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Products of the NIMBioS Working Group:

Gene Tree Reconciliation


Gorecki P, Eulenstein O. 2015. Gene tree diameter for deep coalescence. ​IEEE-ACM Transactions on Computational Biology and Bioinformatics, 12(1): 155-165. ​[Online]

Teufel AI, Masel J, and Liberles DA. 2015. What fraction of duplicates observed in recently sequenced genomes is segregating and destined to fail to fix? Genome Biology and Evolution, 7(8): 2258-2264. [Online]

Gorecki P, Eulenstein O. 2014. Maximizing deep coalescence cost. IEEE-ACM Transactions on Computational Biology and Bioinformatics, 11(1): 231-242. [Online]

Gorecki P, Eulenstein O. 2014. DrML: Probabilistic modeling of gene duplications. Journal of Computational Biology, 21(1): 89-98. [Online]

Jhwueng DC, Huzurbazar S, O'Meara BC, Liu L. 2014. Investigating the performance of AIC in selecting phylogenetic models. ​Statistical Applications in Genetics and Molecular Biology, 13(4): 459-475​. [Online] [PDF]

​Ma Q, Reeves J, Liberles DA, Yu L, Chang Z, Zhao J, Xu Y, and Liu L. 2014. A phylogenetic model for understanding the effect of gene duplication on cancer progression. Nucleic Acides Research, 42: 2870-2878. [Online]​

​Teufel AI, Zhao J, O'Reilly M, Liu L, Liberles DA. 2014. On mechanistic modeling of gene content evolution: Birth-death models and mechanisms of gene birth and gene retention. Computation, 2(3): 112-130. [Online]

Gorecki P, Eulenstein O, Tiuryn J. 2013. Unrooted tree reconciliation: A unified approach. IEEE-ACM Transactions on Computational Biology and Bioinformatics, 10(2): 522-536. [Online]

​Liberles DA, Teufel AI, Liu L, Stadler T. 2013. On the need for mechanistic models in computational genomics. Genome Biology and Evolution, 5: 2008-2018. [Online]

Wehe A, Burleigh JG, Eulenstein O. 2013. Efficient algorithms for knowledge-enhanced supertree and supermatrix phylogenetic problems. IEEE-ACM Transactions on Computational Biology and Bioinformatics, 10(6): 1432-1441. [Online]

Chaudhary R, Burleigh JG, Fernandez-Baca D. 2012. Fast local search for unrooted Robinson-Foulds supertrees. IEEE-ACM Transactions on Computational Biology and Bioinformatics, 9(4): 1004-1013. [Online]

Liu L, Yu L, Kalavacharla V, Liu Z. 2011. A Bayesian model for gene family evolution. BMC Bioinformatics, 12: 426. [Online]

Konrad A, Teufel AI, Grahnen JA, Liberles DA. 2011. Toward a general model for the evolutionary dynamics of gene duplicates. Genome Biology and Evolution, 3: 1197-1209. [Online]


​Liberles D, Liu L, Kubatko L, Leebens-Mack J. May 2014. Workshop on Gene Family Evolution. Las Cruces, NM, USA.​


Liu L, Liberles DA. 2012. Developing a probabilistic model for gene family evolution. National Science Foundation. $300,000. Accepted.

Softoware, Data, and Websites

Liu L. (In preparation). Software: Bayesian Estimation of Gene Family Evolution (BEGFE).

​Ane C. 2014. R package WGDgc and SPIMAPWGD

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NSF logo. NIMBioS is sponsored by the National Science Foundation through NSF Award #DBI-1300426, with additional support from The University of Tennessee, Knoxville. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.
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