/ajb.91.10.1700},
NOTE = {http://www.amjbot.org/cgi/reprint/91/10/1700.pdf},
ANNOTE = {BIBUPDATE : 20070904},
KEYWORDS = {distance between networks, hybridization, phylogenetic network, phylogeny, reconstruction, survey, tripartition distance}
}
@Misc{MNW2002,
AUTHOR = {Moret, Bernard M. E. and Nakhleh, Luay and Warnow, Tandy},
TITLE = {An error metric for phylogenetic networks},
YEAR = {2002},
NOTE = {Technical report TR-02-09, http://www.cs.unm.edu/~treport/tr/03-05/nakhleh.ps.gz},
ANNOTE = {CITE : },
KEYWORDS = {distance between networks, evaluation, phylogenetic network, phylogeny, tripartition distance}
}
@Article{MNWRTPST2004,
AUTHOR = {Moret, Bernard M. E. and Nakhleh, Luay and Warnow, Tandy and Linder, C. Randal and Tholse, Anna and Padolina, Anneke and Sun, Jerry and Timme, Ruth},
TITLE = {Phylogenetic Networks: Modeling, Reconstructibility, and Accuracy},
YEAR = {2004},
JOURNAL = {TCBB},
VOLUME = {1},
NUMBER = {1},
PAGES = {13-23},
URL = {http://dx.doi.org/10.1109/tcbb.2004.10},
NOTE = {http://www.cs.rice.edu/~nakhleh/Papers/tcbb04.pdf},
ANNOTE = {BIBUPDATE : 20070918},
KEYWORDS = {distance between networks, evaluation, phylogenetic network, phylogeny, time consistent network, tripartition distance}
}
@PhdThesis{Nakhleh2004,
AUTHOR = {Nakhleh, Luay},
TITLE = {Phylogenetic Networks},
YEAR = {2004},
SCHOOL = {University of Texas at Austin, U.S.A.},
NOTE = {http://www.library.utexas.edu/etd/d/2004/nakhlehl042/nakhlehl042.pdf},
ANNOTE = {CITE : },
KEYWORDS = {distance between networks, evaluation, generation, phylogenetic network, phylogeny, Program SPNet, reconstruction, split, statistical model, tree sibling network}
}
@InProceedings{NNS2005,
AUTHOR = {Nguyen, Cam Thach and Nguyen, Nguyen Bao and Sung, Wing-Kin},
TITLE = {Fast Algorithms for computing the Tripartition-based Distance between Phylogenetic Networks},
YEAR = {2005},
BOOKTITLE = {ISAAC05},
PAGES = {402-411},
URL = {http://dx.doi.org/10.1007/11602613_41},
NOTE = {http://www.cs.washington.edu/homes/ncthach/Papers/ISAAC2006.pdf},
ANNOTE = {BIBUPDATE : 20070924},
KEYWORDS = {distance between networks, phylogenetic network, phylogeny, tripartition distance}
}
@Article{NNS2007,
AUTHOR = {Nguyen, Cam Thach and Nguyen, Nguyen Bao and Sung, Wing-Kin},
TITLE = {Fast Algorithms for computing the Tripartition-based Distance between Phylogenetic Networks},
YEAR = {2007},
JOURNAL = {JCO},
VOLUME = {13},
NUMBER = {3},
URL = {http://dx.doi.org/10.1007/s10878-006-9025-5},
NOTE = {http://dx.doi.org/10.1007/s10878-006-9025-5},
ANNOTE = {BIBUPDATE : 20071118},
KEYWORDS = {distance between networks, phylogenetic network, phylogeny, tripartition distance}
}
@InProceedings{NSWLMT2003,
AUTHOR = {Nakhleh, Luay and Sun, Jerry and Warnow, Tandy and Linder, C. Randal and Moret, Bernard M. E. and Tholse, Anna},
TITLE = {Towards the Development of Computational Tools for Evaluating Phylogenetic Network Reconstruction Methods},
YEAR = {2003},
BOOKTITLE = {PSB03},
URL = {http://dx.doi.org/10.1142/9789812776303_0030},
NOTE = {http://www.cs.rice.edu/~nakhleh/Papers/psb03.pdf},
ANNOTE = {BIBUPDATE : 20070918},
KEYWORDS = {distance between networks, evaluation, phylogenetic network, phylogeny, polynomial, tripartition distance}
}
@Article{CRV2008b,
