InProceedings publications sorted by year 
2016
1
photophotophoto
Andreas Gunawan, Bhaskar DasGupta and Louxin Zhang. Locating a Tree in a Reticulation-Visible Network in Cubic Time. In RECOMB2016, Vol. 9649:266 of LNBI, Springer, 2016.  
Keywords: cluster containment, explicit network, from clusters, from network, from rooted trees, phylogenetic network, phylogeny, polynomial, reticulation-visible network, tree containment.
Note: http://arxiv.org/abs/1507.02119.
       

2
photophotophotophotophoto
Philippe Gambette, Andreas Gunawan, Anthony Labarre, Stéphane Vialette and Louxin Zhang. Solving the Tree Containment Problem for Genetically Stable Networks in Quadratic Time. In IWOCA15, Vol. 9538:197-208 of LNCS, springer, 2016.  
Keywords: explicit network, from network, from rooted trees, genetically stable network, phylogenetic network, phylogeny, polynomial, tree containment.
Note: https://hal-upec-upem.archives-ouvertes.fr/hal-01226035 .
       

3
photophotophoto
Andreas Gunawan, Bingxin Lu and Louxin Zhang. A program for verification of phylogenetic network models. In ECCB16, Vol. 32(17):i503-i510 of BIO, 2016.  
Keywords: exponential algorithm, from network, from rooted trees, phylogenetic network, phylogeny, software, tree containment.
Note: http://dx.doi.org/10.1093/bioinformatics/btw467.
       

4
photophoto
Ioannis G. Tollis and Konstantinos G. Kakoulis. Algorithms for Visualizing Phylogenetic Networks. In GD16, Vol. 9801:183-195 of LNCS, springer, 2016.  
Keywords: explicit network, galled network, galled tree, NP complete, planar, visualization.
Note: http://arxiv.org/abs/1609.00755.
       

5
photophoto
Nikita Alexeev and Max A. Alekseyev. Combinatorial Scoring of Phylogenetic Networks. In COCOON16, Vol. 9797:560-572 of LNCS, Springer, 2016.  
Keywords: cactus graph, enumeration, explicit network, galled tree, phylogenetic network, phylogeny.
Note: http://arxiv.org/abs/1602.02841.
       

6
photophoto
Jiafan Zhu, Yun Yu and Luay Nakhleh. In the Light of Deep Coalescence: Revisiting Trees Within Networks. In RECOMB-CG16, Vol. 17(suppl. 14):415.271-282 of BMCB, 2016.  
Keywords: branch length, evaluation, explicit network, phylogenetic network, phylogeny, statistical model, tree-based network.
Note: http://arxiv.org/abs/1606.07350.
       

2015
7
photophotophotophotophoto
Philippe Gambette, Andreas Gunawan, Anthony Labarre, Stéphane Vialette and Louxin Zhang. Locating a Tree in A Phylogenetic Network in Quadratic Time. In RECOMB15, Vol. 9029:96-107 of LNCS, Springer, 2015.  
Keywords: evaluation, explicit network, from network, from rooted trees, genetically stable network, nearly-stable network, phylogenetic network, phylogeny, polynomial, tree containment.
Note: https://hal.archives-ouvertes.fr/hal-01116231/en.
       

8
photo
Dan Gusfield. Persistent Phylogeny: A Galled-Tree and Integer Linear Programming Approach. In BCB15, Pages 443-451, 2015.  
Keywords: explicit network, from binary characters, galled tree, integer linear programming, phylogenetic network, phylogeny, reconstruction.
Note: http://arxiv.org/abs/1506.00678.
       

9
photophoto
Quan Nguyen and Teemu Roos. Likelihood-based inference of phylogenetic networks from sequence data by PhyloDAG. In ALCOB2015, Vol. 9199:126-140 of LNCS, springer, 2015.  
Keywords: BIC, explicit network, from sequences, likelihood, phylogenetic network, phylogeny, Program PhyloDAG, reconstruction, software.
Note: http://www.cs.helsinki.fi/u/ttonteri/pub/alcob2015.pdf.
       

10
photo
Vladimir Ulyantsev and Mikhail Melnik. Constructing Parsimonious Hybridization Networks from Multiple Phylogenetic Trees Using a SAT-solver. In ALCOB2015, Vol. 9199:141-153 of LNCS, springer, 2015.  
Keywords: explicit network, from rooted trees, from trees, phylogenetic network, phylogeny, Program PIRN, reconstruction.
       

11
photophotophoto
Jittat Fakcharoenphol, Tanee Kumpijit and Attakorn Putwattana. A Faster Algorithm for the Tree Containment Problem for Binary Nearly Stable Phylogenetic Networks. In Proceedings of the The 12th International Joint Conference on Computer Science and Software Engineering (JCSSE'15), Pages 337-342, IEEE, 2015.  
Keywords: dynamic programming, explicit network, from network, from rooted trees, nearly-stable network, phylogenetic network, phylogeny, polynomial, tree containment.
       

12
photophoto
Misagh Kordi and Mukul S. Bansal. On the Complexity of Duplication-Transfer-Loss Reconciliation with Non-Binary Gene Trees. In ISBRA15, Vol. 9096:187-198 of LNCS, springer, 2015.  
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_ISBRA2015.pdf.
       

13
photophoto
Yun Yu and Luay Nakhleh. A Distance-Based Method for Inferring Phylogenetic Networks in the Presence of Incomplete Lineage Sorting. In ISBRA15, Vol. 9096:378-389 of LNCS, springer, 2015.  
Keywords: bootstrap, explicit network, from distances, heuristic, incomplete lineage sorting, phylogenetic network, phylogeny, reconstruction.
Note: http://bioinfo.cs.rice.edu/sites/bioinfo.cs.rice.edu/files/YuNakhleh-ISBRA15.pdf.
       

14
photophoto
Johannes Fischer and Daniel Peters. A Practical Succinct Data Structure for Tree-Like Graphs. In WALCOM15, Vol. 8973:65-76 of LNCS, springer, 2015.  
Keywords: compression, from network, phylogenetic network, phylogeny.
       

15
photophoto
Yun Yu and Luay Nakhleh. A maximum pseudo-likelihood approach for phylogenetic networks. In RECOMB-CG15, Vol. 16(Suppl 10)(S10):1-10 of BMC Genomics, BioMed Central, 2015.  
Keywords: explicit network, from rooted trees, hybridization, incomplete lineage sorting, likelihood, phylogenetic network, phylogeny, Program PhyloNet, reconstruction, tripartition distance.
Note: http://dx.doi.org/10.1186/1471-2164-16-S10-S10.
       

16
photophoto
Thu-Hien To and Celine Scornavacca. Efficient algorithms for reconciling gene trees and species networks via duplication and loss events. In RECOMB-CG15, Vol. 16(Suppl 10)(S6):1-14 of BMC Genomics, BioMed Central, 2015.  
Keywords: explicit network, from network, from rooted trees, phylogenetic network, phylogeny, polynomial, reconstruction.
Note: http://dx.doi.org/10.1186/1471-2164-16-S10-S6.
       

