University of Wyoming

Liberles Research Group

Recent Publications


Note: Please check that you or your library have paid for access to these journals (where relevant) before downloading .pdf files.

h-factor papers marked with * (22 papers have been cited at least 21 times each including nucleic acid chemistry papers as of 4/2012 according to ISI Web of Science).


2012


1. Anisimova, M. and Liberles, D.A. "Detecting and understanding selection" in Codon Evolution (Eds: Cannarozzi and Schneider). Oxford: Oxford University Press, 2012.


2. Teufel, A.I., Grahnen, J.A., and Liberles, D.A. "Modeling proteins at the interface of structure, evolution, and population genetics" in Computational Modeling of Biological Systems: From Molecules to Pathways (Ed: Dokholyan). New York: Springer-Verlag, 2012.


3. Konrad A., Yarunova, E., Tinta, T., Piskur, J., and Liberles, D.A. 2012. "The global distribution and evolution of deoxyribonucleoside kinases in bacteria." Gene, 492:117-120.


4. Liberles D.A. 2012. "A review of "Convergent Evolution: Limited forms most beautiful."" Trends in Evolutionary Biology, 4:e2.


5. Tinta, T., Christiansen, L.S., Konrad, A., Liberles, D.A., Turk, V., Munch-Petersen, B., Piskur, J., and Clausen A.R. 2012. "Deoxyribonucleoside kinases in two aquatic bacteria with high specificity for thymidine and deoxyadenosine." FEMS Microbiology Letters, in press.


6. Liberles, DA, Teichmann, S, Bahar I, Bastolla U, Bloom J, Bornberg-Bauer E, Colwell LJ, de Koning APJ, Dokholyan NV, Echave J, Elofsson A, Gerloff DL, Goldstein RA, Grahnen JA, Holder M, Lakner C, Lartillot N, Lovell S, Naylor G, Perica T, Pollock DD, Pupko T, Regan L, Roger A, Rubinstein N, Shakhnovich E, Sjolander E, Sunyaev S, Teufel AI, Thorne JL, Thornton JW, Weinreich DM, Whelan S. 2012. "The Interface of Protein Structure, Protein Biophysics, and Molecular Evolution". Protein Science, in press.


2011


1. Liberles, D.A., Tisdell, M.D.M., and Grahnen, J.A. 2011. "Binding constraints on the evolution of enzymes and signaling proteins: The important role of negative pleiotropy." Proceedings of the Royal Society B, 278:1930-1935.


2. Grahnen, J.A., Kubelka, J., and Liberles, D.A. 2011. "Fast side chain replacement in proteins using a coarse grained approach for evaluating the effects of mutation during evolution." Journal of Molecular Evolution, 73:23-33.


3. Konrad, A.*, Teufel, A.I.*, Grahnen, J.A., and Liberles, D.A. 2011. "Towards a general model for the evolutionary dynamics of gene duplicates." Genome Biology and Evolution, 3:1197-1209.


4. Siltberg-Liberles, J., Grahnen, J.A., and Liberles, D.A. 2011. "The evolution of protein structures and structural ensembles under functional constraint." Genes, 2:748-762.


5. Grahnen, J.A., Nandakumar, P., Kubelka, J., and Liberles, D.A. 2011. "Biophysical and Structural Considerations for Protein Evolution." BMC Evolutionary Biology,11:361.



2010


1. Liberles, D.A., Kolesov, G., and Dittmar, K. "Joining biochemistry and population genetics to understand gene duplication." in Evolution After Gene Duplication (Eds: Dittmar and Liberles). New York: Wiley, 2010.


2. Eulenstein, O., Huzurbazar, S., and Liberles, D.A. "Reconciling phylogenetic trees." in Evolution After Gene Duplication (Eds: Dittmar and Liberles). New York: Wiley, 2010.


3. Huzurbazar, S., Kolesov, G., Massey, S.E., Harris, K.C., Churbanov, A., and Liberles, D.A. 2010. "Lineage-specific differences in the amino acid substitution process." Journal of Molecular Biology, 396:1410-1421.


4. Kamneva, O.K., Liberles, D.A., and Ward, N.L. 2010."Genome-wide analysis of insertion and deletion substitutions in organisms of the PVC superphylum."Genome Biology and Evolution, 2:870-886.


5. Anisimova, M., Cannarozzi, G.M., and Liberles, D.A. 2010. "Finding the balance between mathematical and biological optima in multiple sequence alignment." Trends in Evolutionary Biology, 2:e7.


