Publications of Year 2017  
Article (Journal)
1
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Katharina Huber, Leo van Iersel, Vincent Moulton, Celine Scornavacca and Taoyang Wu. Reconstructing phylogenetic level-1 networks from nondense binet and trinet sets. In ALG, Vol. 77(1):173-200, 2017.  
Keywords: explicit network, FPT, from binets, from subnetworks, from trinets, NP complete, phylogenetic network, phylogeny, polynomial, reconstruction.
Note: http://arxiv.org/abs/1411.6804.
       

2

Timothy G. Vaughan. IcyTree: rapid browser-based visualization for phylogenetic trees and networks. In BIO, Vol. 33(15):2392-2394, 2017.  
Keywords: ARG, explicit network, from network, phylogenetic network, phylogeny, Program IcyTree, software, visualization.
Note: http://dx.doi.org/10.1093/bioinformatics/btx155.
       

3
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Edwin Jacox, Mathias Weller, Eric Tannier and Celine Scornavacca. Resolution and reconciliation of non-binary gene trees with transfers, duplications and losses. In BIO, Vol. 33(7):980-987, 2017.  
Keywords: duplication, explicit network, FPT, from rooted trees, from species tree, lateral gene transfer, loss, phylogenetic network, phylogeny, reconstruction.
Note: http://dx.doi.org/10.1093/bioinformatics/btw778.
       

4
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Leo van Iersel, Vincent Moulton, Eveline De Swart and Taoyang Wu. Binets: fundamental building blocks for phylogenetic networks. In BMB, Vol. 79(5):1135-1154, 2017.  
Keywords: approximation, explicit network, from binets, from subnetworks, galled tree, level k phylogenetic network, NP complete, phylogenetic network, phylogeny, reconstruction.
Note: http://dx.doi.org/10.1007/s11538-017-0275-4.
       

5
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Philippe Gambette, Katharina Huber and Guillaume Scholz. Uprooted Phylogenetic Networks. In BMB, Vol. 79(9):2022-2048, 2017.  
Keywords: circular split system, explicit network, from splits, galled tree, phylogenetic network, phylogeny, polynomial, reconstruction, split network, uniqueness.
Note: http://arxiv.org/abs/1511.08387.
       

6
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Charles Semple. Size of a phylogenetic network. In DAM, Vol. 217(2):362-367, 2017.  
Keywords: compressed network, number of vertices, phylogenetic network, phylogeny, stack-free network.
Note: http://www.math.canterbury.ac.nz/~c.semple/papers/S16.pdf.
       

7
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Olga K. Kamneva and Noah A. Rosenberg. Simulation-Based Evaluation of Hybridization Network Reconstruction Methods in the Presence of Incomplete Lineage Sorting. In Evolutionary Bioinformatics, Vol. 13(1176934317691935):1-16, 2017.  
Keywords: evaluation, explicit network, incomplete lineage sorting, simulation.
Note: https://dx.doi.org/10.1177%2F1176934317691935.
       

8
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Andreas Gunawan, Bhaskar DasGupta and Louxin Zhang. A decomposition theorem and two algorithms for reticulation-visible networks. In Information and Computation, Vol. 252:161-175, 2017.  
Keywords: cluster containment, explicit network, from clusters, from network, from rooted trees, phylogenetic network, phylogeny, polynomial, reticulation-visible network, tree containment.
Note: https://www.cs.uic.edu/~dasgupta/resume/publ/papers/Infor_Comput_IC4848_final.pdf.
       

9
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Vincent Moulton, James Oldman and Taoyang Wu. A cubic-time algorithm for computing the trinet distance between level-1 networks. In IPL, Vol. 123:36-41, 2017.  
Keywords: distance between networks, explicit network, from network, phylogenetic network, phylogeny, polynomial, Program TriLoNet.
Note: https://doi.org/10.1016/j.ipl.2017.03.002.
       

10
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Katharina Huber, Vincent Moulton and Taoyang Wu. Hierarchies from lowest stable ancestors in nonbinary phylogenetic networks. In JOC, 2017.  
Keywords: characterization, explicit network, phylogenetic network, phylogeny.
Note: To appear.
       

11
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Philippe Gambette, Katharina Huber and Steven Kelk. On the challenge of reconstructing level-1 phylogenetic networks from triplets and clusters. In JOMB, Vol. 74(7):1729-1751, 2017.  
Keywords: from clusters, from triplets, galled tree, phylogenetic network, phylogeny, reconstruction, uniqueness.
Note: http://dx.doi.org/10.1007/s00285-016-1068-3.
       

12
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Gabriel Cardona and Joan Carles Pons. Reconstruction of LGT networks from tri-LGT-nets. In JOMB, Vol. 75(6-7):1669-1692, 2017.  
Keywords: explicit network, from subnetworks, from tri-LGT-nets, LGT network, phylogenetic network, phylogeny, reconstruction, uniqueness.
Note: https://doi.org/10.1007/s00285-017-1171-0.
       