2014
17
photophoto
Leo van Iersel and Steven Kelk. Kernelizations for the hybridization number problem on multiple nonbinary trees. In WG14, Vol. 8747:299-311 of LNCS, springer, 2014.  
Keywords: explicit network, from rooted trees, kernelization, minimum number, phylogenetic network, phylogeny, Program Treeduce, reconstruction.
Note: http://arxiv.org/abs/1311.4045.
       

18
photophotophotophoto
Ran Libeskind-Hadas, Yi-Chieh Wu, Mukul S. Bansal and Manolis Kellis. Pareto-optimal phylogenetic tree reconciliation. In ISMB14, Vol. 30:i87-i95 of BIO, 2014.  
Keywords: duplication, lateral gene transfer, loss, phylogenetic network, phylogeny, polynomial, Program Xscape, reconstruction.
Note: http://dx.doi.org/10.1093/bioinformatics/btu289.
       
Toggle abstract
2013
19
photo
Yufeng Wu. An Algorithm for Constructing Parsimonious Hybridization Networks with Multiple Phylogenetic Trees. In RECOMB13, Vol. 7821:291-303 of LNCS, springer, 2013.  
Keywords: explicit network, exponential algorithm, from rooted trees, phylogenetic network, phylogeny, Program PIRN, reconstruction.
Note: http://www.engr.uconn.edu/~ywu/Papers/ExactNetRecomb2013.pdf.
       
Toggle abstract
20
photophotophoto
Mukul S. Bansal, Eric J. Alm and Manolis Kellis. Reconciliation Revisited: Handling Multiple Optima when Reconciling with Duplication, Transfer, and Loss. In RECOMB13, Vol. 7821:1-13 of LNCS, springer, 2013.  
Keywords: duplication, from rooted trees, from species tree, loss, phylogenetic network, phylogeny, polynomial, Program RANGER-DTL, reconstruction.
Note: http://people.csail.mit.edu/mukul/Bansal_RECOMB2013.pdf.
       
Toggle abstract
21
photophotophotophotophotophoto
Hoa Vu, Francis Chin, Wing-Kai Hon, Henry Leung, Kunihiko Sadakane, Wing-Kin Sung and Siu-Ming Yiu. Reconstructing k-Reticulated Phylogenetic Network from a Set of Gene Trees. In ISBRA13, Vol. 7875:112-124 of LNCS, springer, 2013.  
Keywords: from rooted trees, k-reticulated, phylogenetic network, phylogeny, polynomial, Program ARTNET, Program CMPT, reconstruction.
Note: http://grid.cs.gsu.edu/~xguo9/publications/2013_Cloud%20computing%20for%20de%20novo%20metagenomic%20sequence%20assembly.pdf#page=123.
       
Toggle abstract
22
photophotophoto
Yun Yu, Nikola Ristic and Luay Nakhleh. Fast algorithms and heuristics for phylogenomics under ILS and hybridization. In RECOMB-CG'13, Vol. 14(Suppl 15):S6 of BMCB, 2013.  
Keywords: from network, from rooted trees, heuristic, phylogenetic network, phylogeny, Program PhyloNet, reconstruction.
       

23
photophotophoto
Zhi-Zhong Chen, Fei Deng and Lusheng Wang. Identifying Duplications and Lateral Gene Transfers Simultaneously and Rapidly. In CIBCB13, Pages 128-135, 2013.  
Keywords: duplication, FPT, from rooted trees, from species tree, phylogenetic network, phylogeny, reconstruction.
Note: http://www.cs.cityu.edu.hk/~lwang/research/singaporet2013.pdf.
       

2012
24
photophoto
Hyun Jung Park and Luay Nakhleh. MURPAR: A fast heuristic for inferring parsimonious phylogenetic networks from multiple gene trees. In ISBRA12, Vol. 7292:213-224 of LNCS, springer, 2012.  
Keywords: explicit network, heuristic, phylogenetic network, phylogeny, reconstruction, software.
       
Toggle abstract
25
photophoto
Pawel Górecki and Jerzy Tiuryn. Inferring evolutionary scenarios in the duplication, loss and horizontal gene transfer model. In Logic and Program Semantics, Vol. 7230:83-105 of LNCS, springer, 2012.  
Keywords: duplication, explicit network, lateral gene transfer, loss, phylogenetic network, phylogeny, reconstruction.
Note: http://dx.doi.org/10.1007/978-3-642-29485-3_7.
       
Toggle abstract
26
photophotophoto
Mukul S. Bansal, Eric J. Alm and Manolis Kellis. Efficient Algorithms for the Reconciliation Problem with Gene Duplication, Horizontal Transfer, and Loss. In ISMB12, Vol. 28(12):i283-i291 of BIO, 2012.  
Keywords: duplication, explicit network, from rooted trees, from species tree, lateral gene transfer, loss, phylogenetic network, phylogeny, Program Angst, Program Mowgli, Program RANGER-DTL, reconstruction.
Note: http://dx.doi.org/10.1093/bioinformatics/bts225.
       
Toggle abstract
27
photophotophotophotophoto
An-Chiang Chu, Jesper Jansson, Richard Lemence, Alban Mancheron and Kun-Mao Chao. Asymptotic Limits of a New Type of Maximization Recurrence with an Application to Bioinformatics. In TAMC12, Vol. 7287:177-188 of LNCS, springer, 2012.  
Keywords: from triplets, galled network, level k phylogenetic network, phylogenetic network.
Note: preliminary version.
       
Toggle abstract
28

Marco Alves, Joãd Alves, Rui Camacho, Pedro Soares and Luísa Pereira. From Networks to Trees. In PACBB'12, Vol. 154:129-136 of Advances in Intelligent and Soft Computing, springer, 2012.  
Keywords: from network, phylogenetic network, phylogeny.
       

29
photophoto
Jesper Jansson and Andrzej Lingas. Computing the rooted triplet distance between galled trees by counting triangles. In CPM12, Vol. 7354:385-398 of LNCS, springer, 2012.  
Keywords: distance between networks, explicit network, from network, galled tree, phylogenetic network, phylogeny, polynomial, triplet distance.
Note: http://www.df.lth.se/~jj/Publications/d_rt_for_Galled_Trees5_CPM_2012.pdf.
       
Toggle abstract
30
photophotophotophoto
Leo van Iersel, Steven Kelk, Nela Lekic and Celine Scornavacca. A practical approximation algorithm for solving massive instances of hybridization number. In WABI12, Vol. 7534(430-440) of LNCS, springer, 2012.  
Keywords: agreement forest, approximation, explicit network, from rooted trees, hybridization, phylogenetic network, phylogeny, Program CycleKiller, Program Dendroscope, Program HybridNET, reconstruction, software.
Note: http://arxiv.org/abs/1205.3417.
       