*6. Denoeud F, Henriet S, Mungpakdee S, Aury JM, Da Silva C, Brinkmann H, Mikhaleva J, Olsen LC, Jubin C, Canestro C, Bouquet J-M, 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, Eikeseth-Ottera H, Noel B, Anthouard V, Porcel-Setterblad B, Kachouri-Lafond R, Nishino A, Ugolini M, Chourrout P, Nishida H, Aasland R, Huzurbazar S, Westhof E, Delsuc F, Lehrach H, Reinhardt R, Weissenbach R, Roy SW, Artiguenave F, Postlethwait J, Manak JR, Thompson EM, Jaillon O, Du Pasquier L, Boudinot P, Liberles DA, Volff J-N, Philippe H, Lenhard B, Roest Crollius H, Wincker P, Chourrout D. 2010. "Plasticity of animal genome architecture unmasked by rapid evolution of pelagic tunicates." Science, 330:1381-1385.



2009


1. Tellgren-Roth, A., Dittmar, K., Massey, S.E., Kemi, C., Roth, C., Savolainen, P., Lyons, L.A., and Liberles, D.A. 2009. "Keeping the blood flowing- Plasminogen activator genes and feeding behavior in vampire bats." Naturwissenschaften, 96:39-47.


2. Liberles, D.A. 2009. "A review of "Reading the Story in DNA."" Systematic Biology, 58:161-162.


*3. Liberles, S.D., Horowitz, L.F., Kuang, D., Contos, J.J., Wilson, K.L., Siltberg-Liberles, J., Liberles, D.A., and Buck, L.B. 2009. "Formyl peptide receptors are candidate chemosensory receptors in the vomeronasal organ." Proc. Natl. Acad. Sci., USA, 106:9842-9847.


4. Muthusamy, N., Ahmed, S.A., Rana , B.K., Navarre, S., Kozlowski, D., Liberles, D.A., and Bergson, C. 2009. "Phylogenetic analysis of the NEEP21/Calcyon/P19 family of endocytic proteins: Evidence for functional evolution in the vertebrate CNS." Journal of Molecular Evolution, 69:319-332.



2008


1. Tellgren-Roth A., Kolesov, G., Sifuentes-Rincon, A.M, and Liberles, D.A. 2008. "Complex microsatellite dynamics in the myostatin gene within ruminants." Journal of Molecular Evolution, 66:258-265.


2. Liberles, D.A. 2008. "Of gene duplication, red queens, linkage, redundancy, and synfunctionalization." Heredity, 101:299-300.


3. Hughes, T. and Liberles, D.A. 2008. "The power law distribution of gene family size is driven by the pseudogenisation rate's heterogeneity between gene families." Gene 414:85-94.


4. Liberles, D.A. and Dittmar, K. 2008. "Characterizing gene family evolution." Biological Procedures, 10:66-73.


5. Massey, S.E., Churbanov, A., Rastogi, S., and Liberles, D.A. 2008. "Characterizing positive and negative selection and their phylogenetic effects." Gene, 418:22-26.


6. Hughes, T. and Liberles, D.A. 2008. "A characterisation of the effects of speciation and whole genome duplication on the distribution of gene family sizes and its application to detecting large scale duplication." Journal of Molecular Evolution, 67:343-357.



2007


1. Ardawatia, H. and Liberles, D.A. 2007. "A systematic analysis of lineage-specific evolution in metabolic pathways." Gene 387:67-74.


*2. Roth, C., Rastogi, S., Arvestad, L., Dittmar, K., Light, S., Ekman, D., and Liberles, D.A. 2007. "Evolution after gene duplication: Models, mechanisms, sequences, systems, and organisms." Journal of Experimental Zoology, 308B:58-73.


3. Kodra, J.T., Skovgaard, M., Madsen, D., and Liberles, D.A. "Linking sequence to function in drug design with ancestral sequence reconstruction." in Ancestral Sequence Reconstruction (Ed: Liberles). Oxford: Oxford University Press, 2007.


4. Pupko, T., Doron-Faigenboim, A., Liberles, D.A., and Cannarozzi, G.M. "Probabilistic models and their impact on the accuracy of reconstructed ancestral protein sequences." in Ancestral Sequence Reconstruction (Ed: Liberles). Oxford: Oxford University Press, 2007.


5. Hughes, T., Ekman, D., Ardawatia, H., Elofsson, A., and Liberles, D.A. 2007. "Evaluating dosage compensation as a cause of duplicate gene retention in Paramecium tetraurelia." Genome Biology, 8:213.


*6. Anisimova, M. and Liberles, D.A. 2007. "The quest for natural selection in the age of comparative genomics." Heredity, 99:567-579.


