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 * (15 papers have been cited at least 15 times each including nucleic acid chemistry papers as of 8/2008).

2008

1. Tellgren-Roth Å., 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, in press.

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, in press.

7. Tellgren-Roth, Å., Dittmar, K., Massey, S.E., Kemi, C., Roth, C., Savolainen, P., Lyons, L.A., and Liberles, D.A. 2008. “Keeping the blood flowing- Plasminogen activator genes and feeding behavior in vampire bats.” Naturwissenschaften, in press.

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. 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. 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. 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., Ståhl, 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.

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. "Påvisning 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, Å., 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., Söderberg, 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 Hammarström, 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.