Toggle abstract
31
photophoto
Hyun Jung Park and Luay Nakhleh. Inference of reticulate evolutionary histories by maximum likelihood: The performance of information criteria. In RECOMB-CG'12, Vol. 13(suppl 19):S12 of BMCB, 2012.  
Keywords: AIC, BIC, explicit network, heuristic, likelihood, phylogenetic network, phylogeny, reconstruction, statistical model.
Note: http://www.biomedcentral.com/1471-2105/13/S19/S12.
       

32
photophotophotophotophoto
Maureen Stolzer, Han Lai, Minli Xu, Deepa Sathaye, Benjamin Vernot and Dannie Durand. Inferring Duplications, Losses, Transfers, and Incomplete Lineage Sorting with Non-Binary Species Trees. In ECCB12, Vol. 28(18):i409-i415 of BIO, 2012.  
Keywords: duplication, explicit network, from rooted trees, lateral gene transfer, loss, phylogenetic network, phylogeny, Program Notung, reconstruction.
Note: http://dx.doi.org/10.1093/bioinformatics/bts386.
       
Toggle abstract
33
photophotophotophotophoto
Thi-Hau Nguyen, Jean-Philippe Doyon, Stéphanie Pointet, Anne-Muriel Chifolleau Arigon, Vincent Ranwez and Vincent Berry. Accounting for Gene Tree Uncertainties Improves Gene Trees and Reconciliation Inference. In WABI12, Vol. 7534:123-134 of LNCS, springer, 2012.  
Keywords: duplication, heuristic, lateral gene transfer, phylogenetic network, phylogeny, Program Mowgli, reconstruction.
Note: http://hal.archives-ouvertes.fr/hal-00718347/en/.
       
Toggle abstract
34
photophotophotophoto
Katharina Huber, Vincent Moulton, Andreas Spillner, Sabine Storandt and Radoslaw Suchecki. Computing a consensus of multilabeled trees. In ALENEX12, Pages 84-92, 2012.  
Keywords: duplication, explicit network, exponential algorithm, phylogenetic network, phylogeny.
Note: http://siam.omnibooksonline.com/2012ALENEX/data/papers/020.pdf.
       
Toggle abstract
35
photo
Cayla McBee. Generalizing Fourier Calculus on Evolutionary Trees to Splits Networks. In ISPAN'12, Pages 149-155, 2012.  
Keywords: abstract network, from sequences, phylogenetic network, phylogeny, split network, statistical model.
       
Toggle abstract
2011
36
photophotophotophotophoto
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/.
       
Toggle abstract
37
photophotophoto
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.
       
Toggle abstract
38
photophoto
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.
       
Toggle abstract
39
photophoto
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.
       

40
photophotophotophoto
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.
       
Toggle abstract
2010
41
photophotophotophoto
Leo van Iersel, Steven Kelk, Regula Rupp and Daniel H. Huson. Phylogenetic Networks Do not Need to Be Complex: Using Fewer Reticulations to Represent Conflicting Clusters. In ISMB10, Vol. 26(12):i124-i131 of BIO, 2010.  
Keywords: from clusters, level k phylogenetic network, Program Dendroscope, Program HybridInterleave, Program HybridNumber, reconstruction.
Note: http://dx.doi.org/10.1093/bioinformatics/btq202, with proofs: http://arxiv.org/abs/0910.3082.
       
Toggle abstract
42
photophotophotophotophoto
Tetsuo Asano, Jesper Jansson, Kunihiko Sadakane, Ryuhei Uehara and Gabriel Valiente. Faster Computation of the Robinson-Foulds Distance between Phylogenetic Networks. In CPM10, Vol. 6129:190-201 of LNCS, springer, 2010.  
Keywords: distance between networks, explicit network, level k phylogenetic network, phylogenetic network, polynomial, spread.
Note: http://hdl.handle.net/10119/9859, slides available at http://cs.nyu.edu/parida/CPM2010/MainPage_files/18.pdf.
       
Toggle abstract
43
photo
Yufeng Wu. Close Lower and Upper Bounds for the Minimum Reticulate Network of Multiple Phylogenetic Trees. In ISMB10, Vol. 26(12):i140-i148 of BIO, 2010.  
Keywords: explicit network, from rooted trees, hybridization, minimum number, phylogenetic network, phylogeny, Program PIRN, software.
Note: http://dx.doi.org/10.1093/bioinformatics/btq198.
       
Toggle abstract
44
photo
Yufeng Wu and Jiayin Wang. Fast Computation of the Exact Hybridization Number of Two Phylogenetic Trees. In ISBRA10, Vol. 6053:203-214 of LNCS, springer, 2010.  
Keywords: agreement forest, explicit network, from rooted trees, hybridization, integer linear programming, minimum number, phylogenetic network, phylogeny, Program HybridNumber, Program SPRDist, SPR distance.
Note: http://www.engr.uconn.edu/~ywu/Papers/ISBRA10WuWang.pdf.
       
Toggle abstract
45
photophotophoto
Hyun Jung Park, Guohua Jin and Luay Nakhleh. Algorithmic strategies for estimating the amount of reticulation from a collection of gene trees. In CSB10, 2010.  
Keywords: bound, from rooted trees, heuristic, phylogenetic network, phylogeny, reconstruction, SPR distance.
Note: http://www.cs.rice.edu/~nakhleh/Papers/ParkEtAl-CSB2010.pdf.
       

46
photophotophoto
Chris Whidden, Robert G. Beiko and Norbert Zeh. Fast FPT Algorithms for Computing Rooted Agreement Forests: Theory and Experiments. In Proceedings of the ninth International Symposium on Experimental Algorithms (SEA'10), Vol. 6049:141-153 of LNCS, springer, 2010.  
Keywords: agreement forest, explicit network, FPT, from rooted trees, hybridization, minimum number, phylogenetic network, phylogeny, Program HybridInterleave, reconstruction, SPR distance.
Note: https://www.cs.dal.ca/sites/default/files/technical_reports/CS-2010-03.pdf.
       
Toggle abstract
2009
47
photophoto
Thu-Hien To and Michel Habib. Level-k Phylogenetic Networks Are Constructable from a Dense Triplet Set in Polynomial Time. In CPM09, (5577):275-288, springer, 2009.  
Keywords: explicit network, from triplets, level k phylogenetic network, minimum number, phylogenetic network, phylogeny, polynomial, reconstruction.
Note: http://arxiv.org/abs/0901.1657.
       
Toggle abstract
48
photophotophoto
Philippe Gambette, Vincent Berry and Christophe Paul. The structure of level-k phylogenetic networks. In CPM09, Vol. 5577:289-300 of LNCS, springer, 2009.  
Keywords: coalescent, explicit network, galled tree, level k phylogenetic network, phylogenetic network, Program Recodon.
Note: http://hal-lirmm.ccsd.cnrs.fr/lirmm-00371485/en/.
       