*7. Hughes, T. and Liberles, D.A. 2007. "The pattern of evolution of smaller scale duplicates in mammalian genomes is more consistent with neo- than sub-functionalisation." Journal of Molecular Evolution, 65:574-588.



2006


1. Li, T., Caraco, M.D., Gaucher, E.A., Liberles, D.A., Thomson, J.M., Chamberlin, S.G., and Benner, S.A. 2006. "Examination of transition redundant approach-to-equilibrium (TREx) Clocks in Mammalian Systems." BMC Evolutionary Biology, 6:25.


*2. Berglund-Sonnhammer, A.C., Steffansson, P., Betts, M.J., and Liberles, D.A. 2006. "Optimal gene trees from sequences and species trees using a soft interpretation of parsimony." Journal of Molecular Evolution, 63:240-250.


3. Arnesen, T., Betts, M.J., Pendino, F., Liberles, D.A., Anderson, D., Caro, J., Kong, X., Varhaug, J.E., and Lillehaug, J.R. 2006. "Characterization of a processed gene duplicate, hARD2, encoding a novel human protein acetyltransferase." BMC Biochemistry, 7:13.


4. Roth, C. and Liberles, D.A. 2006. "A systematic search for positive selection in higher plants (embryophytes)." BMC Plant Biology, 6:12.


5. Rastogi, S., Reuter, N., and Liberles, D.A. 2006. "Evaluation of models for the evolution of protein sequences and functions under structural constraint." Biophysical Chemistry 124:134-144.


6. Skovgaard, M., Kodra, J.T., Gram, D.X., Knudsen, S.M., Madsen, D., and Liberles, D.A. 2006. "Using evolutionary information and ancestral sequences to understand the sequence-function relationship in Glp1 agonists." Journal of Molecular Biology, 363:977-988.


2005


1. Liberles, D.A. "Using phylogeny to understand genomic evolution." in Parsimony, Phylogeny, and Genomics (Ed: Albert). Oxford:Oxford University Press, 2005. (reprint available upon request)


*2. Roth, C., Betts, M.J., Steffansson, P., Saelensminde, G., and Liberles, D.A. 2005. "The Adaptive Evolution Database (TAED): A phylogeny-based tool for comparative genomics." Nucleic Acids Research, 33:D495-D497.


*3. Bellinge, R.H.S., Liberles, D.A., Iaschi, S.P.A., O'Brien, P.A., and Tay, G.K. 2005. "Myostatin and its implications on animal breeding- a review." Animal Genetics, 36:1-6.


*4. Berglund, A.C., Wallner, B., Elofsson, A., and Liberles, D.A. 2005. "Tertiary windowing to detect positive diversifying selection." Journal of Molecular Evolution, 60:499-504.


5. Liberles, D.A. 2005. "Datasets for evolutionary comparative genomics." Genome Biology, 6:117. see also journal cover.


6. Roth, C., Betts, M.J., and Liberles, D.A. "Protein content in chordate and embryophyte genomes." in Bioinformatics: New Research, Volume 1. New York:Nova Science Publishers, 2005. (reprint available upon request)


*7. Bhusan, S., Stahl, A., Nilsson, S., Lefebvre, B., Seki, M., Roth, C., McWilliam, D., Wright, S.J., Liberles, D.A., Shinozaki, K., Bruce, B.D., Boutry, M., and Glaser, E. 2005. "Catalysis, subcellular localization, expression, and evolution of the targeting peptides degrading protease, AtPreP2." Plant and Cell Physiology, 46:985-996.


*8. Rastogi, S. and Liberles, D.A. 2005. "Subfunctionalization of duplicated genes as a transition state to neofunctionalization." BMC Evolutionary Biology, 5:28.


9. Rossnes, R., Eidhammer, I., and Liberles, D.A. 2005. "Phylogenetic reconstruction of ancestral character states for gene expression and mRNA splicing data." BMC Bioinformatics, 6:127.


2004


1. Braun, F.N. and Liberles, D.A. 2004. "Repeat modulated population genetic effects in fungal proteins." Journal of Molecular Evolution, 59:97-102.


2. Hughes, T., Hyun, Y., and Liberles, D.A. 2004. "Visualising very large phylogenetic trees in three dimensional hyperbolic space." BMC Bioinformatics, 5:48. (Figure 2 featured on cover of March, 2010 issue of Nature Methods.)


3. Gaucher, E.A., Graddy, L.G., Li, T., Simmen, R.C.M., Simmen, F.A., Schreiber, D.R., Liberles, D.A., Janis, C.M., and Benner, S.A. 2004. "The planetary biology of cytochrome P450 aromatases." BMC Biology, 2:19.


