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Items: 1 to 50 of 87

1.

A New Editorial Beginning at Journal of Molecular Evolution.

Liberles DA.

J Mol Evol. 2019 Apr;87(2-3):69-71. doi: 10.1007/s00239-019-09888-2. No abstract available.

PMID:
30770947
2.

Evolution in the light of fitness landscape theory.

Fragata I, Blanckaert A, Dias Louro MA, Liberles DA, Bank C.

Trends Ecol Evol. 2019 Jan;34(1):69-82. doi: 10.1016/j.tree.2018.10.009. Epub 2018 Dec 21. Review.

PMID:
30583805
3.

Evolution and Structure of Proteins and Proteomes.

Liberles DA, Teufel AI.

Genes (Basel). 2018 Nov 28;9(12). pii: E583. doi: 10.3390/genes9120583.

4.

Protocols for the Molecular Evolutionary Analysis of Membrane Protein Gene Duplicates.

Yohe LR, Liu L, Dávalos LM, Liberles DA.

Methods Mol Biol. 2019;1851:49-62. doi: 10.1007/978-1-4939-8736-8_3.

PMID:
30298391
5.

Using the Mutation-Selection Framework to Characterize Selection on Protein Sequences.

Teufel AI, Ritchie AM, Wilke CO, Liberles DA.

Genes (Basel). 2018 Aug 13;9(8). pii: E409. doi: 10.3390/genes9080409. Review.

6.

Protein evolution depends on multiple distinct population size parameters.

Platt A, Weber CC, Liberles DA.

BMC Evol Biol. 2018 Feb 8;18(1):17. doi: 10.1186/s12862-017-1085-x. Review.

7.

A new parameter-rich structure-aware mechanistic model for amino acid substitution during evolution.

Chi PB, Kim D, Lai JK, Bykova N, Weber CC, Kubelka J, Liberles DA.

Proteins. 2018 Feb;86(2):218-228. doi: 10.1002/prot.25429. Epub 2017 Dec 12.

8.

The Adaptive Evolution Database (TAED): A New Release of a Database of Phylogenetically Indexed Gene Families from Chordates.

Hermansen RA, Oswald BP, Knight S, Shank SD, Northover D, Korunes KL, Michel SN, Liberles DA.

J Mol Evol. 2017 Aug;85(1-2):46-56. doi: 10.1007/s00239-017-9806-8. Epub 2017 Aug 9.

PMID:
28795237
9.

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.

10.

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.

11.

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

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

Syst Biol. 2017 Nov 1;66(6):1054-1064. doi: 10.1093/sysbio/syw121.

PMID:
28057858
12.
13.

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.

14.

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. Epub 2016 Apr 18.

PMID:
27088604
15.

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. Epub 2016 Feb 26.

PMID:
26920685
16.

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.

17.

Selection on protein structure, interaction, and sequence.

Chi PB, Liberles DA.

Protein Sci. 2016 Jul;25(7):1168-78. doi: 10.1002/pro.2886. Epub 2016 Feb 11. Review.

18.

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.

19.

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.

20.

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.

21.

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):11-19. doi: 10.1002/gepi.21870. Epub 2014 Nov 4.

22.

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.

PMID:
24845553
23.

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. Epub 2014 Feb 6.

PMID:
24500774
24.

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.

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.

26.

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.

27.

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.

28.

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.

29.

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. Epub 2012 Sep 3.

PMID:
22967797
30.

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.

31.

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.

32.

Deoxyribonucleoside kinases in two aquatic bacteria with high specificity for thymidine and deoxyadenosine.

Tinta T, Christiansen LS, Konrad A, Liberles DA, Turk V, Munch-Petersen B, Piškur J, Clausen AR.

FEMS Microbiol Lett. 2012 Jun;331(2):120-7. doi: 10.1111/j.1574-6968.2012.02565.x. Epub 2012 Apr 25.

33.

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.

34.

The global distribution and evolution of deoxyribonucleoside kinases in bacteria.

Konrad A, Yarunova E, Tinta T, Piškur J, Liberles DA.

Gene. 2012 Jan 15;492(1):117-20. doi: 10.1016/j.gene.2011.10.039. Epub 2011 Oct 26.

PMID:
22057012
35.

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.

36.

Fast side chain replacement in proteins using a coarse-grained approach for evaluating the effects of mutation during evolution.

Grahnen JA, Kubelka J, Liberles DA.

J Mol Evol. 2011 Aug;73(1-2):23-33. doi: 10.1007/s00239-011-9454-3. Epub 2011 Jul 29.

PMID:
21800121
37.

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.

38.

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.

39.

Plasticity of animal genome architecture unmasked by rapid evolution of a pelagic tunicate.