Toggle abstract
49
photophotophotophotophoto
Daniel H. Huson, Regula Rupp, Vincent Berry, Philippe Gambette and Christophe Paul. Computing Galled Networks from Real Data. In ISMBECCB09, Vol. 25(12):i85-i93 of BIO, 2009.  
Keywords: abstract network, cluster containment, explicit network, FPT, from clusters, from rooted trees, galled network, NP complete, phylogenetic network, phylogeny, polynomial, Program Dendroscope, reconstruction.
Note: http://hal-lirmm.ccsd.cnrs.fr/lirmm-00368545/en/.
       
Toggle abstract
50
photophoto
Lichen Bao and Sergey Bereg. Counting Faces in Split Networks. In ISBRA09, Vol. 5251:284-295 of LNCS, 2009.  
Note: http://dx.doi.org/10.1007/978-3-642-01551-9_12.
       
Toggle abstract
51
photo
Poornima Venugopal and Sergey Bereg. Layout of Phylogenetic Networks and Multi-Labeled Trees. In BIOT'09, Pages 91, 2009.  
Keywords: explicit network, phylogenetic network, phylogeny, Program PADRE, visualization.
Note: http://www.biotconf.org/PDFs/1456.pdf.
       

52
photophoto
Chris Whidden and Norbert Zeh. A Unifying View on Approximation and FPT of Agreement Forests. In WABI09, Vol. 5724:390-402 of LNCS, Springer, 2009.  
Keywords: agreement forest, approximation, explicit network, FPT, minimum number, phylogenetic network, phylogeny, reconstruction.
Note: https://www.cs.dal.ca/sites/default/files/technical_reports/CS-2009-02.pdf.
       
Toggle abstract
2008
53
photophotophotophotophotophoto
Leo van Iersel, Judith Keijsper, Steven Kelk, Leen Stougie, Ferry Hagen and Teun Boekhout. Constructing level-2 phylogenetic networks from triplets. In RECOMB08, Vol. 4955:450-462 of LNCS, springer, 2008.  
Keywords: explicit network, from triplets, level k phylogenetic network, NP complete, phylogenetic network, phylogeny, polynomial, Program Level2, reconstruction.
Note: http://homepages.cwi.nl/~iersel/level2full.pdf. An appendix with proofs can be found here http://arxiv.org/abs/0707.2890.
       
Toggle abstract
54
photophotophoto
Rune Lyngsø, Yun S. Song and Jotun Hein. Accurate Computation of Likelihoods in the Coalescent with Recombination via Parsimony. In RECOMB08, Vol. 4955:463-477 of LNCS, springer, 2008.  
Keywords: coalescent, likelihood, phylogenetic network, phylogeny, recombination, statistical model.
Note: http://dx.doi.org/10.1007/978-3-540-78839-3_41.
       
Toggle abstract
55
photophoto
Leo van Iersel and Steven Kelk. Constructing the Simplest Possible Phylogenetic Network from Triplets. In ISAAC08, Vol. 5369:472-483 of LNCS, springer, 2008.  
Keywords: explicit network, from triplets, galled tree, level k phylogenetic network, minimum number, phylogenetic network, phylogeny, polynomial, Program Marlon, Program Simplistic.
Note: http://arxiv.org/abs/0805.1859.
       

56
photophoto
Cuong Than and Luay Nakhleh. SPR-based Tree Reconciliation: Non-binary Trees and Multiple Solutions. In APBC08, Pages 251-260, 2008.  
Keywords: evaluation, from rooted trees, lateral gene transfer, phylogenetic network, phylogeny, Program LatTrans, Program PhyloNet, reconstruction, SPR distance.
Note: http://www.cs.rice.edu/~nakhleh/Papers/apbc08.pdf.
       

57
photophoto
Daniel H. Huson and Regula Rupp. Summarizing Multiple Gene Trees Using Cluster Networks. In WABI08, Vol. 5251:296-305 of LNCS, springer, 2008.  
Keywords: abstract network, from clusters, from rooted trees, phylogenetic network, phylogeny, polynomial, Program Dendroscope.
Note: http://dx.doi.org/10.1007/978-3-540-87361-7_25, slides from the MIEP Conference available at http://www.lirmm.fr/MIEP08/slides/11_13_rupp.pdf.
       
Toggle abstract
58
photophoto
Lichen Bao and Sergey Bereg. Clustered SplitsNetworks. In COCOA08, Vol. 5165:469-478 of LNCS, springer, 2008.  
Keywords: abstract network, from distances, NeighborNet, realization, reconstruction.
Note: http://dx.doi.org/10.1007/978-3-540-85097-7_44, slides available at http://www.utdallas.edu/~besp/cocoa08talk.pdf.
       
Toggle abstract
59
photophoto
Victoria Kusherbaeva and Nikolay Vyahhi. Stochastic Approach to Binary Matrix Partitioning for Phylogenetic Networks. In Proceedings of the SYRCODIS 2008 Colloquium on Databases and Information Systems (SYRCoDIS'08), Vol. 355 of CEUR Workshop Proceedings, 2008.  
Keywords: clustering, phylogenetic network, phylogeny, reconstruction.
Note: http://ftp.informatik.rwth-aachen.de/Publications/CEUR-WS/Vol-355/kusherbaeva.pdf.
       

60
photophoto
Sagi Snir and Tamir Tuller. Novel Phylogenetic Network Inference by Combining Maximum Likelihood and Hidden Markov Models. In WABI08, Vol. 5251:354-368 of LNCS, springer, 2008.  
Keywords: explicit network, from sequences, HMM, lateral gene transfer, likelihood, phylogenetic network, phylogeny, statistical model.
Note: http://dx.doi.org/10.1007/978-3-540-87361-7_30.
       
Toggle abstract
61
photophotophotophoto
Stefan Grünewald, Andreas Spillner, Kristoffer Forslund and Vincent Moulton. Constructing Phylogenetic Supernetworks from Quartets. In WABI08, Vol. 5251:284-295 of LNCS, springer, 2008.  
Keywords: abstract network, from quartets, from unrooted trees, phylogenetic network, phylogeny, Program QNet, Program SplitsTree, reconstruction, split network.
Note: http://dx.doi.org/10.1007/978-3-540-87361-7_24.
       
Toggle abstract
62
photophotophotophoto
Gabriel Cardona, Mercè Llabrés, Francesc Rosselló and Gabriel Valiente. Phylogenetic Networks: Justification, Models, Distances and Algorithms. In VI Jornadas de Matemática Discreta y Algorítmica (JMDA'08), 2008.  
Keywords: distance between networks, mu distance, phylogenetic network, phylogeny, polynomial, survey, time consistent network, tree child network, tripartition distance, triplet distance.
Note: http://bioinfo.uib.es/media/uploaded/jmda2008_submission_61-1.pdf.
       

