Products of the NIMBioS Working Group:
Gene Tree Reconciliation
Publications
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]
Grants/Proposals
Liberles D, Liu L, Kubatko L, Leebens-Mack J. May 2014. Workshop on Gene Family Evolution. Las Cruces, NM, USA.
Grants/Proposals
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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