Who is Who in Phylogenetic Networks

PhdThesis publications sorted by year
2020
1 Marefatollah Mansouri. Combinatorial properties of phylogenetic networks. PhD thesis, Vienna University of Technology (Austria), Institute of Discrete Mathematics and Geometry, 2020. Keywords: counting, explicit network, galled tree, level k phylogenetic network, normal network, phylogenetic network, phylogeny. Note: https://dmg.tuwien.ac.at/bgitten/Theses/mansouri.pdf.
2019
2 Konstantinos Mampentzidis. Comparison and Construction of Phylogenetic Trees and Networks. PhD thesis, Aarhus University, Denmark, 2019. Keywords: distance between networks, explicit network, from network, phylogenetic network, phylogeny, polynomial, triplet distance. Note: https://pure.au.dk/ws/files/172250681/thesis_Konstantinos_Mampentzidis.pdf.
2018
3 Sajad Mirzaei. Efficient Algorithms for Trees and Networks in Evolutionary Genomics. PhD thesis, University of Connecticut, 2018. Keywords: branch length, explicit network, haplotype network, heuristic, Program PIRN, reconstruction. Note: https://opencommons.uconn.edu/dissertations/1853.         4 Guillaume Scholz. New algorithms and mathematical tools for phylogenetics beyond trees. PhD thesis, University of East Anglia, 2018. Keywords: circular split system, explicit network, explicit network, from splits, galled tree, phylogenetic network, phylogeny, polynomial, reconstruction, split network, uniqueness. Note: https://ueaeprints.uea.ac.uk/id/eprint/66952.         5 Andreas Gunawan. On the tree and cluster containment problems for phylogenetic networks. PhD thesis, National University of Singapore, 2018. Keywords: cluster containment, explicit network, galled network, genetically stable network, nearly-stable network, phylogenetic network, phylogeny, reticulation-visible network, tree containment. Note: https://scholarbank.nus.edu.sg/handle/10635/144270.
2017
6 Hussein A. Hejase. Scalable Phylogenetic Analysis and Functional Interpretation of Genomes with Complex Evolutionary Histories. PhD thesis, Michigan State University, 2017. Keywords: explicit network, from rooted trees, heuristic, phylogenetic network, phylogeny, Program FastNet, reconstruction. Note: https://dx.doi.org/10.25335/M5T855.         7 Paul Bastide. Shifted stochastic processes evolving on trees : application to models of adaptive evolution on phylogenies. PhD thesis, Université Paris Saclay, 2017. Keywords: ancestral trait reconstruction, bayesian, explicit network, phylogenetic network, phylogeny, Program PhyloNetworks SNaQ, reconstruction, statistical model. Note: https://tel.archives-ouvertes.fr/tel-01629648/en/, slides..         8 Dingqiao Wen. Bayesian Inference of Phylogenetic Networks from Sequence Data. PhD thesis, Rice University, 2017. Keywords: bayesian, explicit network, phylogenetic network, phylogeny, reconstruction.
2016
9 Jonathan Mitchell. Distinguishing Convergence on Phylogenetic Networks. PhD thesis, University of Tasmania, Australia, 2016. Keywords: phylogenetic network, phylogeny, statistical model. Note: http://arxiv.org/abs/1606.07160.         10 Benjamin Albrecht. Computing Hybridization Networks Using Agreement Forests. PhD thesis, Ludwig-Maximilians-Universität München, 2016. Note: https://edoc.ub.uni-muenchen.de/19444/.         11 Nihan Tokac. Efficiency of Algorithms in Phylogenetics. PhD thesis, Durham University, U.K., 2016. Keywords: explicit network, from distances, phylogenetic network, phylogeny, reconstruction, tree-child network. Note: http://etheses.dur.ac.uk/11768/.         12 Pei Wu. Quartet weights in phylogenetic network reconstruction. PhD thesis, University of Chinese Academy of Sciences, 2016. Keywords: abstract network, from distances, from quartets, phylogenetic network, phylogeny, reconstruction, split, split network. Note: https://www.researchgate.net/publication/324475948_Quartet_weights_in_phylogenetic_network_reconstruction.         13 Monika Balvociute. Flat Embeddings of Genetic and Distance Data. PhD thesis, University of Otago, 2016. Keywords: abstract network, flat, phylogenetic network, phylogeny, planar, Program FlatNJ, Program SplitsTree, split, split network. Note: http://hdl.handle.net/10523/6286.