63
photophoto
Ernst Althaus and Rouven Naujoks. Reconstructing Phylogenetic Networks with One Recombination. In Proceedings of the seventh International Workshop on Experimental Algorithms (WEA'08), Vol. 5038:275-288 of LNCS, springer, 2008.  
Keywords: enumeration, explicit network, exponential algorithm, from sequences, generation, parsimony, phylogenetic network, phylogeny, reconstruction, unicyclic network.
Note: http://dx.doi.org/10.1007/978-3-540-68552-4_21.
       
Toggle abstract
64
photophotophoto
Cuong Than, Guohua Jin and Luay Nakhleh. Integrating Sequence and Topology for Efficient and Accurate Detection of Horizontal Gene Transfer. In Proceedings of the Sixth RECOMB Comparative Genomics Satellite Workshop (RECOMB-CG'08), Vol. 5267:113-127 of LNCS, springer, 2008.  
Keywords: bootstrap, explicit network, from rooted trees, from sequences, lateral gene transfer, phylogenetic network, phylogeny, Program Nepal, Program PhyloNet, reconstruction.
Note: http://www.cs.rice.edu/~nakhleh/Papers/recombcg-08.pdf, slides available at http://igm.univ-mlv.fr/RCG08/RCG08slides/Cuong_Than_RCG08.pdf.
       

2007
65
photophoto
Daniel H. Huson and Tobias Kloepper. Beyond Galled Trees - Decomposition and Computation of Galled Networks. In RECOMB07, Vol. 4453:211-225 of LNCS, springer, 2007.  
Keywords: FPT, from splits, from trees, galled network, phylogenetic network, phylogeny, Program SplitsTree, reconstruction.
Note: http://dx.doi.org/10.1007/978-3-540-71681-5_15, errata..
       

66
photophotophotophoto
Guohua Jin, Luay Nakhleh, Sagi Snir and Tamir Tuller. Efficient Parsimony-based Methods for Phylogenetic Network Reconstruction. In ECCB06, Vol. 23(2):e123-e128 of BIO, 2007.  
Keywords: parsimony, phylogenetic network, phylogeny, Program Nepal, reconstruction.
Note: http://www.cs.rice.edu/~nakhleh/Papers/eccb06.pdf.
       

67
photophotophotophoto
Guohua Jin, Luay Nakhleh, Sagi Snir and Tamir Tuller. A New Linear-time Heuristic Algorithm for Computing the Parsimony Score of Phylogenetic Networks: Theoretical Bounds and Empirical Performance. In ISBRA07, Vol. 4463:61-72 of LNCS, springer, 2007.  
Keywords: approximation, heuristic, parsimony, phylogenetic network, phylogeny, Program Nepal.
Note: http://www.cs.rice.edu/~nakhleh/Papers/isbra07.pdf.
       

68
photophotophotophoto
Iyad A. Kanj, Luay Nakhleh, Cuong Than and Ge Xia. Seeing the Trees and Their Branches in the Network is Hard. In Proceedings of the Tenth Italian Conference on Theoretical Computer Science (ICTCS'07), 2007.  
Keywords: evaluation, from network, from rooted trees, NP complete, phylogenetic network, phylogeny, tree containment.
Note: http://www.cs.rice.edu/~nakhleh/Papers/ictcs07.pdf.
       

69
photophoto
Yufeng Wu and Dan Gusfield. Improved Algorithms for Inferring the Minimum Mosaic of a Set of Recombinants. In CPM07, Vol. 4580:150-161 of LNCS, springer, 2007.  
Note: http://wwwcsif.cs.ucdavis.edu/~gusfield/CPM2007mosaic.pdf.
       

70
photophoto
Yufeng Wu and Dan Gusfield. A new recombination lower bound and the minimum perfect phylogenetic forest problem. In COCOON07, Vol. 4598:16-26 of LNCS, springer, 2007.  
Keywords: perfect, phylogenetic network, phylogeny.
Note: http://dx.doi.org/10.1007/978-3-540-73545-8_5.
       

71
photophotophotophoto
Andreas W. M. Dress, Katharina Huber, Jacobus Koolen and Vincent Moulton. An Algorithm for Computing Virtual Cut Points in Finite Metric Spaces. In COCOA07, Vol. 4616:4-10 of LNCS, springer, 2007.  
Keywords: from distances.
Note: http://dx.doi.org/10.1007/978-3-540-73556-4_3.
       

72
photophoto
Patricia Buendia and Giri Narasimhan. Searching for Recombinant Donors in a Phylogenetic Network of Serial Samples. In ISBRA07, Vol. 4463:109-120 of LNCS, springer, 2007.  
Keywords: evaluation, phylogenetic network, phylogeny, recombination, recombination detection.
Note: http://dx.doi.org/10.1007/978-3-540-72031-7_10.
       

73
photo
D. S. Rao, G. N. Kumar, Dheeresh K. Mallick and Prasanta K. Jana. Parallel Construction of Conflict Graph for Phylogenetic Network Problem. In Pattern Recognition and Machine Intelligence (PReMI'07), Vol. 4815:398-405 of LNCS, springer, 2007.  
Note: http://dx.doi.org/10.1007/978-3-540-77046-6_49.
       

74
photophotophoto
Hadas Birin, Zohar Gal-Or, Isaac Elias and Tamir Tuller. Inferring Models of Rearrangements, Recombinations, and Horizontal Transfers by the Minimum Evolution Criterion. In WABI07, Vol. 4645:111-123 of LNCS, springer, 2007.  
Keywords: explicit network, from sequences, phylogenetic network, phylogeny, reconstruction.
Note: http://safrabio.cs.tau.ac.il/download/Papers/Birin_et_al.pdf.
       

2006
75
photophotophoto
Barbara R. Holland, Lars S. Jermiin and Vincent Moulton. Improved Consensus Network Techniques for Genome-Scale Phylogeny. In Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005 (SMBE'05), Vol. 23(5):848-855 of MBE, 2006.  
Keywords: consensus.
Note: http://dx.doi.org/10.1093/molbev/msj061.
       

76
photophotophoto
Daniel H. Huson, Mike Steel and James B. Whitfield. Reducing Distortion in Phylogenetic Networks. In WABI06, Vol. 4175:150-161 of LNCS, springer, 2006.  
Keywords: phylogenetic network, reconstruction.
Note: http://www.math.canterbury.ac.nz/~m.steel/research/Non_UC/files/distortion.pdf.
       

77
photophotophoto
Iyad A. Kanj, Luay Nakhleh and Ge Xia. Reconstructing Evolution of Natural Languages: Complexity and Parameterized Algorithms. In COCOON06, Vol. 4112:299-308 of LNCS, springer, 2006.  
Note: http://www.cs.rice.edu/~nakhleh/Papers/cocoon06.pdf.
       

