Publications related to 'lateral gene transfer'
 
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Article (Journal)
1
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Bhaskar DasGupta, Sergio Ferrarini, Uthra Gopalakrishnan and Nisha Raj Paryani. Inapproximability results for the lateral gene transfer problem. In JCO, Vol. 11(4):387-405, 2006.  
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/t-scenario-3-reviewed-3.pdf.
       

2
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Dave MacLeod, Robert L. Charlebois, W. Ford Doolittle and Eric Bapteste. Deduction of probable events of lateral gene transfer through comparison of phylogenetic trees by recursive consolidation and rearrangement. In BMCEB, Vol. 5(27), 2005.  
Keywords: explicit network, from rooted trees, lateral gene transfer, phylogenetic network, phylogeny, Program HorizStory, reconstruction, software.
Note: http://dx.doi.org/10.1186/1471-2148-5-27.
       
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3
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Robert G. Beiko and Nicholas Hamilton. Phylogenetic identification of lateral genetic transfer events. In BMCEB, Vol. 6(15), 2006.  
Keywords: evaluation, from rooted trees, from unrooted trees, lateral gene transfer, Program EEEP, Program HorizStory, Program LatTrans, reconstruction, software, SPR distance.
Note: http://dx.doi.org/10.1186/1471-2148-6-15.
       
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4
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Maria S. Poptsova and J. Peter Gogarten. The power of phylogenetic approaches to detect horizontally transferred genes. In BMCEB, Vol. 7(45), 2007.  
Keywords: evaluation, from rooted trees, lateral gene transfer, Program EEEP.
Note: http://dx.doi.org/10.1186/1471-2148-7-45.
       
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5
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Wayne P. Maddison. Gene Trees in Species Trees. In Systematic Biology, Vol. 46(3):523-536, 1997.  
Keywords: from rooted trees, from species tree, lateral gene transfer, phylogeny, reconstruction, time consistent network.
Note: http://dx.doi.org/10.2307/2413694.
       

6
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Roderic D.M. Page and Michael A. Charleston. Trees within trees: phylogeny and historical associations. In TEE, Vol. 13(9):356-359, 1998.  
Keywords: duplication, explicit network, from rooted trees, from species tree, lateral gene transfer, phylogenetic network, phylogeny, reconstruction, survey.
Note: http://taxonomy.zoology.gla.ac.uk/rod/papers/tree.pdf.
       

7
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Cuong Than, Derek Ruths, Hideki Innan and Luay Nakhleh. Confounding Factors in HGT Detection: Statistical Error, Coalescent Effects, and Multiple Solutions. In JCB, Vol. 14(4):517-535, 2007.  
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-jcb.pdf.
       

8
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Sagi Snir and Tamir Tuller. The NET-HMM approach: Phylogenetic Network Inference by Combining Maximum Likelihood and Hidden Markov Models. In JBCB, Vol. 7(4):625-644, 2009.  
Keywords: explicit network, from sequences, HMM, lateral gene transfer, likelihood, phylogenetic network, phylogeny, statistical model.
Note: http://research.haifa.ac.il/~ssagi/published%20papers/Snir-NET-HMM-JBCB-2009.pdf.
       
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9
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Simone Linz, Charles Semple and Tanja Stadler. Analyzing and reconstructing reticulation networks under timing constraints. In JOMB, Vol. 61(5):715-737, 2010.  
Keywords: explicit network, from rooted trees, hybridization, lateral gene transfer, NP complete, phylogenetic network, phylogeny, reconstruction, time consistent network.
Note: http://dx.doi.org/10.1007/s00285-009-0319-y..
       
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10
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Tal Dagan, Yael Artzy-Randrup and William Martin. Modular networks and cumulative impact of lateral transfer in prokaryote genome evolution. In PNAS, Vol. 105:10039-10044, 2008.  
Keywords: from sequences, from species tree, heuristic, lateral gene transfer, phylogenetic network, phylogeny, reconstruction.
Note: http://dx.doi.org/10.1073/pnas.0800679105.
       
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11
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Ali Tofigh, Mike Hallett and Jens Lagergren. Simultaneous Identification of Duplications and Lateral Gene Transfers. In TCBB, Vol. 8(2):517-535, 2011.  
Keywords: duplication, explicit network, FPT, from rooted trees, from species tree, lateral gene transfer, loss, NP complete, phylogenetic network, phylogeny, reconstruction.
Note: http://dx.doi.org/10.1109/TCBB.2010.14.
       