2015
14 Nela Lekic. Trees, agreement forests and treewidth: combinatorial algorithms for constructing phylogenetic networks. PhD thesis, Maastricht University, The Netherlands, 2015. Keywords: explicit network, from rooted trees, phylogenetic network, phylogeny, reconstruction.         15 Claudia Solís-Lemus. Statistical methods to infer population structure with coalescence and gene flow. PhD thesis, University of Wisconsin-Madison, 2015. Keywords: explicit network, from quartets, from unrooted trees, likelihood, phylogenetic network, phylogeny, Program PhyloNetworks SNaQ, semidirected network. Note: https://www.stat.wisc.edu/~claudia/thesis.pdf.
2014
16 Josh Voorkamp né Collins. Untangling Evolution. PhD thesis, University of Otago, New Zealand, 2014. Keywords: agreement forest, explicit network, from rooted trees, generation, phylogenetic network, phylogeny, reconstruction. Note: http://otago.ourarchive.ac.nz/handle/10523/4802.         17 Yi-Chieh Wu. Computational evolutionary genomics : phylogenomic models spanning domains, genes, individuals, and species. PhD thesis, Massachusetts Institute of Technology, U.S.A., 2014. Keywords: duplication, from sequences, from species tree, lateral gene transfer, loss, phylogeny, Program TreeFix-DTL, reconstruction. Note: http://hdl.handle.net/1721.1/87937.         18 Yun Yu. Models and Methods for Evolutionary Histories Involving Hybridization and Incomplete Lineage Sorting. PhD thesis, Rice University, U.S.A., 2014. Keywords: hybridization, incomplete lineage sorting, phylogenetic network, phylogeny, Program PhyloNet, reconstruction, software. Note: http://hdl.handle.net/1911/77583.
2013
19 Sha Zhu. Stochastic tree models and probabilistic modelling of gene trees of given species networks. PhD thesis, University of Canterbury, New Zealand, 2013. Keywords: from network, generation, phylogenetic network, phylogeny, simulation, statistical model. Note: http://hdl.handle.net/10092/7944.         20 Thi-Hau Nguyen. Réconciliations: corriger des arbres de gènes et inférer la fiabilité des événements évolutifs. PhD thesis, Université Montpellier 2, France, 2013. Keywords: duplication, explicit network, from rooted trees, heuristic, lateral gene transfer, phylogenetic network, phylogeny, Program Mowgli, Program MowgliNNI, reconstruction. Note: http://www.biu-montpellier.fr/florabium/servlet/DocumentFileManager?source=ged&document=ged:IDOCS:247665&resolution=&recordId=theses%3ABIU_THESE%3A1789&file=.         21 Chris Whidden. Efficient Computation and Application of Maximum Agreement Forests. PhD thesis, Dalhousie University, Canada, 2013. Keywords: agreement forest, explicit network, FPT, from rooted trees, minimum number, phylogenetic network, phylogeny, reconstruction. Note: http://hdl.handle.net/10222/35349.         22 Sarah Bastkowski. From Trees to Networks and Back. PhD thesis, University of East Anglia, 2013. Keywords: abstract network, NeighborNet, phylogenetic network, phylogeny, Program FlatNJ, Program QNet, Program SplitsTree, reconstruction, software, split network. Note: http://spectre-suite-of-phylogenetic-tools-for-reticulate-evolution.readthedocs.io/en/latest/_downloads/spectre_bastkowskis_thesis.pdf.
