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Items: 1 to 20 of 42


Characterizing the roles of changing population size and selection on the evolution of flux control in metabolic pathways.

Orlenko A, Chi PB, Liberles DA.

BMC Evol Biol. 2017 May 25;17(1):117. doi: 10.1186/s12862-017-0962-7.


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.


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. eCollection 2016. Review.


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.


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. Epub 2014 Nov 4.


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. Epub 2013 Dec 25.


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.


A phylogenetic analysis of normal modes evolution in enzymes and its relationship to enzyme function.

Lai J, Jin J, Kubelka J, Liberles DA.

J Mol Biol. 2012 Sep 21;422(3):442-59. doi: 10.1016/j.jmb.2012.05.028. Epub 2012 May 28. Erratum in: J Mol Biol. 2013 Aug 23;425(16):3019-23.


The interface of protein structure, protein biophysics, and molecular evolution.

Liberles DA, Teichmann SA, Bahar I, Bastolla U, Bloom J, Bornberg-Bauer E, Colwell LJ, de Koning AP, Dokholyan NV, Echave J, Elofsson A, Gerloff DL, Goldstein RA, Grahnen JA, Holder MT, Lakner C, Lartillot N, Lovell SC, Naylor G, Perica T, Pollock DD, Pupko T, Regan L, Roger A, Rubinstein N, Shakhnovich E, Sjölander K, Sunyaev S, Teufel AI, Thorne JL, Thornton JW, Weinreich DM, Whelan S.

Protein Sci. 2012 Jun;21(6):769-85. doi: 10.1002/pro.2071. Epub 2012 Apr 23. Review.


Biophysical and structural considerations for protein sequence evolution.

Grahnen JA, Nandakumar P, Kubelka J, Liberles DA.

BMC Evol Biol. 2011 Dec 16;11:361. doi: 10.1186/1471-2148-11-361.


Toward a general model for the evolutionary dynamics of gene duplicates.

Konrad A, Teufel AI, Grahnen JA, Liberles DA.

Genome Biol Evol. 2011;3:1197-209. doi: 10.1093/gbe/evr093. Epub 2011 Sep 13.


Binding constraints on the evolution of enzymes and signalling proteins: the important role of negative pleiotropy.

Liberles DA, Tisdell MD, Grahnen JA.

Proc Biol Sci. 2011 Jul 7;278(1714):1930-5. doi: 10.1098/rspb.2010.2637. Epub 2011 Apr 13. Review.


The evolution of protein structures and structural ensembles under functional constraint.

Siltberg-Liberles J, Grahnen JA, Liberles DA.

Genes (Basel). 2011 Oct 28;2(4):748-62. doi: 10.3390/genes2040748.

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