78
photophotophotophoto
Cuong Than, Derek Ruths, Hideki Innan and Luay Nakhleh. Identifiability Issues in Phylogeny-Based Detection of Horizontal Gene Transfer. In Proceedings of the Fourth RECOMB Comparative Genomics Satellite Workshop (RECOMB-CG'06), Vol. 4205:215-229 of LNCS, springer, 2006. 1 comment  
Keywords: enumeration, explicit network, from rooted trees, from species tree, lateral gene transfer, phylogenetic network, phylogeny, Program LatTrans, Program PhyloNet.
Note: http://www.cs.rice.edu/~nakhleh/Papers/recombcg06-final.pdf.
       

79
photophoto
Yufeng Wu and Dan Gusfield. Efficient Computation of Minimum Recombination with Genotypes (not Haplotypes) In CSB06, Pages 147-156, 2006.  
Note: http://www.lifesciencessociety.org/CSB2006/Papers/131_Wu.pdf.
       

80
photophoto
Juan Diego Trujillo and Carlos Cotta. An Evolutionary Approach to the Inference of Phylogenetic Networks. In Proceedings of the ninth Conference on Parallel Problem Solving from Nature (PPSN'IX), Vol. 4193:332-341 of LNCS, springer, 2006.  
Note: http://www.lcc.uma.es/~ccottap/papers/trujillo06ppsn.pdf.
       

81
photophotophotophotophoto
Vladimir Makarenkov, Alix Boc, Charles Delwiche, Alpha B. Diallo and Hervé Philippe. New Efficient Algorithm for Modeling Partial and Complete Gene Transfer Scenarios. In IFCS06, Pages 341-349, springer, 2006.  
Note: http://www.labunix.uqam.ca/~makarenv/makarenv/IFCS_2006_M_et_al.pdf.
       

2005
82
photophoto
Vineet Bafna and Vikas Bansal. Improved recombination lower bounds for haplotype data. In RECOMB05, Vol. 3500:569-584 of LNCS, springer, 2005.  
Keywords: bound, minimum number, phylogeny, recombination.
Note: http://www.cse.ucsd.edu/users/vbafna/pub/recomblb05.pdf.
       

83
photophoto
Sergey Bereg and Kathryn Bean. Constructing Phylogenetic Networks from Trees. In BIBE05, Pages 299-305, 2005. 1 comment  
Keywords: evaluation, from distances, phylogenetic network, phylogeny, Program SplitsTree, Program T REX, reconstruction, split, split network.
Note: http://dx.doi.org/10.1109/BIBE.2005.19.
       
Toggle abstract
84
photophoto
Sergey Bereg and Yuanyi Zhang. Phylogenetic Networks Based on the Molecular Clock Hypothesis. In BIBE05, Pages 320-323, 2005.  
Note: http://dx.doi.org/10.1109/BIBE.2005.46.
       
Toggle abstract
85
photophotophotophoto
Ho-Leung Chan, Jesper Jansson, Tak-Wah Lam and Siu-Ming Yiu. Reconstructing an Ultrametric Galled Phylogenetic Network from a Distance Matrix. In MFCS05, Vol. 3618:224-235 of LNCS, springer, 2005.  
Keywords: from distances, galled tree, phylogenetic network, phylogeny, reconstruction.
Note: http://dx.doi.org/10.1007/11549345_20.
       

86
photo
Elena Dubrova. Phylogenetic networks with edge-disjoint recombination cycles. In Proceedings of SPIE Bioengineered and Bioinspired Systems II (SPIE-BBS II), Vol. 5839:381-388, 2005.  
Keywords: galled tree, phylogenetic network, polynomial, site consistency.
Note: http://dx.doi.org/10.1117/12.607910.
       
Toggle abstract
87
photophoto
Dan Gusfield and Vikas Bansal. A Fundamental Decomposition Theory for Phylogenetic Networks and Incompatible Characters. In RECOMB05, Vol. 3500:217-232 of LNCS, springer, 2005.  
Keywords: explicit network, from sequences, phylogenetic network, phylogeny, polynomial, recombination, reconstruction.
Note: http://wwwcsif.cs.ucdavis.edu/~gusfield/gusfieldrecomb.pdf.
       

88
photophotophotophoto
Ying-Jun He, Trinh N. D. Huynh, Jesper Jansson and Wing-Kin Sung. Inferring Phylogenetic Relationships Avoiding Forbidden Rooted Triplets. In APBC05, Pages 339-348, 2005.  
Note: https://dflund.se/~jj/Publications/forb_triplets4_APBC2005.pdf.
       

89
photophotophotophoto
Trinh N. D. Huynh, Jesper Jansson, Nguyen Bao Nguyen and Wing-Kin Sung. Constructing a Smallest Refining Galled Phylogenetic Network. In RECOMB05, Vol. 3500:265-280 of LNCS, springer, 2005.  
Keywords: from rooted trees, galled tree, NP complete, phylogenetic network, phylogeny, polynomial, Program SPNet, reconstruction.
Note: http://www.df.lth.se/~jj/Publications/refining_gn3_RECOMB2005.pdf.
       

90
photophotophotophoto
Daniel H. Huson, Tobias Kloepper, Peter J. Lockhart and Mike Steel. Reconstruction of Reticulate Networks from Gene Trees. In RECOMB05, Vol. 3500:233-249 of LNCS, springer, 2005.  
Keywords: from rooted trees, from splits, phylogenetic network, phylogeny, reconstruction, split, split network, visualization.
Note: http://dx.doi.org/10.1007/11415770_18.
       

91
photophoto
Daniel H. Huson and Tobias Kloepper. Computing recombination networks from binary sequences. In ECCB05, Vol. 21(suppl. 2):ii159-ii165 of BIO, 2005.  
Keywords: from sequences, phylogenetic network, phylogeny, recombination.
Note: http://dx.doi.org/10.1093/bioinformatics/bti1126.
       
Toggle abstract
92
photophoto
Jesper Jansson and Wing-Kin Sung. The Maximum Agreement of Two Nested Phylogenetic Networks. In ISAAC04, Vol. 3341:581-593 of LNCS, springer, 2005.  
Keywords: dynamic programming, MASN, nested network, NP complete, phylogenetic network, phylogeny, polynomial.
Note: http://www.df.lth.se/~jj/Publications/nested7_ISAAC2004.pdf.
       

93
photophotophoto
Jesper Jansson, Nguyen Bao Nguyen and Wing-Kin Sung. Algorithms for Combining Rooted Triplets into a Galled Phylogenetic Network. In SODA05, Pages 349-358, 2005. 1 comment  
Keywords: approximation, explicit network, from triplets, galled tree, phylogenetic network, phylogeny, polynomial, reconstruction.
Note: http://portal.acm.org/citation.cfm?id=1070481.
       

94
photophotophoto
Rune Lyngsø, Yun S. Song and Jotun Hein. Minimum Recombination Histories by Branch and Bound. In WABI05, Vol. 3692:239-250 of LNCS, springer, 2005.  
Keywords: ARG, branch and bound, from sequences, minimum number, Program Beagle, recombination, reconstruction, software.
Note: http://www.cs.ucdavis.edu/~yssong/Pub/WABI05-239.pdf.
       