13
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Mohammad Hossein Reyhani and Hadi Poormohammadi. RPNCH: A Method for Constructing Rooted Phylogenetic Networks from Rooted Triplets based on Height Function. In Journal of Paramedical Sciences, Vol. 8(4):14-20, 2017.  
Keywords: from triplets, heuristic, phylogenetic network, phylogeny, reconstruction.
Note: http://journals.sbmu.ac.ir/jps/article/view/16707.
       

14
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Christopher Bryant, Mareike Fischer, Simone Linz and Charles Semple. On the Quirks of Maximum Parsimony and Likelihood on Phylogenetic Networks. In JTB, Vol. 417:100-108, 2017.  
Keywords: explicit network, from sequences, likelihood, parsimony, phylogenetic network, phylogeny.
Note: http://arxiv.org/abs/1505.06898.
       

15
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Celine Scornavacca, Joan Carles Pons and Gabriel Cardona. Fast algorithm for the reconciliation of gene trees and LGT networks. In JTB, Vol. 418:129-137, 2017.  
Keywords: duplication, explicit network, from network, from rooted trees, lateral gene transfer, LGT network, loss, parsimony, phylogenetic network, phylogeny, polynomial, reconstruction.
       

16
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Magnus Bordewich, Simone Linz and Charles Semple. Lost in space? Generalising subtree prune and regraft to spaces of phylogenetic networks. In JTB, Vol. 423:1-12, 2017.  
Keywords: distance between networks, explicit network, phylogenetic network, phylogeny, reticulation-visible network, SPR distance, tree child network, tree-based network.
Note: https://simonelinz.files.wordpress.com/2017/04/bls171.pdf.
       

17
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Claudia Solís-Lemus, Paul Bastide and Cécile Ané. PhyloNetworks: A Package for Phylogenetic Networks. In MBE, Vol. 34(12):3292-3298, 2017.  
Keywords: from sequences, from trees, likelihood, phylogenetic network, phylogeny, Program PhyloNetworks SNaQ, reconstruction, software.
Note: https://doi.org/10.1093/molbev/msx235.
       

18
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Klaus Schliep, Alastair J. Potts, David A. Morrison and Guido W. Grimm. Intertwining phylogenetic trees and networks. In Methods in Ecology and Evolution, Vol. 8(10):1212-1220, 2017.  
Keywords: abstract network, from network, from unrooted trees, phylogenetic network, phylogeny, split network, visualization.
Note: http://dx.doi.org/10.1111/2041-210X.12760.
       

19
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Philippe Gambette, Leo van Iersel, Mark Jones, Manuel Lafond, Fabio Pardi and Celine Scornavacca. Rearrangement Moves on Rooted Phylogenetic Networks. In PLoS Computational Biology, Vol. 13(8):e1005611.1-21, 2017.  
Keywords: distance between networks, explicit network, from network, NNI distance, phylogenetic network, phylogeny, SPR distance.
Note: https://hal-upec-upem.archives-ouvertes.fr/hal-01572624/en/.
       

20
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Sha Zhu and James H. Degnan. Displayed Trees Do Not Determine Distinguishability Under the Network Multispecies Coalescent. In SB, Vol. 66(2):283-298, 2017.  
Keywords: branch length, coalescent, explicit network, from network, likelihood, phylogenetic network, phylogeny, Program Hybrid-coal, Program Hybrid-Lambda, Program PhyloNet, software, uniqueness.
Note: presentation available at https://www.youtube.com/watch?v=JLYGTfEZG7g.
       

21
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Juan Wang and Maozu Guo. A Metric on the Space of kth-order reduced Phylogenetic Networks. In Scientific Reports, Vol. 7(3189):1-10, 2017.  
Keywords: distance between networks, explicit network, from network, kth-order reduced network, phylogenetic network, phylogeny, polynomial.
Note: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5466651/.
       

22
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Satyan L. Devadoss and Samantha Petti. A Space of Phylogenetic Networks. In SIAM Journal on Applied Algebra and Geometry, Vol. 1(1):683-705, 2017.  
Keywords: abstract network, circular split system, phylogenetic network, phylogeny, split network.
Note: http://arxiv.org/abs/1607.06978.
       

23
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Monika Balvociute, David Bryant and Andreas Spillner. When can splits be drawn in the plane? In SIAM Journal on Discrete Mathematics, Vol. 31(2):839-856, 2017.  
Keywords: abstract network, characterization, flat, phylogenetic network, planar, split, split network.
Note: http://arxiv.org/abs/1509.06104v1.
       

24
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Julia Matsieva, Steven Kelk, Celine Scornavacca, Chris Whidden and Dan Gusfield. A Resolution of the Static Formulation Question for the Problem of Computing the History Bound. In TCBB, Vol. 14(2):404-417, 2017.  
Keywords: ARG, explicit network, from sequences, minimum number, phylogenetic network, phylogeny.
       

