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Results: 1 to 20 of 66

1.

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
[PubMed - in process]
2.

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
[PubMed - in process]
3.

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.

PMID:
24371277
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

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.

PMID:
24115604
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

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.

PMID:
23914788
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

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.

PMID:
23221607
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

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.

PMID:
23043301
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

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
[PubMed - indexed for MEDLINE]
9.

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.

PMID:
22651983
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

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.

PMID:
22528593
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

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.

PMID:
22462611
[PubMed - indexed for MEDLINE]
12.

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.

PMID:
22171550
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

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
[PubMed - indexed for MEDLINE]
14.

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.

PMID:
21920903
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

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
[PubMed - indexed for MEDLINE]
16.

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.

PMID:
21490020
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

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.

PMID:
24710290
[PubMed]
Free PMC Article
18.

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, Cong EH, 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.

PMID:
21097902
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

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.

PMID:
21048002
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

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.

PMID:
20004669
[PubMed - indexed for MEDLINE]
Free PMC Article

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