4. Liberles, D.A. "Detecting and Characterizing Adaptive Evolution in Chordate Proteins." in Comparative Genomics of Vertebrates: Concepts and Bioinformatic Tools. INSERM, 2004.


5. Liberles, D.A. 2004. "Pavisning og karakterisering av positivt seleksjonstrykk i proteinkodende gener." NBS Nytt, 28 (1/2):14-16. (translation by Eivind Hovig) (page proof version as .pdf)


6. Tellgren, A., Berglund, A.C., Savolainen, P., Janis, C.M., and Liberles, D.A. 2004. "Myostatin rapid sequence evolution in ruminants predates domestication." Molecular Phylogenetics and Evolution, 33:782-790.


2003


*1. Mazet, F., Yu, J.K., Liberles, D.A., Holland, L.Z., and Shimeld, S.M. 2003. "Phylogenetic relationships of the Fox (Forkhead) gene family in the Bilateria." Gene, 316:79-89.


2. Braun, F.N. and Liberles D.A. 2003. "Retention of enzyme gene duplicates by subfunctionalization." International Journal of Biological Macromolecules, 33:19-22.


2002


*1. Peltier, J.B., Emanuelsson, O., Kalume, D.E., Ytterberg, J., Friso, G., Rudella, A., Liberles, D.A., Soderberg, L., Roepstorff, P., von Heijne, G., and van Wijk, K.J. 2002. "Central functions of the lumenal and peripheral thylakoid proteome of Arabidopsis thaliana determined by experimentation and genome-wide prediction." The Plant Cell, 14:211-236.


2. Davids, W., Gamieldien, J., Liberles, D.A., and Hide, W. 2002. "Positive selection scanning reveals decoupling of enzymatic activities of carbamoyl phosphate synthetase in H. pylori." Journal of Molecular Evolution, 54:458-464.


3. Liberles, D.A., Thoren, A., von Heijne, G., and Elofsson, A. 2002. "The use of phylogenetic profiles for gene predictions." Current Genomics, 3:131-138.


*4. Siltberg, J. and Liberles, D.A. 2002. "A simple covarion-based approach to analyse nucleotide substitution rates." Journal of Evolutionary Biology, 15:588-594.


5. Liberles, D.A. and Wayne, M.L. 2002. "Tracking adaptive evolutionary events in genomic sequences." Genome Biology, 3(6):reviews1018.1-1018.4.


6. Milchert, L.E.F., Liberles, D.A., and Elofsson, A. 2002. "The salmon genome (and other issues in bioinformatics)." Genome Biology, 3(7):reports4022.1-4022.4.


*7. Zhao, Y., Kacskovics, I., Pan, Q., Liberles, D.A., Geli, J., Rabbani, H., and Hammarstrom, L. 2002. "Artiodactyl IgD- the missing link." Journal of Immunology, 169:4408-4416.


2001


*1. Peltier, J.B., Ytterberg, J., Liberles, D.A., Roepstorff, P., and van Wijk, K.J. 2001. "Identification of a 350 kDa ClpP protease complex with 10 different Clp isoforms in chloroplasts of Arabidopsis thaliana." Journal of Biological Chemistry, 276:16318-16327.


*2. Liberles, D.A., Schreiber, D.R., Govindarajan, S., Chamberlin, S.G., and Benner, S.A. 2001. "The Adaptive Evolution Database (TAED)." Genome Biology, 2(8):research0028.1-0028.6.


*3. Liberles, D.A. 2001. "Evaluation of Methods for Determination of a Reconstructed History of Gene Sequence Evolution." Molecular Biology and Evolution, 18:2040-2047.


4. Liberles, D.A. 2001. "Evolution enters the genomic era." Genome Biology, 2(11):reports4026.1-4026.5.


5. Liberles, D.A. 2001. "SNPing variation from genomes." Genome Biology, 3(1):reports4001.1-4001.4.


2000


*1. Benner, S.A., Chamberlin, S.G., Liberles, D.A., Govindarajan, S., Knecht, L. 2000. "Functional Inferences From Reconstructed Evolutionary Biology Involving Rectified Databases- An Evolutionarily Grounded Approach to Functional Genomics." Research in Microbiology, 151:97-106.


2. Peltier, M.R., Raley, L.C., Liberles, D.A., Benner, S.A., and Hansen, P.J. 2000. "Evolutionary History of the Uterine Serpins." Journal of Experimental Zoology, 288:165-174.


Also, please feel free to contact me for copies of manuscripts from my pre-bioinformatics life working on nucleic acid chemistry.