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12
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Hyun Jung Park, Guohua Jin and Luay Nakhleh. Bootstrap-based Support of HGT Inferred by Maximum Parsimony. In BMCEB, Vol. 10:131, 2010.  
Keywords: bootstrap, explicit network, from sequences, lateral gene transfer, parsimony, phylogenetic network, phylogeny, Program Nepal, reconstruction.
Note: http://dx.doi.org/10.1186/1471-2148-10-131.
       
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13
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Sophie Abby, Eric Tannier, Manolo Gouy and Vincent Daubin. Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests. In BMCB, Vol. 11:324, 2010.  
Keywords: explicit network, from rooted trees, from species tree, heuristic, lateral gene transfer, phylogenetic network, phylogeny, Program EEEP, Program PhyloNet, Program Prunier, reconstruction, software.
Note: http://www.biomedcentral.com/1471-2105/11/324.
       
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14
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Tao Sang and Yang Zhong. Testing Hybridization Hypotheses Based on Incongruent Gene Trees. In Systematic Biology, Vol. 49(3):422-434, 2000.  
Keywords: bootstrap, from rooted trees, hybridization, lateral gene transfer, lineage sorting, phylogenetic network, phylogeny, reconstruction, statistical model.
Note: http://dx.doi.org/10.1080/10635159950127321.
       

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Nicolas Galtier. A model of horizontal gene transfer and the bacterial phylogeny problem. In Systematic Biology, Vol. 56(4):633-642, 2007.  
Keywords: explicit network, generation, lateral gene transfer, phylogenetic network, phylogeny, Program HGT_simul, software, statistical model.
Note: http://dx.doi.org/10.1080/10635150701546231.
       
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16

Mark T. Holder, Jennifer A. Anderson and Alisha K. Holloway. Difficulties in Detecting Hybridization. In Systematic Biology, Vol. 50(6):978-982, 2001.  
Keywords: bootstrap, from rooted trees, hybridization, lateral gene transfer, lineage sorting, phylogenetic network, phylogeny, reconstruction, statistical model.
Note: http://dx.doi.org/10.1080/106351501753462911.
       
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17
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Marc Thuillard and Vincent Moulton. Identifying and reconstructing lateral transfers from distance matrices by combining the Minimum Contradiction Method and Neighbor-Net. In JBCB, Vol. 9(4):453-470, 2011.  
Keywords: from distances, lateral gene transfer, minimum contradiction, NeighborNet, phylogenetic network, phylogeny, reconstruction.
Note: http://dx.doi.org/10.1142/S0219720011005409, slides available at http://www.newton.ac.uk/programmes/PLG/seminars/062015501.html.
       
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18
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Gergely J. Szöllösi and Vincent Daubin. Modeling Gene Family Evolution and Reconciling Phylogenetic Discord. In Evolutionary Genomics, Statistical and Computational Methods, Volume 2, Methods in Molecular Biology, Vol. 856:29-51, Chapter 2, springer, 2011.  
Keywords: duplication, from multilabeled tree, lateral gene transfer, likelihood, phylogeny, reconstruction, statistical model.
Note: ArXiv version entitled The pattern and process of gene family evolution.
       
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19
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Mukul S. Bansal, Guy Banay, J. Peter Gogarten and Ron Shamir. Detecting Highways of Horizontal Gene Transfer. In JCB, Vol. 18(9):1087-1114, 2011.  
Keywords: explicit network, from rooted trees, from species tree, lateral gene transfer, phylogenetic network, phylogeny, polynomial, reconstruction.
Note: http://people.csail.mit.edu/mukul/HighwayFull_preprint.pdf.
       
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20
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Jean-Philippe Doyon, Vincent Ranwez, Vincent Daubin and Vincent Berry. Models, algorithms and programs for phylogeny reconciliation. In Briefings in Bioinformatics, Vol. 12(5):392-400, 2011.  
Keywords: explicit network, lateral gene transfer, phylogenetic network, phylogeny, reconstruction, survey.
       
