Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests, BMC Bioinformatics, vol.11, issue.1, p.324, 2010. ,
DOI : 10.1186/1471-2105-11-324
URL : https://hal.archives-ouvertes.fr/inria-00527151
A New Fast Method for Detecting and Validating Horizontal Gene Transfer Events Using Phylogenetic Trees and Aggregation Functions, Pattern Recognition in Computational Molecular Biology: Techniques and Approaches, pp.483-504, 2016. ,
DOI : 10.1137/040608635
Efficient algorithms for the reconciliation problem with gene duplication, horizontal transfer and loss, Bioinformatics, vol.28, issue.12, pp.28-283, 2012. ,
DOI : 10.1093/bioinformatics/bts225
URL : https://academic.oup.com/bioinformatics/article-pdf/28/12/i283/16907823/bts225.pdf
Comparative Genomics on Artificial Life, Computability in Europe, Lecture Notes in Computer Science, 2016. ,
DOI : 10.1073/pnas.1202997109
URL : https://hal.archives-ouvertes.fr/hal-01334930
Sorting heuristics for the feedback arc set problem, 2011. ,
Inferring incomplete lineage sorting, duplications, transfers and losses with reconciliations, Journal of Theoretical Biology, vol.432, 2017. ,
DOI : 10.1016/j.jtbi.2017.08.008
Gene transfers, like fossils, can date the tree of life, Biorxiv, 2017. ,
DOI : 10.1101/193813
Telling the evolutionary time, 2003. ,
Approximating Minimum Feedback Sets and Multicuts in Directed Graphs, Algorithmica, vol.20, issue.2, pp.151-174, 1998. ,
DOI : 10.1007/PL00009191
URL : http://theory.lcs.mit.edu/~madhu/papers/fes-journ.ps
A Method for Investigating Relative Timing Information on Phylogenetic Trees, Systematic Biology, vol.58, issue.2, pp.167-183, 2009. ,
DOI : 10.1093/sysbio/syp018
URL : https://academic.oup.com/sysbio/article-pdf/58/2/167/17836344/syp018.pdf
Computers and Intractability; A Guide to the Theory of NP-Completeness, 1990. ,
Horizontal Gene Transfer: Pitfalls and Promises, The Biological Bulletin, vol.196, issue.3, pp.359-61, 1999. ,
DOI : 10.2307/1542970
Gene tree reconciliation including transfers with replacement is hard and FPT. arXiv preprint, 2017. ,
Gene tree species tree reconciliation with gene conversion. arXiv preprint, 2017. ,
URL : https://hal.archives-ouvertes.fr/hal-01495707
ecceTERA: comprehensive gene tree-species tree reconciliation using parsimony: Table 1., Bioinformatics, vol.32, issue.13, 2016. ,
DOI : 10.1093/bioinformatics/btw105
URL : https://academic.oup.com/bioinformatics/article-pdf/32/13/2056/16920517/btw105.pdf
An approximate max-flow min-cut theorem for uniform multicommodity flow problems with applications to approximation algorithms, Proc. 29th Annual Symp. Foundations of Computer Science, pp.422-431, 1988. ,
DOI : 10.1109/sfcs.1988.21958
: Phylogenomic Simulation of Gene, Locus, and Species Trees, Systematic Biology, vol.65, issue.2, pp.334-344, 2016. ,
DOI : 10.1093/sysbio/syv082
URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4748750/pdf
Lateral gene transfer and the nature of bacterial innovation, nature, issue.6784, p.405299, 2000. ,
Inferring Horizontal Gene Transfer, PLOS Computational Biology, vol.1079, issue.1, p.1004095, 2015. ,
DOI : 10.1371/journal.pcbi.1004095.s002
URL : https://doi.org/10.1371/journal.pcbi.1004095
Phylogenetics. Oxford lecture series in mathematics and its applications, 2003. ,
Efficient computation of feedback arc set at web-scale, Proceedings of the VLDB Endowment, pp.133-144, 2016. ,
DOI : 10.14778/3021924.3021930
Inferring duplications, losses, transfers and incomplete lineage sorting with nonbinary species trees, Bioinformatics, vol.28, issue.18, pp.28-409, 2012. ,
DOI : 10.1093/bioinformatics/bts386
URL : https://academic.oup.com/bioinformatics/article-pdf/28/18/i409/16906592/bts386.pdf
Phylogenetic modeling of lateral gene transfer reconstructs the pattern and relative timing of speciations, Proceedings of the National Academy of Sciences of the United States of America, pp.17513-17518, 2012. ,
Efficient exploration of the space of reconciled gene trees, Syst Biol, issue.6, pp.62901-912, 2013. ,
Lateral Gene Transfer from the Dead, Systematic Biology, vol.62, issue.3, pp.386-397, 2013. ,
DOI : 10.1093/sysbio/syt003
Genome-scale phylogenetic analysis finds extensive gene transfer among fungi, Philosophical Transactions of the Royal Society B: Biological Sciences, vol.5, issue.1678, p.20140335, 2015. ,
DOI : 10.1093/bioinformatics/btt021