AUTHOR = {Cardona, Gabriel and Rossell{\~A}³, Francesc and Valiente, Gabriel},
TITLE = {A Perl Package and an Alignment Tool for Phylogenetic Networks},
YEAR = {2008},
JOURNAL = {BMCB},
VOLUME = {9},
PAGES = {175},
URL = {http://dx.doi.org/10.1186/1471-2105-9-175},
NOTE = {http://dx.doi.org/10.1186/1471-2105-9-175},
ANNOTE = {BIBUPDATE : 20080506},
KEYWORDS = {distance between networks, phylogenetic network, phylogeny, Program Bio PhyloNetwork, tree child network, tree sibling network}
}
@Article{Nakhleh2010,
AUTHOR = {Nakhleh, Luay},
TITLE = {A Metric on the Space of Reduced Phylogenetic Networks},
YEAR = {2010},
JOURNAL = {TCBB},
VOLUME = {7},
NUMBER = {2},
URL = {http://dx.doi.org/10.1109/TCBB.2009.2},
NOTE = {http://www.cs.rice.edu/~nakhleh/Papers/tcbb-Metric.pdf},
ANNOTE = {http://doi.ieeecomputersociety.org/10.1109/TCBB.2009.2},
KEYWORDS = {distance between networks, phylogenetic network, phylogeny}
}
@Article{WPC2008,
AUTHOR = {Woolley, Steven M. and Posada, David and Crandall, Keith A.},
TITLE = {A Comparison of Phylogenetic Network Methods Using Computer Simulation},
YEAR = {2008},
JOURNAL = {PLoS ONE},
VOLUME = {3},
NUMBER = {4},
PAGES = {e1913},
URL = {http://dx.doi.org/10.1371/journal.pone.0001913},
NOTE = {http://dx.doi.org/10.1371/journal.pone.0001913},
ANNOTE = {BIBUPDATE : 20080421},
KEYWORDS = {abstract network, distance between networks, evaluation, median network, MedianJoining, minimum spanning network, NeighborNet, parsimony, phylogenetic network, phylogeny, Program Arlequin, Program CombineTrees, Program Network, Program SHRUB, Program SplitsTree, Program TCS, split decomposition}
}
@PhdThesis{Vriesendorp2007,
AUTHOR = {Vriesendorp, Bastienne},
TITLE = {Phylogenenetworks, exploring reticulate evolution and its consequences for phylogenetic reconstruction},
YEAR = {2007},
SCHOOL = {Wageningen University, The Netherlands},
NOTE = {http://library.wur.nl/wda/dissertations/dis4239.pdf},
ANNOTE = {CITE : },
KEYWORDS = {consensus, distance between networks, evaluation, hybridization, median network, NeighborNet, parsimony, phylogenetic network, phylogeny, Program SplitsTree, split decomposition, survey}
}
@Article{CLRV2008b,
AUTHOR = {Cardona, Gabriel and Llabr{\~A}İs, Merc{\~A}¨ and Rossell{\~A}³, Francesc and Valiente, Gabriel},
TITLE = {A Distance Metric for a Class of Tree-Sibling Phylogenetic Networks},
YEAR = {2008},
JOURNAL = {BIO},
VOLUME = {24},
NUMBER = {13},
PAGES = {1481-1488},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn231},
NOTE = {http://dx.doi.org/10.1093/bioinformatics/btn231},
ANNOTE = {BIBUPDATE : 20080505, 20080520},
KEYWORDS = {distance between networks, phylogenetic network, phylogeny, polynomial, tree sibling network}
}
@Article{CLRV2009a,
AUTHOR = {Cardona, Gabriel and Llabr{\~A}İs, Merc{\~A}¨ and Rossell{\~A}³, Francesc and Valiente, Gabriel},
TITLE = {Metrics for phylogenetic networks I: Generalizations of the Robinson-Foulds metric},
YEAR = {2009},
JOURNAL = {TCBB},
VOLUME = {6},
NUMBER = {1},
PAGES = {46-61},
URL = {http://dx.doi.org/10.1109/TCBB.2008.70},
NOTE = {http://dx.doi.org/10.1109/TCBB.2008.70},
ANNOTE = {BIBUPDATE : 20080725},
KEYWORDS = {distance between networks, explicit network, phylogenetic network, phylogeny, time consistent network, tree child network, tripartition distance}