2012
23 Hyun Jung Park. Towards Accurate Reconstruction of Phylogenetic Networks. PhD thesis, Rice University, U.S.A., 2012. Keywords: explicit network, likelihood, parsimony, phylogenetic network, phylogeny, reconstruction. Note: http://scholarship.rice.edu/handle/1911/64705.         24 Devin Robert Bickner. On normal networks. PhD thesis, Iowa State University, U.S.A., 2012. Keywords: distance between networks, explicit network, from network, from trees, normal network, phylogenetic network, phylogeny, polynomial, reconstruction, SPR distance. Note: http://gradworks.umi.com/3511361.pdf.         25 Alix Boc. Détection des transferts horizontaux de gènes : modèles et algorithmes appliqués à l'évolution des espèces et des langues. PhD thesis, Université du Québec à Montréal, Canada, 2012. Keywords: explicit network, from rooted trees, from species tree, phylogenetic network, phylogeny, Program T REX, reconstruction. Note: http://www.collectionscanada.gc.ca/obj/thesescanada/vol2/QMUQ/TC-QMUQ-4658.pdf.
2011
26 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.         27 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.         28 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.         29 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/.
2010
30 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/.         31 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.         32 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.
2009
33 Leo van Iersel. Algorithms, Haplotypes and Phylogenetic Networks. PhD thesis, Eindhoven University of Technology, The Netherlands, 2009. Keywords: evaluation, explicit network, exponential algorithm, FPT, from triplets, galled tree, level k phylogenetic network, mu distance, phylogenetic network, phylogeny, polynomial, Program Level2, Program Marlon, Program Simplistic, Program T REX, reconstruction. Note: http://www.win.tue.nl/~liersel/thesis_vaniersel_viewing.pdf.         34 Martin Lott. New Methods for Constructing Phylogenetic Networks from Multi-Labelled Trees. PhD thesis, University of East Anglia, U.K., 2009. Keywords: duplication, explicit network, from multilabeled tree, phylogenetic network, phylogeny, Program PADRE, reconstruction, software. Note: http://www.ic0.net/thesis-martin-final.pdf.         35 Klaus Schliep. Some applications of statistical phylogenetics. PhD thesis, Massey University, New Zealand, 2009. Keywords: abstract network, phylogenetic network, Program Phangorn, reconstruction, split network. Note: http://muir.massey.ac.nz/handle/10179/931.         36 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.         37 Qiong Wu. Phylogenetic Networks: New Constructions and Applications. PhD thesis, Université of East Anglia, U.K., 2009. Keywords: abstract network, phylogenetic network, phylogeny, reconstruction, split network. Note: http://ethos.bl.uk/OrderDetails.do?did=1&uin=uk.bl.ethos.514315.         38 Lichen Bao. Phylogenetic network construction and the application. PhD thesis, University of Texas at Dallas, U.S.A., 2009. Keywords: from distances, phylogenetic network, phylogeny, reconstruction, split, split network. Note: http://proquest.umi.com/pqdlink?did=1952801881&sid=1&Fmt=6&clientId=176295&RQT=309&VName=PQD.
2008
39 Simone Linz. Reticulation in evolution. PhD thesis, Heinrich-Heine-University, Düsseldorf, Germany, 2008. Keywords: agreement forest, FPT, from rooted trees, lateral gene transfer, phylogenetic network, phylogeny, SPR distance, statistical model. Note: http://docserv.uni-duesseldorf.de/servlets/DocumentServlet?id=8505.         40 Tobias Kloepper. Algorithms for the Calculation and Visualisation of Phylogenetic Networks. PhD thesis, Eberhard-Karls-Universität Tübingen, Germany, 2008. Keywords: from rooted trees, from sequences, from unrooted trees, galled network, phylogenetic network, phylogeny, Program SplitsTree, reconstruction, split network, visualization. Note: https://publikationen.uni-tuebingen.de/xmlui/handle/10900/49159.         41 Anthony Labarre. Combinatorial aspects of genome rearrangements and haplotype networks. PhD thesis, Université Libre de Bruxelles, Belgium, 2008. Keywords: abstract network, from unrooted trees, haplotype network, phylogenetic network, phylogeny, reconstruction. Note: http://homepages.ulb.ac.be/~alabarre/publications/phd-thesis.pdf.         42 Jaroslaw Byrka. Randomized Approximation Algorithms: Facility Location, Phylogenetic Networks, Nash Equilibria. PhD thesis, Eindhoven University of Technology, Netherlands, 2008. Note: http://disopt.epfl.ch/webdav/site/disopt/users/191068/public/phdthesis_byrka.pdf.