95
photophoto
Luay Nakhleh and Li-San Wang. Phylogenetic Networks, Trees, and Clusters. In IWBRA05, Vol. 3515:919-926 of LNCS, springer, 2005.  
Keywords: cluster containment, evaluation, from clusters, from network, from rooted trees, phylogenetic network, phylogeny, polynomial, tree child network, tree containment.
Note: http://www.cs.rice.edu/~nakhleh/Papers/NakhlehWang.pdf.
       

96
photophoto
Luay Nakhleh and Li-San Wang. Phylogenetic Networks: Properties and Relationship to Trees and Clusters. In TCSB2, Vol. 3680:82-99 of LNCS, springer, 2005.  
Keywords: cluster containment, evaluation, from clusters, from network, from rooted trees, phylogenetic network, phylogeny, polynomial, tree child network, tree containment.
Note: http://www.cs.rice.edu/~nakhleh/Papers/LNCS_TCSB05.pdf.
       

97
photophotophotophoto
Luay Nakhleh, Guohua Jin, Fengmei Zhao and John Mellor-Crummey. Reconstructing Phylogenetic Networks Using Maximum Parsimony. In CSB05, Pages 93-102, 2005.  
Keywords: parsimony, phylogenetic network, phylogeny, Program Nepal, reconstruction.
Note: http://www.cs.rice.edu/~nakhleh/Papers/CSB05.pdf.
       

98
photophotophoto
Cam Thach Nguyen, Nguyen Bao Nguyen and Wing-Kin Sung. Fast Algorithms for computing the Tripartition-based Distance between Phylogenetic Networks. In ISAAC05, Pages 402-411, 2005.  
Keywords: distance between networks, phylogenetic network, phylogeny, tripartition distance.
Note: http://www.cs.washington.edu/homes/ncthach/Papers/ISAAC2006.pdf.
       

99
photophotophoto
Luay Nakhleh, Derek Ruths and Li-San Wang. RIATA-HGT: A Fast and Accurate Heuristic for Reconstructing Horizontal Gene Transfer. In COCOON05, Vol. 3595:84-93 of LNCS, springer, 2005.  
Keywords: from rooted trees, heuristic, lateral gene transfer, phylogenetic network, phylogeny, Program PhyloNet.
Note: http://www.cs.rice.edu/~nakhleh/Papers/COCOON05.pdf.
       

100
photophotophoto
Yun S. Song, Yufeng Wu and Dan Gusfield. Efficient computation of close lower and upper bounds on the minimum number of recombinations in biological sequence evolution. In ISMB05, Vol. 21:i413-i422 of BIO, 2005.  
Keywords: minimum number, Program HapBound, Program SHRUB, recombination.
Note: http://dx.doi.org/10.1093/bioinformatics/bti1033.
       
Toggle abstract
101
photophotophotophoto
Bhaskar DasGupta, Sergio Ferrarini, Uthra Gopalakrishnan and Nisha Raj Paryani. Inapproximability results for the lateral gene transfer problem. In Proceedings of the Ninth Italian Conference on Theoretical Computer Science (ICTCS'05), Pages 182-195, springer, 2005.  
Keywords: approximation, from rooted trees, from species tree, inapproximability, lateral gene transfer, parsimony, phylogenetic network, phylogeny.
Note: http://www.cs.uic.edu/~dasgupta/resume/publ/papers/ictcs-final.pdf.
       

102
photophotophoto
Mohd Abdul Hai Zahid, Ankush Mittal and Ramesh C. Joshi. A Classification Based Approach for Root Unknown Phylogenetic Networks under Constrained Recombination. In Proceedings of the Second International Conference on Distributed Computing and Internet Technology (ICDCIT'05), Vol. 3816:592-603, 2005.  
Note: http://www.isical.ac.in/~zahid_t/publications/papers/paper_ICDCIT.pdf.
       

103
photophotophoto
Dung Nguyen, Alix Boc and Vladimir Makarenkov. HGT-Simulator : logiciel pour simuler des transferts horizontaux. In SFC05, 2005.  
Note: http://lacim.uqam.ca/~sfc05/Articles/Nguyen_%20Boc_Makarenkov.pdf.
       

104
photo
Wei-Shun Su, Tso-Ching Lee and Yaw-Ling Lin. Efficient Algorithms for Constructing Phylogenetic Networks with Restricted Recombinations. In NCS05, Pages 1-7, 2005.  
Keywords: explicit network, from sequences, phylogenetic network, phylogeny, reconstruction.
Note: http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.168.6735.
       

2004
105
photophotophotophoto
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.
       
Toggle abstract
106
photophoto
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.
       

107
photophoto
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.
       

108
photophotophoto
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.
       

109
photophotophoto
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.
       

110
photophotophotophoto
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.
       

111
photo
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.
       

112
photophotophoto
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.
       

2003
113
photophotophoto
Louigi Addario-Berry, Mike Hallett and Jens Lagergren. Towards Identifying Lateral Gene Transfer Events. In PSB03, 2003.  
Keywords: evaluation, from rooted trees, from species tree, lateral gene transfer, phylogenetic network, phylogeny, Program LatTrans, reconstruction.
Note: http://www.nada.kth.se/~jensl/AHLPsb.pdf.
       

114
photophoto
Alix Boc and Vladimir Makarenkov. New Efficient Algorithm for Detection of Horizontal Gene Transfer Events. In WABI03, Vol. 2812:190-201 of LNCS, springer, 2003.  
Note: http://www.info2.uqam.ca/~makarenv/articles/article_WABI.pdf.
       

115
photophotophoto
Dan Gusfield, Satish Eddhu and Charles Langley. Efficient reconstruction of phylogenetic networks with constrained recombination. In CSB03, Pages 363-374, 2003.  
Keywords: explicit network, from sequences, galled tree, phylogenetic network, phylogeny, recombination, reconstruction.
Note: http://wwwcsif.cs.ucdavis.edu/~gusfield/ieeefinal.pdf.
       

116
photophoto
Barbara R. Holland and Vincent Moulton. Consensus networks: A method for visualising incompatibilities in collections of trees. In WABI03, Vol. 2812:165-176 of LNCS, springer, 2003.  
Keywords: consensus.
Note: http://dx.doi.org/10.1093/molbev/msj061.
       

117
photophotophotophotophotophoto
Luay Nakhleh, Jerry Sun, Tandy Warnow, C. Randal Linder, Bernard M. E. Moret and Anna Tholse. Towards the Development of Computational Tools for Evaluating Phylogenetic Network Reconstruction Methods. In PSB03, 2003.  
Keywords: distance between networks, evaluation, phylogenetic network, phylogeny, polynomial, tripartition distance.
Note: http://www.cs.rice.edu/~nakhleh/Papers/psb03.pdf.
       