}
@Article{CLRV2009b,
AUTHOR = {Cardona, Gabriel and Llabr{\~A}İs, Merc{\~A}¨ and Rossell{\~A}³, Francesc and Valiente, Gabriel},
TITLE = {Metrics for phylogenetic networks II: Nodal and triplets metrics},
YEAR = {2009},
JOURNAL = {TCBB},
VOLUME = {6},
NUMBER = {3},
PAGES = {454-469},
URL = {http://dx.doi.org/10.1109/TCBB.2008.127},
NOTE = {http://dx.doi.org/10.1109/TCBB.2008.127},
ANNOTE = {BIBUPDATE : 20080725},
KEYWORDS = {distance between networks, phylogenetic network, phylogeny}
}
@InProceedings{CLRV2008e,
AUTHOR = {Cardona, Gabriel and Llabr{\~A}İs, Merc{\~A}¨ and Rossell{\~A}³, Francesc and Valiente, Gabriel},
TITLE = {Phylogenetic Networks: Justification, Models, Distances and Algorithms},
YEAR = {2008},
BOOKTITLE = {VI Jornadas de Matem{\~A}Ħtica Discreta y Algor{\~A}tmica (JMDA'08)},
NOTE = {http://bioinfo.uib.es/media/uploaded/jmda2008_submission_61-1.pdf},
ANNOTE = {BIBUPDATE : 20080725},
KEYWORDS = {distance between networks, mu distance, phylogenetic network, phylogeny, polynomial, survey, time consistent network, tree child network, tripartition distance, triplet distance}
}
@Article{CLRV2010b,
AUTHOR = {Cardona, Gabriel and Llabr{\~A}İs, Merc{\~A}¨ and Rossell{\~A}³, Francesc and Valiente, Gabriel},
TITLE = {Path lengths in tree-child time consistent hybridization networks},
YEAR = {2010},
JOURNAL = {Information Sciences},
VOLUME = {180},
NUMBER = {3},
PAGES = {366-383},
URL = {http://dx.doi.org/10.1016/j.ins.2009.09.013},
NOTE = {http://arxiv.org/abs/0807.0087?context=cs.CE},
ANNOTE = {BIBUPDATE : 20080725},
KEYWORDS = {distance between networks, phylogenetic network, phylogeny, time consistent network, tree child network}
}
@Article{CLRV2009d,
AUTHOR = {Cardona, Gabriel and Llabr{\~A}İs, Merc{\~A}¨ and Rossell{\~A}³, Francesc and Valiente, Gabriel},
TITLE = {On Nakhleh's metric for reduced phylogenetic networks},
YEAR = {2009},
JOURNAL = {TCBB},
VOLUME = {6},
NUMBER = {4},
PAGES = {629-638},
URL = {http://dx.doi.org/10.1109/TCBB.2009.33},
NOTE = {Preliminary versions: http://arxiv.org/abs/0809.0110 and http://arxiv.org/abs/0801.2354v1},
ANNOTE = {BIBUPDATE : 20080925},
KEYWORDS = {distance between networks, phylogenetic network, phylogeny}
}
@Article{CLRV2014,
AUTHOR = {Cardona, Gabriel and Llabr{\~A}İs, Merc{\~A}¨ and Rossell{\~A}³, Francesc and Valiente, Gabriel},
TITLE = {The comparison of tree-sibling time consistent phylogenetic networks is graph-isomorphism complete},
YEAR = {2014},
JOURNAL = {The Scientific World Journal},
VOLUME = {2014},
NUMBER = {254279},
PAGES = {1-6},
URL = {http://dx.doi.org/10.1155/2014/254279},
NOTE = {http://arxiv.org/abs/0902.4640},
KEYWORDS = {abstract network, distance between networks, from network, isomorphism, phylogenetic network, tree sibling network}
}
@InBook{Valiente2009,
AUTHOR = {Valiente, Gabriel},
TITLE = {Combinatorial Pattern Matching Algorithms in Computational Biology Using Perl and R},
YEAR = {2009},
PAGES = {184-208},
PUBLISHER = {Taylor {\&} Francis/CRC Press},
URL = {http://dx.doi.org/10.1201/9781420069747},
NOTE = {http://books.google.fr/books?id=F4YIIUWb7yMC},
KEYWORDS = {counting, distance between networks, galled tree, generation, phylogenetic network, phylogeny, survey, time consistent network, tree child network, tree sibling network}