Denoeud F, Henriet S, Mungpakdee S, Aury JM, Da Silva C, Brinkmann H, Mikhaleva J, Olsen LC, Jubin C, Cañestro C, Bouquet JM, Danks G, Poulain J, Campsteijn C, Adamski M, Cross I, Yadetie F, Muffato M, Louis A, Butcher S, Tsagkogeorga G, Konrad A, Singh S, Jensen MF, Huynh Cong E, Eikeseth-Otteraa H, Noel B, Anthouard V, Porcel BM, Kachouri-Lafond R, Nishino A, Ugolini M, Chourrout P, Nishida H, Aasland R, Huzurbazar S, Westhof E, Delsuc F, Lehrach H, Reinhardt R, Weissenbach J, Roy SW, Artiguenave F, Postlethwait JH, Manak JR, Thompson EM, Jaillon O, Du Pasquier L, Boudinot P, Liberles DA, Volff JN, Philippe H, Lenhard B, Roest Crollius H, Wincker P, Chourrout D.

Science. 2010 Dec 3;330(6009):1381-5. doi: 10.1126/science.1194167. Epub 2010 Nov 18.

40.

Genome-wide influence of indel Substitutions on evolution of bacteria of the PVC superphylum, revealed using a novel computational method.

Kamneva OK, Liberles DA, Ward NL.

Genome Biol Evol. 2010;2:870-86. doi: 10.1093/gbe/evq071. Epub 2010 Nov 3.

41.

Lineage-specific differences in the amino acid substitution process.

Huzurbazar S, Kolesov G, Massey SE, Harris KC, Churbanov A, Liberles DA.

J Mol Biol. 2010 Mar 12;396(5):1410-21. doi: 10.1016/j.jmb.2009.11.075. Epub 2010 Jan 15.

42.

Phylogenetic analysis of the NEEP21/calcyon/P19 family of endocytic proteins: evidence for functional evolution in the vertebrate CNS.

Muthusamy N, Ahmed SA, Rana BK, Navarre S, Kozlowski DJ, Liberles DA, Bergson C.

J Mol Evol. 2009 Oct;69(4):319-32. doi: 10.1007/s00239-009-9273-y. Epub 2009 Sep 17.

43.

Formyl peptide receptors are candidate chemosensory receptors in the vomeronasal organ.

Liberles SD, Horowitz LF, Kuang D, Contos JJ, Wilson KL, Siltberg-Liberles J, Liberles DA, Buck LB.

Proc Natl Acad Sci U S A. 2009 Jun 16;106(24):9842-7. doi: 10.1073/pnas.0904464106. Epub 2009 Jun 3.

44.

Whole-genome duplications in the ancestral vertebrate are detectable in the distribution of gene family sizes of tetrapod species.

Hughes T, Liberles DA.

J Mol Evol. 2008 Oct;67(4):343-57. doi: 10.1007/s00239-008-9145-x. Epub 2008 Sep 25.

PMID:
18815825
45.

Keeping the blood flowing-plasminogen activator genes and feeding behavior in vampire bats.

Tellgren-Roth A, Dittmar K, Massey SE, Kemi C, Tellgren-Roth C, Savolainen P, Lyons LA, Liberles DA.

Naturwissenschaften. 2009 Jan;96(1):39-47. doi: 10.1007/s00114-008-0446-0. Epub 2008 Sep 13.

PMID:
18791694
46.

Gene duplication: red queens, linkage, redundancy and synfunctionalization.

Liberles DA.

Heredity (Edinb). 2008 Oct;101(4):299-300. doi: 10.1038/hdy.2008.81. Epub 2008 Aug 13. No abstract available.

47.

Characterizing positive and negative selection and their phylogenetic effects.

Massey SE, Churbanov A, Rastogi S, Liberles DA.

Gene. 2008 Jul 15;418(1-2):22-6. doi: 10.1016/j.gene.2008.03.017. Epub 2008 Apr 8.

PMID:
18486364
48.

The power-law distribution of gene family size is driven by the pseudogenisation rate's heterogeneity between gene families.

Hughes T, Liberles DA.

Gene. 2008 May 15;414(1-2):85-94. doi: 10.1016/j.gene.2008.02.014. Epub 2008 Mar 10.

PMID:
18378100
49.

Complex microsatellite dynamics in the myostatin gene within ruminants.

Tellgren-Roth A, Kolesov G, Sifuentes-Rincón AM, Liberles DA.

J Mol Evol. 2008 Mar;66(3):258-65. doi: 10.1007/s00239-008-9080-x. Epub 2008 Mar 5.

PMID:
18320259
50.

Characterizing gene family evolution.

Liberles DA, Dittmar K.

Biol Proced Online. 2008 Jun 20;10:66-73. doi: 10.1251/bpo144.

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