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Alix Boc and Vladimir Makarenkov. Towards an accurate identification of mosaic genes and partial horizontal gene transfers. In NAR, Vol. 39(21):e144, 2011.  
Keywords: explicit network, from sequences, lateral gene transfer, phylogenetic network, phylogeny, Program T REX, reconstruction.
Note: http://dx.doi.org/10.1093/nar/gkr735.
       
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Pawel Górecki. H-trees: a model of evolutionary scenario with horizontal gene transfer. In Fundamenta Informaticae, Vol. 103:105-128, 2010.  
Keywords: duplication, lateral gene transfer, loss, phylogenetic network, phylogeny, uniqueness.
       

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Alix Boc, Alpha B. Diallo and Vladimir Makarenkov. T-REX: a web server for inferring, validating and visualizing phylogenetic trees and networks. In NAR, Vol. 40(W1):W573-W579, 2012.  
Keywords: from rooted trees, from species tree, lateral gene transfer, phylogenetic network, phylogeny, Program T REX, reconstruction, reticulogram, software.
Note: http://dx.doi.org/10.1093/nar/gks485.
       
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24
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Thi-Hau Nguyen, Vincent Ranwez, Stéphanie Pointet, Anne-Muriel Chifolleau Arigon, Jean-Philippe Doyon and Vincent Berry. Reconciliation and local gene tree rearrangement can be of mutual profit. In ALMOB, Vol. 8(12), 2013.  
Keywords: duplication, explicit network, from rooted trees, heuristic, lateral gene transfer, phylogenetic network, phylogeny, Program Mowgli, Program MowgliNNI, Program Prunier, reconstruction, software.
       
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25
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Mukul S. Bansal, Guy Banay, Timothy J. Harlow, J. Peter Gogarten and Ron Shamir. Systematic inference of highways of horizontal gene transfer in prokaryotes. In BIO, Vol. 29(5):571-579, 2013.  
Keywords: duplication, explicit network, from species tree, from unrooted trees, lateral gene transfer, phylogenetic network, phylogeny, Program HiDe, Program RANGER-DTL, reconstruction.
Note: http://people.csail.mit.edu/mukul/Bansal_Highways_Bioinformatics_2013.pdf.
       

26
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Gergely J. Szöllösi, Eric Tannier, Nicolas Lartillot and Vincent Daubin. Lateral Gene Transfer from the Dead. In Systematic Biology, Vol. 62(3):386-397, 2013.  
Keywords: duplication, lateral gene transfer, likelihood, loss, phylogeny, Program TERA, reconstruction.
Note: http://dx.doi.org/10.1093/sysbio/syt003.
       
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27
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Gergely J. Szöllösi, Wojciech Rosikiewicz, Bastien Boussau, Eric Tannier and Vincent Daubin. Efficient Exploration of the Space of Reconciled Gene Trees. In Systematic Biology, Vol. 62(6):901-912, 2013.  
Keywords: duplication, explicit network, lateral gene transfer, likelihood, loss, phylogeny, Program ALE, reconstruction.
Note: http://arxiv.org/abs/1306.2167.
       
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28
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Zhi-Zhong Chen, Fei Deng and Lusheng Wang. Simultaneous Identification of Duplications, Losses, and Lateral Gene Transfers. In TCBB, Vol. 9(5):1515-1528, 2012.  
Keywords: duplication, explicit network, FPT, from rooted trees, from species tree, lateral gene transfer, loss, phylogenetic network, phylogeny, reconstruction.
Note: http://www.cs.cityu.edu.hk/~lwang/research/tcbb2012c.pdf.
       
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29
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Joel Sjöstrand, Ali Tofigh, Vincent Daubin, Lars Arvestad, Bengt Sennblad and Jens Lagergren. A Bayesian Method for Analyzing Lateral Gene Transfer. In Systematic Biology, Vol. 63(3):409-420, 2014.  
Keywords: bayesian, duplication, from rooted trees, from sequences, from species tree, lateral gene transfer, loss, phylogenetic network, phylogeny, Program JPrIME-DLTRS, reconstruction.
Note: http://dx.doi.org/10.1093/sysbio/syu007.
       

30
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Vincent Ranwez, Celine Scornavacca, Jean-Philippe Doyon and Vincent Berry. Inferring gene duplications, transfers and losses can be done in a discrete framework. In JOMB, Vol. 72(7):1811-1844, 2016.  
Keywords: duplication, explicit network, from rooted trees, from species tree, lateral gene transfer, loss, phylogenetic network, phylogeny, reconstruction.
       