}
@InProceedings{AJSUV2010,
AUTHOR = {Asano, Tetsuo and Jansson, Jesper and Sadakane, Kunihiko and Uehara, Ryuhei and Valiente, Gabriel},
TITLE = {Faster Computation of the Robinson-Foulds Distance between Phylogenetic Networks},
YEAR = {2010},
BOOKTITLE = {CPM10},
VOLUME = {6129},
PAGES = {190-201},
SERIES = {LNCS},
PUBLISHER = {springer},
URL = {http://dx.doi.org/10.1007/978-3-642-13509-5_18},
NOTE = {http://hdl.handle.net/10119/9859, slides available at http://cs.nyu.edu/parida/CPM2010/MainPage_files/18.pdf},
KEYWORDS = {distance between networks, explicit network, level k phylogenetic network, phylogenetic network, polynomial, spread}
}
@Misc{CMF2010,
AUTHOR = {Cardona, Gabriel and Llabr{\~A}İs, Merc{\~A}¨ and Rossell{\~A}³, Francesc},
TITLE = {A metric for galled networks},
YEAR = {2010},
NOTE = {http://arxiv4.library.cornell.edu/abs/1009.0652},
KEYWORDS = {distance between networks, explicit network, from network, galled network, phylogenetic network, phylogeny}
}
@Article{CLR2010b,
AUTHOR = {Cardona, Gabriel and Llabr{\~A}İs, Merc{\~A}¨ and Rossell{\~A}³, Francesc},
TITLE = {Two Results on Distances for Phylogenetic Networks},
YEAR = {2010},
JOURNAL = {Advances in Intelligent and Soft Computing},
VOLUME = {74},
PAGES = {93-100},
URL = {http://dx.doi.org/10.1007/978-3-642-13214-8_12},
NOTE = {http://www.merilibrary.com/books/bioinformatics/advances%20in%20bioinformatics.pdf#page=103},
KEYWORDS = {distance between networks, explicit network, phylogenetic network, phylogeny, tree sibling network}
}
@Article{KRFJZK2012,
AUTHOR = {Kirkpatrick, Bonnie and Reshef, Yakir and Finucane, Hilary and Jiang, Haitao and Zhu, Binhai and Karp, Richard M.},
TITLE = {Comparing Pedigree Graphs},
YEAR = {2012},
JOURNAL = {JCB},
VOLUME = {19},
NUMBER = {9},
PAGES = {998-1014},
URL = {http://dx.doi.org/10.1089/cmb.2011.0254},
NOTE = {http://arxiv.org/abs/1009.0909, preliminary version as poster at WABI 2010},
KEYWORDS = {distance between networks, from network, pedigree}
}
@InProceedings{JanssonLingas2012,
AUTHOR = {Jansson, Jesper and Lingas, Andrzej},
TITLE = {Computing the rooted triplet distance between galled trees by counting triangles},
YEAR = {2012},
BOOKTITLE = {CPM12},
VOLUME = {7354},
PAGES = {385-398},
SERIES = {LNCS},
PUBLISHER = {springer},
URL = {http://dx.doi.org/10.1007/978-3-642-31265-6_31},
NOTE = {http://www.df.lth.se/~jj/Publications/d_rt_for_Galled_Trees5_CPM_2012.pdf},
KEYWORDS = {distance between networks, explicit network, from network, galled tree, phylogenetic network, phylogeny, polynomial, triplet distance}
}
@Article{AJSUV2012,
AUTHOR = {Asano, Tetsuo and Jansson, Jesper and Sadakane, Kunihiko and Uehara, Ryuhei and Valiente, Gabriel},
TITLE = {Faster computation of the Robinson{\^a}Foulds distance between phylogenetic networks},
YEAR = {2012},
JOURNAL = {Information Sciences},
VOLUME = {197},
PAGES = {77-90},
URL = {http://dx.doi.org/10.1016/j.ins.2012.01.038},
KEYWORDS = {distance between networks, explicit network, level k phylogenetic network, phylogenetic network, polynomial, spread}
}
@PhdThesis{Birckner2012,
AUTHOR = {Bickner, Devin Robert},
TITLE = {On normal networks},
YEAR = {2012},
SCHOOL = {Iowa State University, U.S.A.},