25
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Misagh Kordi and Mukul S. Bansal. On the Complexity of Duplication-Transfer-Loss Reconciliation with Non-Binary Gene Trees. In TCBB, Vol. 14(3):587-599, 2017.  
Keywords: duplication, from rooted trees, from species tree, lateral gene transfer, loss, NP complete, phylogenetic network, phylogeny, reconstruction.
Note: http://compbio.engr.uconn.edu/papers/Kordi_DTLreconciliationPreprint2015.pdf.
       

InProceedings
26
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Ruzbeh Tusserkani, Hadi Poormohammadi, Azin Azadi and Changiz Eslahchi. Inferring phylogenies from minimal information. In AEEICB17, Pages 202-206, IEEE, 2017.  
Keywords: from triplets, phylogenetic network, phylogeny, Program TripNet, reconstruction.
       

27
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Jesper Jansson, Ramesh Rajaby and Wing-Kin Sung. An Efficient Algorithm for the Rooted Triplet Distance Between Galled Trees. In AlCoB17, Vol. 10252:115-126 of LNCS, Springer, 2017.  
Keywords: distance between networks, from network, phylogenetic network, phylogeny, polynomial, reconstruction, triplet distance.
Note: .
       

28
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Bingxin Lu, Louxin Zhang and Hon Wai Leong. A program to compute the soft Robinson-Foulds distance between phylogenetic networks. In APBC17, Vol. 18(Suppl. 2):111 of BMC Genomics, 2017.  
Keywords: cluster containment, distance between networks, explicit network, exponential algorithm, from network, phylogenetic network, phylogeny, Program icelu-PhyloNetwork.
Note: http://dx.doi.org/10.1186/s12864-017-3500-5.
       

29
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Kuang-Yu Chang, Yun Cui, Siu-Ming Yiu and Wing-Kai Hon. Reconstructing One-Articulated Networks with Distance Matrices. In ISBRA17, Vol. 10330:34-45 of LNCS, Springer, 2017.  
Keywords: explicit network, from distances, k-reticulated, phylogenetic network, phylogeny, reconstruction.
Note: https://link.springer.com/content/pdf/10.1007%2F978-3-319-59575-7.pdf#page=100.
       

30
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Han Lai, Maureen Stolzer and Dannie Durand. Fast Heuristics for Resolving Weakly Supported Branches Using Duplication, Transfers, and Losses. In RECOMB-CG17, Vol. 10562:298-320 of LNCS, Springer, 2017.  
Keywords: duplication, explicit network, from rooted trees, from species tree, lateral gene transfer, loss, phylogenetic network, phylogeny, Program Notung, reconstruction.
       

PhdThesis
31
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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.
       

32
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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..
       

Misc
33
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Joan Carles Pons, Charles Semple and Mike Steel. Nonbinary tree-based networks: characterisations, metrics, and support trees. 2017.  
Keywords: characterization, explicit network, from network, phylogenetic network, phylogeny, time consistent network, tree-based network.
Note: https://arxiv.org/abs/1710.07836.
       

34
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Jonathan Klawitter. The SNPR neighbourhood of tree-child networks. 2017.  
Keywords: distance between networks, phylogenetic network, phylogeny, SPR distance, tree child network.
Note: https://arxiv.org/abs/1707.09579
       

35
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Simone Linz and Charles Semple. Attaching leaves and picking cherries to characterise the hybridisation number for a set of phylogenies. 2017.  
Keywords: agreement forest, cherry-picking, explicit network, from rooted trees, phylogenetic network, phylogeny, reconstruction, tree child network.
Note: https://arxiv.org/abs/1712.04131.
       

36
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Janosch Döcker, Leo van Iersel, Steven Kelk and Simone Linz. Deciding the existence of a cherry-picking sequence is hard on two trees. 2017.  
Keywords: cherry-picking, explicit network, hybridization, minimum number, NP complete, phylogenetic network, phylogeny, reconstruction, temporal-hybridization number, time consistent network, tree child network.
Note: https://arxiv.org/abs/1712.02965.
       

37
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Luay Nakhleh. Phylogenetic Networks: From Displayed Trees to a Distribution of Gene Trees. Phyloseminar #70, 2017.  
Keywords: bayesian, coalescent, explicit network, phylogenetic network, phylogeny, Program PhyloNet, reconstruction, statistical model.
Note: https://www.youtube.com/watch?v=dkQsvLUUDcQ.
       

38
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Celine Scornavacca. Occam's razor in phylogenetic network reconstruction. Phyloseminar #71, 2017.  
Keywords: explicit network, from rooted trees, parsimony, phylogenetic network, phylogeny, reconstruction.
Note: https://www.youtube.com/watch?v=W6tEVulgQu8.
       

39
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Cécile Ané. From reconstructing to using phylogenetic networks. Phyloseminar #72, 2017.  
Keywords: explicit network, from sequences, likelihood, phylogenetic network, phylogeny, Program PhyloNetworks SNaQ, reconstruction, semidirected network.
Note: https://www.youtube.com/watch?v=PF4j_JOQP0c.