2007
43 Monique M. Morin. Phylogenetic Networks: Simulation, Characterization, and Reconstruction. PhD thesis, The University of New Mexico, U.S.A., 2007. Keywords: evaluation, explicit network, hybridization, lateral gene transfer, phylogenetic network, phylogeny, Program NetGen, simulation, software. Note: http://www.cs.unm.edu/~morin/morin_phd.pdf.         44 Alice Lesser. Optimal and Hereditarily Optimal Realizations of Metric Spaces. PhD thesis, Uppsala University, Sweden, 2007. Keywords: from distances, optimal realization, phylogenetic network, phylogeny, realization. Note: http://www.diva-portal.org/diva/getDocument?urn_nbn_se_uu_diva-8297-2__fulltext.pdf.         45 Bastienne Vriesendorp. Phylogenenetworks, exploring reticulate evolution and its consequences for phylogenetic reconstruction. PhD thesis, Wageningen University, The Netherlands, 2007. Keywords: consensus, distance between networks, evaluation, hybridization, median network, NeighborNet, parsimony, phylogenetic network, phylogeny, Program SplitsTree, split decomposition, survey. Note: http://library.wur.nl/wda/dissertations/dis4239.pdf.         46 Yuanyi Zhang. Optimization Algorithms for Phylogenetic Networks. PhD thesis, University of Texas at Dallas, U.S.A., 2007. Keywords: abstract network, explicit network, from distances, phylogenetic network, phylogeny, reconstruction, split, split network, visualization. Note: http://proquest.umi.com/pqdlink?did=1421626541&sid=1&Fmt=6&clientId=176295&RQT=309&VName=PQD.
2006
47 Pawel Górecki. Detection of horizontal gene transfer. PhD thesis, Warsaw University, Poland, 2006. Keywords: explicit network, from rooted trees, from species tree, lateral gene transfer, NP complete, parsimony, phylogenetic network, phylogeny, polynomial, reconstruction.         48 Olivier Gauthier. Utilisation de réseaux en analyse phylogénétique. PhD thesis, Université de Montréal, Canada, 2006. Note: http://igm.univ-mlv.fr/phylnet/PhylogeneticNetworks/docs/GauthierPhdThesis.pdf.
2004
49 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.         50 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.
2001
51 Barbara R. Holland. Evolutionary analyses of large data sets: Trees and beyond. PhD thesis, Massey University, New Zealand, 2001. Keywords: median network, split. Note: http://mro.massey.ac.nz/handle/10179/2078.
1999
52 Arne Röhl. Phylogenetische Netzwerke. PhD thesis, Universität Hamburg, Germany, 1999. Note: http://www.sub.uni-hamburg.de/opus/volltexte/1999/53/html/Phylogenetische_Netzwerke.html.
1997
53 David Bryant. Building Trees, Hunting for Trees, and Comparing Trees: theory and method in phylogenetic analysis. PhD thesis, Dept. Mathematics, University of Canterbury, New Zealand, 1997. Note: http://citeseer.ist.psu.edu/685475.html.
1995
54 Rainer Wetzel. Zur Visualisierung abstrakter Ahnlichkeitsbeziehungen. PhD thesis, Universität Bielefeld, Germany, 1995. Keywords: abstract network, circular split system, visualization.
1986
55 Patrice Bertrand. Étude de la représentation pyramidale. PhD thesis, Université de Paris-Dauphine, France, 1986. Keywords: abstract network, pyramid.