URL = {http://gradworks.umi.com/35/11/3511361.html},
NOTE = {http://gradworks.umi.com/3511361.pdf},
KEYWORDS = {distance between networks, explicit network, from network, from trees, normal network, phylogenetic network, phylogeny, polynomial, reconstruction, SPR distance}
}
@Misc{AlcalaRossello2012,
AUTHOR = {Alcal{\~A} Mena, Adri{\~A} and Rossell{\~A}³, Francesc},
TITLE = {Ternary graph isomorphism in polynomial time, after Luks},
YEAR = {2012},
URL = {http://arxiv.org/abs/1209.0871},
NOTE = {http://arxiv.org/abs/1209.0871},
KEYWORDS = {distance between networks, explicit network, from network, isomorphism, phylogenetic network, phylogeny, polynomial, Program SAGE}
}
@MastersThesis{Alcala2012,
AUTHOR = {Alcal{\~A} Mena, Adri{\~A} },
TITLE = {Trivalent Graph isomorphism in polynomial time},
YEAR = {2012},
SCHOOL = {Universidad de Cantabria, Spain},
URL = {http://arxiv.org/abs/1209.1040},
NOTE = {http://arxiv.org/abs/1209.1040},
KEYWORDS = {distance between networks, explicit network, from network, isomorphism, phylogenetic network, phylogeny, polynomial, Program SAGE}
}
@Article{JanssonLingas2014,
AUTHOR = {Jansson, Jesper and Lingas, Andrzej},
TITLE = {Computing the rooted triplet distance between galled trees by counting triangles},
YEAR = {2014},
JOURNAL = {Journal of Discrete Algorithms},
VOLUME = {25},
PAGES = {66-78},
URL = {http://dx.doi.org/10.1016/j.jda.2013.10.002},
KEYWORDS = {distance between networks, explicit network, from network, galled network, phylogenetic network, phylogeny, polynomial, triplet distance}
}
@Article{HLMW2016,
AUTHOR = {Huber, Katharina and Linz, Simone and Moulton, Vincent and Wu, Taoyang},
TITLE = {Spaces of phylogenetic networks from generalized nearest-neighbor interchange operations},
YEAR = {2016},
JOURNAL = {JOMB},
VOLUME = {72},
NUMBER = {2},
PAGES = {699-725},
URL = {http://dx.doi.org/10.1007/s00285-015-0899-7},
KEYWORDS = {bound, distance between networks, from network, LST distance, phylogenetic network, phylogeny}
}
@Article{HMW2016,
AUTHOR = {Huber, Katharina and Moulton, Vincent and Wu, Taoyang},
TITLE = {Transforming phylogenetic networks: Moving beyond tree space},
YEAR = {2016},
JOURNAL = {JTB},
VOLUME = {404},
PAGES = {30-39},
URL = {http://dx.doi.org/10.1016/j.jtbi.2016.05.030},
NOTE = {http://arxiv.org/abs/1601.01788},
KEYWORDS = {distance between networks, level k phylogenetic network, phylogenetic network, phylogeny}
}
@Article{Wang2016,
AUTHOR = {Wang, Juan},
TITLE = {A Metric on the Space of Partly Reduced Phylogenetic Networks},
YEAR = {2016},
JOURNAL = {BMRI},
VOLUME = {2016},
NUMBER = {7534258},
PAGES = {1-9},
URL = {http://dx.doi.org/10.1155/2016/7534258},
NOTE = {http://downloads.hindawi.com/journals/bmri/aip/7534258.pdf},
KEYWORDS = {distance between networks, partly reduced networks, phylogenetic network, phylogeny, polynomial, reduced networks}
}
@Article{FHMW2017,
AUTHOR = {Francis, Andrew R. and Huber, Katharina and Moulton, Vincent and Wu, Taoyang},
TITLE = {Bounds for phylogenetic network space metrics},
YEAR = {2017},
JOURNAL = {JOMB},
URL = {https://dx.doi.org/10.1007/s00285-017-1171-0},
NOTE = {https://arxiv.org/abs/1702.05609, to appear},
KEYWORDS = {bound, distance between networks, from network, NNI distance, SPR distance, TBR distance}
