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Items: 1 to 20 of 78


Analysis of a mechanistic Markov model for gene duplicates evolving under subfunctionalization.

Stark TL, Liberles DA, Holland BR, O'Reilly MM.

BMC Evol Biol. 2017 Jan 31;17(1):38. doi: 10.1186/s12862-016-0848-0.


ProtASR: An Evolutionary Framework for Ancestral Protein Reconstruction with Selection on Folding Stability.

Arenas M, Weber CC, Liberles DA, Bastolla U.

Syst Biol. 2017 Jan 5. pii: syw121. doi: 10.1093/sysbio/syw121. [Epub ahead of print]


Extracting functional trends from whole genome duplication events using comparative genomics.

Hermansen RA, Hvidsten TR, Sandve SR, Liberles DA.

Biol Proced Online. 2016 May 10;18:11. doi: 10.1186/s12575-016-0041-2. Review.


The Atlantic salmon genome provides insights into rediploidization.

Lien S, Koop BF, Sandve SR, Miller JR, Kent MP, Nome T, Hvidsten TR, Leong JS, Minkley DR, Zimin A, Grammes F, Grove H, Gjuvsland A, Walenz B, Hermansen RA, von Schalburg K, Rondeau EB, Di Genova A, Samy JK, Olav Vik J, Vigeland MD, Caler L, Grimholt U, Jentoft S, Våge DI, de Jong P, Moen T, Baranski M, Palti Y, Smith DR, Yorke JA, Nederbragt AJ, Tooming-Klunderud A, Jakobsen KS, Jiang X, Fan D, Hu Y, Liberles DA, Vidal R, Iturra P, Jones SJ, Jonassen I, Maass A, Omholt SW, Davidson WS.

Nature. 2016 May 12;533(7602):200-5. doi: 10.1038/nature17164.


Flux Control in Glycolysis Varies Across the Tree of Life.

Orlenko A, Hermansen RA, Liberles DA.

J Mol Evol. 2016 Mar;82(2-3):146-61. doi: 10.1007/s00239-016-9731-2.


Models for gene duplication when dosage balance works as a transition state to subsequent neo-or sub-functionalization.

Teufel AI, Liu L, Liberles DA.

BMC Evol Biol. 2016 Feb 20;16:45. doi: 10.1186/s12862-016-0616-1.


Selection on protein structure, interaction, and sequence.

Chi PB, Liberles DA.

Protein Sci. 2016 Jul;25(7):1168-78. doi: 10.1002/pro.2886. Review.


A generalized birth and death process for modeling the fates of gene duplication.

Zhao J, Teufel AI, Liberles DA, Liu L.

BMC Evol Biol. 2015 Dec 8;15:275. doi: 10.1186/s12862-015-0539-2.


Characterizing selective pressures on the pathway for de novo biosynthesis of pyrimidines in yeast.

Hermansen RA, Mannakee BK, Knecht W, Liberles DA, Gutenkunst RN.

BMC Evol Biol. 2015 Oct 28;15:232. doi: 10.1186/s12862-015-0515-x.


What Fraction of Duplicates Observed in Recently Sequenced Genomes Is Segregating and Destined to Fail to Fix?

Teufel AI, Masel J, Liberles DA.

Genome Biol Evol. 2015 Jul 27;7(8):2258-64. doi: 10.1093/gbe/evv139.


Genetic simulation tools for post-genome wide association studies of complex diseases.

Chen HS, Hutter CM, Mechanic LE, Amos CI, Bafna V, Hauser ER, Hernandez RD, Li C, Liberles DA, McAllister K, Moore JH, Paltoo DN, Papanicolaou GJ, Peng B, Ritchie MD, Rosenfeld G, Witte JS, Gillanders EM, Feuer EJ.

Genet Epidemiol. 2015 Jan;39(1):11-9. doi: 10.1002/gepi.21870.


Molecular traces of alternative social organization in a termite genome.

Terrapon N, Li C, Robertson HM, Ji L, Meng X, Booth W, Chen Z, Childers CP, Glastad KM, Gokhale K, Gowin J, Gronenberg W, Hermansen RA, Hu H, Hunt BG, Huylmans AK, Khalil SM, Mitchell RD, Munoz-Torres MC, Mustard JA, Pan H, Reese JT, Scharf ME, Sun F, Vogel H, Xiao J, Yang W, Yang Z, Yang Z, Zhou J, Zhu J, Brent CS, Elsik CG, Goodisman MA, Liberles DA, Roe RM, Vargo EL, Vilcinskas A, Wang J, Bornberg-Bauer E, Korb J, Zhang G, Liebig J.

Nat Commun. 2014 May 20;5:3636. doi: 10.1038/ncomms4636.


The phylogenetic distribution and evolution of enzymes within the thymidine kinase 2-like gene family in metazoa.

Konrad A, Lai J, Mutahir Z, Piškur J, Liberles DA.

J Mol Evol. 2014 Apr;78(3-4):202-16. doi: 10.1007/s00239-014-9611-6.


A phylogenetic model for understanding the effect of gene duplication on cancer progression.

Ma Q, Reeves JH, Liberles DA, Yu L, Chang Z, Zhao J, Cui J, Xu Y, Liu L.

Nucleic Acids Res. 2014 Mar;42(5):2870-8. doi: 10.1093/nar/gkt1320.


On the need for mechanistic models in computational genomics and metagenomics.

Liberles DA, Teufel AI, Liu L, Stadler T.

Genome Biol Evol. 2013;5(10):2008-18. doi: 10.1093/gbe/evt151.


State-of the art methodologies dictate new standards for phylogenetic analysis.

Anisimova M, Liberles DA, Philippe H, Provan J, Pupko T, von Haeseler A.

BMC Evol Biol. 2013 Aug 1;13:161. doi: 10.1186/1471-2148-13-161. Review.


Analysis of genome content evolution in pvc bacterial super-phylum: assessment of candidate genes associated with cellular organization and lifestyle.

Kamneva OK, Knight SJ, Liberles DA, Ward NL.

Genome Biol Evol. 2012;4(12):1375-90. doi: 10.1093/gbe/evs113.


The salmonid myostatin gene family: a novel model for investigating mechanisms that influence duplicate gene fate.

Lawson CB, Niino T, Hermansen RA, Brok-Volchanskaya V, Jackson MF, Garikipati DK, Liberles DA, Rodgers BD.

BMC Evol Biol. 2012 Oct 8;12:202. doi: 10.1186/1471-2148-12-202.


The evolution of catalytic residues and enzyme mechanism within the bacterial nucleoside phosphorylase superfamily 1.

Konrad A, Piškur J, Liberles DA.

Gene. 2012 Dec 1;510(2):154-61. doi: 10.1016/j.gene.2012.08.046.


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