David A Liberles

Summary

Affiliation: Stockholm University
Country: Sweden

Publications

  1. ncbi A systematic analysis of lineage-specific evolution in metabolic pathways
    Himanshu Ardawatia
    Computational Biology Unit, BCCS, University of Bergen, 5020 Bergen, Norway
    Gene 387:67-74. 2007
  2. ncbi The Adaptive Evolution Database (TAED)
    D A Liberles
    Department of Chemistry, University of Florida, Gainesville, FL 32611 USA
    Genome Biol 2:PREPRINT0003. 2001
  3. ncbi The adaptive evolution database (TAED)
    D A Liberles
    Departments of Chemistry, University of Florida, Gainesville, FL 32611, USA
    Genome Biol 2:RESEARCH0028. 2001
  4. ncbi Evaluation of methods for determination of a reconstructed history of gene sequence evolution
    D A Liberles
    Department of Biochemistry and Biophysics and Stockholm Bioinformatics Center, Stockholm University, Stockholm, Sweden
    Mol Biol Evol 18:2040-7. 2001
  5. ncbi Evolution enters the genomic era
    D A Liberles
    Department of Biochemistry and Biophysics and Stockholm Bioinformatics Center, Stockholm University, 10691 Stockholm, Sweden
    Genome Biol 2:REPORTS4026. 2001
  6. ncbi Tracking adaptive evolutionary events in genomic sequences
    David A Liberles
    Department of Biochemistry and Biophysics and Stockholm Bioinformatics Center, Stockholm University, 10691 Stockholm, Sweden
    Genome Biol 3:REVIEWS1018. 2002
  7. ncbi The salmon genome (and other issues in bioinformatics)
    Lena E F Milchert
    Department of Biochemistry and Biophysics and Stockholm Bioinformatics Center, Stockholm University, 10691 Stockholm, Sweden
    Genome Biol 3:REPORTS4022. 2002
  8. ncbi Optimal gene trees from sequences and species trees using a soft interpretation of parsimony
    Ann-Charlotte Berglund-Sonnhammer
    Stockholm Bioinformatics Center, Stockholm University, 10691, Stockholm, Sweden
    J Mol Evol 63:240-50. 2006
  9. ncbi Positive selection scanning reveals decoupling of enzymatic activities of carbamoyl phosphate synthetase in Helicobacter pylori
    Wagied Davids
    Department of Biochemistry and Biophysics and Stockholm Bioinformatics Center, Stockholm University, 10691 Stockholm, Sweden
    J Mol Evol 54:458-64. 2002
  10. ncbi Analysis of transitions at two-fold redundant sites in mammalian genomes. Transition redundant approach-to-equilibrium (TREx) distance metrics
    Tang Li
    Foundation for Applied Molecular Evolution, Gainesville, FL 32604, USA
    BMC Evol Biol 6:25. 2006