}
@InProceedings{LZL2017,
AUTHOR = {Lu, Bingxin and Zhang, Louxin and Leong, Hon Wai},
TITLE = {A program to compute the soft Robinson-Foulds distance between phylogenetic networks},
YEAR = {2017},
BOOKTITLE = {APBC17},
VOLUME = {18},
NUMBER = {Suppl. 2},
PAGES = {111},
SERIES = {BMC Genomics},
URL = {http://dx.doi.org/10.1186/s12864-017-3500-5},
NOTE = {http://dx.doi.org/10.1186/s12864-017-3500-5},
KEYWORDS = {cluster containment, distance between networks, explicit network, exponential algorithm, from network, phylogenetic network, phylogeny, Program icelu-PhyloNetwork}
}
@Article{MOW2017,
AUTHOR = {Moulton, Vincent and Oldman, James and Wu, Taoyang},
TITLE = {A cubic-time algorithm for computing the trinet distance between level-1 networks},
YEAR = {2017},
JOURNAL = {IPL},
VOLUME = {123},
PAGES = {36-41},
URL = {https://doi.org/10.1016/j.ipl.2017.03.002},
NOTE = {https://doi.org/10.1016/j.ipl.2017.03.002},
KEYWORDS = {distance between networks, explicit network, from network, phylogenetic network, phylogeny, polynomial, Program TriLoNet}
}
@Article{BLS2017,
AUTHOR = {Bordewich, Magnus and Linz, Simone and Semple, Charles},
TITLE = {Lost in space? Generalising subtree prune and regraft to spaces of phylogenetic networks},
YEAR = {2017},
JOURNAL = {JTB},
VOLUME = {423},
PAGES = {1-12},
URL = {https://doi.org/10.1016/j.jtbi.2017.03.032},
NOTE = {https://simonelinz.files.wordpress.com/2017/04/bls171.pdf},
KEYWORDS = {distance between networks, SPR distance}
}
@InProceedings{JRS2017,
AUTHOR = {Jansson, Jesper and Rajaby, Ramesh and Sung, Wing-Kin},
TITLE = {An Efficient Algorithm for the Rooted Triplet Distance Between Galled Trees},
YEAR = {2017},
BOOKTITLE = {AlCoB17},
VOLUME = {10252},
PAGES = {115-126},
SERIES = {LNCS},
PUBLISHER = {Springer},
URL = {http://dx.doi.org/10.1007/978-3-319-58163-7_8},
NOTE = {},
KEYWORDS = {distance between networks, from network, phylogenetic network, phylogeny, polynomial, reconstruction, triplet distance}
}
@Article{GIJLPS2017,
AUTHOR = {Gambette, Philippe and van Iersel, Leo and Jones, Mark and Lafond, Manuel and Pardi, Fabio and Scornavacca, Celine},
TITLE = {Rearrangement Moves on Rooted Phylogenetic Networks},
YEAR = {2017},
JOURNAL = {PLoS Computational Biology},
VOLUME = {13},
NUMBER = {8},
PAGES = {e1005611.1-21},
URL = {http://dx.doi.org/10.1371/journal.pcbi.1005611},
NOTE = {https://hal-upec-upem.archives-ouvertes.fr/hal-01572624/en/},
KEYWORDS = {distance between networks, explicit network, from network, NNI distance, phylogenetic network, phylogeny, SPR distance}
}
@Article{WangGuo2017,
AUTHOR = {Wang, Juan and Guo, Maozu},
TITLE = {A Metric on the Space of kth-order reduced Phylogenetic Networks},
YEAR = {2017},
JOURNAL = {Scientific Reports},
VOLUME = {7},
NUMBER = {3189},
PAGES = {1-10},
URL = {https://dx.doi.org/10.1038/s41598-017-03363-y},
NOTE = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5466651/},
KEYWORDS = {distance between networks, explicit network, from network, kth-order reduced network, phylogenetic network, phylogeny, polynomial}
}
@Misc{Klawitter2017,
AUTHOR = {Klawitter, Jonathan},
TITLE = {The SNPR neighbourhood of tree-child networks},
YEAR = {2017},
NOTE = {https://arxiv.org/abs/1707.09579