31
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Gergely J. Szöllösi, Adrián Arellano Davín, Eric Tannier, Vincent Daubin and Bastien Boussau. Genome-scale phylogenetic analysis finds extensive gene transfer among fungi. In Philosophical Transactions of the Royal Society of London B: Biological Sciences, Vol. 370(1678):1-11, 2015.  
Keywords: duplication, from sequences, lateral gene transfer, loss, phylogenetic network, phylogeny, Program ALE, reconstruction.
Note: http://dx.doi.org/10.1098/rstb.2014.0335.
       

32
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François Chevenet, Jean-Philippe Doyon, Celine Scornavacca, Edwin Jacox, Emmanuelle Jousselin and Vincent Berry. SylvX: a viewer for phylogenetic tree reconciliations. In BIO, Vol. 32(4):608-610, 2016.  
Keywords: duplication, explicit network, from rooted trees, from species tree, lateral gene transfer, loss, phylogenetic network, phylogeny, Program SylvX, software, visualization.
Note: https://www.researchgate.net/profile/Emmanuelle_Jousselin/publication/283446016_SylvX_a_viewer_for_phylogenetic_tree_reconciliations/links/5642146108aec448fa621efa.pdf.
       

33
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Gabriel Cardona, Joan Carles Pons and Francesc Rosselló. A reconstruction problem for a class of phylogenetic networks with lateral gene transfers. In ALMOB, Vol. 10(28):1-15, 2015.  
Keywords: explicit network, from rooted trees, lateral gene transfer, phylogenetic network, phylogeny, Program LGTnetwork, reconstruction, software, tree-based network.
Note: http://dx.doi.org/10.1186/s13015-015-0059-z.
       

34
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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.
       

35
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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.
       

InProceedings
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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.
       

37
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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.
       

38
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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.
       

39
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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.
       

40
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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.
       

41
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Mike Hallett, Jens Lagergren and Ali Tofigh. Simultaneous Identification of Duplications and Lateral Transfers. In RECOMB04, Pages 347-356, 2004.  
Keywords: duplication, explicit network, FPT, from rooted trees, from species tree, lateral gene transfer, loss, NP complete, parsimony, phylogenetic network, phylogeny, polynomial, reconstruction.
Note: http://www.nada.kth.se/~jensl/p164-hallett.pdf.
       

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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.
       

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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.
       
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44
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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.
       

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

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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.
       

47
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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/.
       
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48
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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.
       
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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.
       
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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.
       
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51
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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.
       
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52
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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/.
       
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53
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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.
       
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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.
       

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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.
       

InBook
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Vladimir Makarenkov, Dmytro Kevorkov and Pierre Legendre. Phylogenetic Network Construction Approaches. In Applied Mycology and Biotechnology, Vol. 6:61-97, 2006.  
Keywords: from distances, hybridization, lateral gene transfer, median network, NeighborNet, netting, Program Arlequin, Program Network, Program Pyramids, Program Reticlad, Program SplitsTree, Program T REX, Program TCS, Program WeakHierarchies, pyramid, reticulogram, split, split decomposition, split network, survey, weak hierarchy.
Note: http://www.labunix.uqam.ca/~makarenv/makarenv/MKL_article.pdf.
       

PhdThesis
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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.
       

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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.
       

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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.
       

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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.
       

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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=.
       

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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.
       

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

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Tamir Tuller and Sagi Snir. The NET-HMM: a HMM Based Likelihood Model for Evolutionary Networks. 2007.  
Keywords: lateral gene transfer, likelihood, phylogenetic network, phylogeny, reconstruction, statistical model.
Note: Poster presented at the eleventh Annual International Conference on Research in Computational Molecular Biology (RECOMB'07), http://www.qb3.org/recomb07/posters/Tuller013043013RECOMB_HMM1.pdf.
       

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Ali Tofigh, Joel Sjöstrand, Bengt Sennblad, Lars Arvestad and Jens Lagergren. Detecting LGTs using a novel probabilistic model integrating duplications, LGTs, losses, rate variation, and sequence evolution. 2009.  
Keywords: duplication, lateral gene transfer, loss, phylogenetic network, phylogeny, reconstruction.
Note: http://kth.diva-portal.org/smash/record.jsf?searchId=1&pid=diva2:233574.