118
photophoto
Yun S. Song and Jotun Hein. Parsimonious reconstruction of sequence evolution and haplotype blocks: Finding the minimum number of recombination events. In WABI03, Vol. 2812:287-302 of LNCS, springer, 2003.  
Keywords: minimum number, recombination.
Note: http://www.cs.ucdavis.edu/~yssong/Pub/SH-WABI03.pdf.
       

119
photophotophotophoto
Esra Erdem, Vladimir Lifschitz, Luay Nakhleh and Don Ringe. Reconstructing the evolutionary history of Indo-European languages using answer set programming. In PADL03, Vol. 2562:160-176 of LNCS, springer, 2003.  
Note: http://people.sabanciuniv.edu/~esraerdem/papers/padl03.ps.
       

120
photo
Pawel Górecki. Single step reconciliation algorithm for duplication, loss and horizontal gene transfer model. In ECCB03, 2003.  
Keywords: duplication, explicit network, from rooted trees, from species tree, lateral gene transfer, NP complete, parsimony, phylogenetic network, phylogeny, polynomial, reconstruction.
Note: http://www.inra.fr/eccb2003/posters/pdf/short/S_gorecki.ps.
       

2002
121
photophoto
David Bryant and Vincent Moulton. Neighbor-Net: An Agglomerative Method for the Construction of Planar Phylogenetic Networks. In WABI02, Vol. 2452:375-391 of LNCS, springer, 2002.  
Keywords: abstract network, circular split system, from distances, NeighborNet, phylogenetic network, phylogeny, Program SplitsTree, reconstruction, split network.
Note: http://dx.doi.org/10.1007/3-540-45784-4_28.
       

122
photophoto
Olivier Gauthier and François-Joseph Lapointe. A comparison of alternative methods for detecting reticulation events in phylogenetic analysis. In IFCS02, Pages 365-369, springer, 2002.  
       

123
photo
Dan Gusfield. Haplotyping as Perfect Phylogeny: Conceptual Framework and Efficient Solutions. In RECOMB02, 2002.  
Keywords: haplotyping, perfect, phylogeny.
Note: http://wwwcsif.cs.ucdavis.edu/~gusfield/acmhapre.pdf .
       

2001
124
photophoto
Mike Hallett and Jens Lagergren. Efficient algorithms for lateral gene transfers problems. In RECOMB01, Pages 141-148, 2001.  
Keywords: from rooted trees, lateral gene transfer, NP complete, phylogeny, polynomial, Program McKiTscH, reconstruction.
Note: http://dx.doi.org/10.1145/369133.369188.
       

125
photophotophoto
Lusheng Wang, Kaizhong Zhang and Louxin Zhang. Perfect phylogenetic networks with recombination. In SAC01, Pages 46-50, 2001.  
Keywords: from sequences, galled tree, NP complete, perfect, phylogenetic network, phylogeny, polynomial, recombination, reconstruction.
Note: http://dx.doi.org/10.1145/372202.372271.
       

126
photophotophoto
Andreas W. M. Dress, Katharina Huber and Vincent Moulton. Hereditarily Optimal Realizations: Why are they Relevant in Phylogenetic Analysis, and how does one Compute them? In Proceedings of the Euroconference on Algebraic Combinatorics and Applications (Alcoma'99), Pages 110-117, springer, 2001.  
Keywords: abstract network, from distances, optimal realization, phylogenetic network.
Note: http://www.math.uni-bielefeld.de/fsp-math/Preprints/139.pdf.
       

2000
127
photophoto
Pierre Legendre and Vladimir Makarenkov. Improving the additive tree representation of a dissimilarity matrix using reticulations. In IFCS00, Pages 35-40, springer, 2000.  
Keywords: phylogenetic network, phylogeny, reconstruction, reticulogram.
Note: http://www.info2.uqam.ca/~makarenv/makarenv/Article_IFCS.pdf.
       

1999
128
photophoto
Vincent Berry and David Bryant. Faster reliable phylogenetic analysis. In RECOMB99, Pages 59-68, 1999.  
Keywords: abstract network, from quartets, phylogenetic network, phylogeny, polynomial, Program SplitsTree, reconstruction, split network, weakly compatible.
Note: http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.95.9151.
       

1998
129
photophotophoto
Bin Ma, Lusheng Wang and Ming Li. Fixed topology alignment with recombination. In CPM98, Vol. 1448:174-188 of LNCS, springer, 1998.  
Keywords: approximation, explicit network, from network, from sequences, galled tree, inapproximability, phylogenetic network, phylogeny, recombination.
Note: http://dx.doi.org/10.1007/BFb0030789.
       

1994
130
photo
Hans-Jürgen Bandelt. Phylogenetic Networks. In Verhandlungen des Naturwissenschaftlichen Vereins Hamburg, Vol. 34:51-71, 1994.  
       

131
photophoto
John Kececioglu and Dan Gusfield. Reconstructing a history of recombinations from a set of sequences. In SODA94, Pages 471-480, 1994.  
Keywords: from sequences, NP complete, polynomial, recombination, reconstruction.
Note: http://portal.acm.org/citation.cfm?id=314626#.
       

132
photophoto
Hans-Jürgen Bandelt and Andreas W. M. Dress. A relational approach to split decomposition. In H.-H. Bock, W. Lenski and M. M. Richter editors, Information Systems and Data Analysis, Proceedings of the 17th Annual Conference of the Gesellschaft Für Klassifikation (GFKL93), Vol. 42:123-131 of Studies in Classification, Data Analysis, and Knowledge Organization, springer, 1994.  
Keywords: characterization, from quartets, phylogenetic network, weakly compatible.
       

1983
133
photo
Gareth J. Nelson. Reticulation in Cladograms. In Advances in Cladistics: Proceedings of the Second meeting of the Willi Hennig Society (HENNIG II), Pages 105-111, Columbia University Press, 1983.  
Keywords: explicit network, from rooted trees, from species tree, hybridization, parsimony, phylogeny.
       

134
photo
Hans-Erik Wanntorp. Reticulated cladograms and the identification of hybrid taxa. In Advances in Cladistics: Proceedings of the Second meeting of the Willi Hennig Society (HENNIG II), Pages 81-88, Columbia University Press, 1983.  
Keywords: explicit network, from rooted trees, from species tree, hybridization, parsimony, phylogeny.
       

135
photo
Christopher J. Humphries. Primary data in hybrid analysis. In Advances in Cladistics: Proceedings of the Second meeting of the Willi Hennig Society (HENNIG II), Pages 89-103, Columbia University Press, 1983.  
Keywords: explicit network, from rooted trees, from species tree, hybridization, parsimony, phylogeny.
       

136
photo
Warren H. Wagner. Reticulistics: the recognition of hybrids and their role in cladistics and classification. In Advances in Cladistics: Proceedings of the Second meeting of the Willi Hennig Society (HENNIG II), Pages 63-79, 1983.  
Keywords: explicit network, from rooted trees, from species tree, hybridization, parsimony, phylogeny.