Collaborators

Detail Information

Publications28

  1. ncbi A systematic analysis of lineage-specific evolution in metabolic pathways
    Himanshu Ardawatia
    Computational Biology Unit, BCCS, University of Bergen, 5020 Bergen, Norway
    Gene 387:67-74. 2007
    ....
  2. ncbi The Adaptive Evolution Database (TAED)
    D A Liberles
    Department of Chemistry, University of Florida, Gainesville, FL 32611 USA
    Genome Biol 2:PREPRINT0003. 2001
    ....
  3. ncbi The adaptive evolution database (TAED)
    D A Liberles
    Departments of Chemistry, University of Florida, Gainesville, FL 32611, USA
    Genome Biol 2:RESEARCH0028. 2001
    ....
  4. ncbi Evaluation of methods for determination of a reconstructed history of gene sequence evolution
    D A Liberles
    Department of Biochemistry and Biophysics and Stockholm Bioinformatics Center, Stockholm University, Stockholm, Sweden
    Mol Biol Evol 18:2040-7. 2001
    ..The examination of these and other measures to detect changes of gene function along branches of a phylogenetic tree will become increasingly important in the postgenomic era...
  5. ncbi Evolution enters the genomic era
    D A Liberles
    Department of Biochemistry and Biophysics and Stockholm Bioinformatics Center, Stockholm University, 10691 Stockholm, Sweden
    Genome Biol 2:REPORTS4026. 2001
    ..A report on the 18th Congress of the European Society for Evolutionary Biology (ESEB), Aarhus, Denmark, 20-25 August, 2001...
  6. ncbi Tracking adaptive evolutionary events in genomic sequences
    David A Liberles
    Department of Biochemistry and Biophysics and Stockholm Bioinformatics Center, Stockholm University, 10691 Stockholm, Sweden
    Genome Biol 3:REVIEWS1018. 2002
    ..Positive selection appears to be important in the interaction between genotype, protein structure, function, and organismal phenotype...
  7. ncbi The salmon genome (and other issues in bioinformatics)
    Lena E F Milchert
    Department of Biochemistry and Biophysics and Stockholm Bioinformatics Center, Stockholm University, 10691 Stockholm, Sweden
    Genome Biol 3:REPORTS4022. 2002
    ..A report on the fourth annual conference of the Society for Bioinformatics in the Nordic Countries (SOCBIN), Bioinformatics 2002, Bergen, Norway, 4-7 April 2002...
  8. ncbi Optimal gene trees from sequences and species trees using a soft interpretation of parsimony
    Ann-Charlotte Berglund-Sonnhammer
    Stockholm Bioinformatics Center, Stockholm University, 10691, Stockholm, Sweden
    J Mol Evol 63:240-50. 2006
    ..The algorithm has also been made available for download as a software package, Softparsmap...
  9. ncbi Positive selection scanning reveals decoupling of enzymatic activities of carbamoyl phosphate synthetase in Helicobacter pylori
    Wagied Davids
    Department of Biochemistry and Biophysics and Stockholm Bioinformatics Center, Stockholm University, 10691 Stockholm, Sweden
    J Mol Evol 54:458-64. 2002
    ..Implications of these findings for a metabolic enzyme under positive selection are discussed in terms of the mechanisms of H. pylori pathogenesis...
  10. ncbi Analysis of transitions at two-fold redundant sites in mammalian genomes. Transition redundant approach-to-equilibrium (TREx) distance metrics
    Tang Li
    Foundation for Applied Molecular Evolution, Gainesville, FL 32604, USA
    BMC Evol Biol 6:25. 2006
    ..Multiple transitions at synonymous sites may cause equilibration and loss of information. Further, to be useful to correlate events in the genomic record, different genes within a genome must suffer transitions at similar rates...
  11. ncbi Catalysis, subcellular localization, expression and evolution of the targeting peptides degrading protease, AtPreP2
    Shashi Bhushan
    Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, 10691 Stockholm, Sweden
    Plant Cell Physiol 46:985-96. 2005
    ..thaliana plants. Phylogenetic evidence indicated that AtPreP1 and AtPreP2 are recent gene duplicates that may have diverged through subfunctionalization...
  12. ncbi A systematic search for positive selection in higher plants (Embryophytes)
    Christian Roth
    Computational Biology Unit, BCCS, University of Bergen, 5020 Bergen, Norway
    BMC Plant Biol 6:12. 2006
    ..The database and these examples have now been studied in further detail to better understand the molecular basis for plant genome evolution...
  13. ncbi Phylogenetic reconstruction of ancestral character states for gene expression and mRNA splicing data
    Roald Rossnes
    Bergen Centre for Computational Science, University of Bergen, 5020 Bergen, Norway
    BMC Bioinformatics 6:127. 2005
    ..A minimum evolution general method for continuous character analysis in a phylogenetic perspective is presented that allows for reconstruction of ancestral character states and for measuring along branch evolution...
  14. ncbi Subfunctionalization of duplicated genes as a transition state to neofunctionalization
    Shruti Rastogi
    Computational Biology Unit, BCCS, University of Bergen, 5020 Bergen, Norway
    BMC Evol Biol 5:28. 2005
    ..The relative importance of these two processes is unclear...
  15. ncbi The Adaptive Evolution Database (TAED): a phylogeny based tool for comparative genomics
    Christian Roth
    Computational Biology Unit, BCCS, University of Bergen, 5020 Bergen, Norway
    Nucleic Acids Res 33:D495-7. 2005
    ..The calculated information is available both as a gene family database and as a phylogenetically indexed resource, called 'The Adaptive Evolution Database' (TAED), available at http://www.bioinfo.no/tools/TAED...
  16. ncbi Complex microsatellite dynamics in the myostatin gene within ruminants
    Asa Tellgren-Roth
    Department of Molecular Biology, University of Wyoming, Laramie, WY 82071, USA
    J Mol Evol 66:258-65. 2008
    ..Finally, these models are evaluated in the context of patterns of microsatellite conservation between closely related mammalian genomes...
  17. ncbi The pattern of evolution of smaller-scale gene duplicates in mammalian genomes is more consistent with neo- than subfunctionalisation
    Timothy Hughes
    Computational Biology Unit, BCCS, University of Bergen, 5020, Bergen, Norway
    J Mol Evol 65:574-88. 2007
    ....
  18. ncbi Artiodactyl IgD: the missing link
    Yaofeng Zhao
    Center for Biotechnology, Department of Bioscience at Novum, Karolinska Institute, SE 14157 Huddinge, Sweden
    J Immunol 169:4408-16. 2002
    ..The presence of Cdelta genes in artiodactyls, possibly in most mammals, suggests that IgD may have some as yet unknown biological properties, distinct from those of IgM, conferring a survival advantage...
  19. ncbi Using evolutionary information and ancestral sequences to understand the sequence-function relationship in GLP-1 agonists
    Marie Skovgaard
    Novo Nordisk A S, Novo Nordisk Park, DK 2760 Måløv, Denmark
    J Mol Biol 363:977-88. 2006
    ..This represents a new approach using evolutionary data in protein engineering...
  20. ncbi Evolution after gene duplication: models, mechanisms, sequences, systems, and organisms
    Christian Roth
    Department of Molecular Biology, University of Wyoming, Laramie, Wyoming 82071, USA
    J Exp Zool B Mol Dev Evol 308:58-73. 2007
    ..single gene duplication. Lastly, the role that these processes may have played in driving speciation is examined...
  21. ncbi Evaluation of models for the evolution of protein sequences and functions under structural constraint
    Shruti Rastogi
    Department of Molecular Biology, University of Wyoming, Laramie, WY 82071, USA
    Biophys Chem 124:134-44. 2006
    ..To demonstrate the applicability of these methods, the dynamics of evolution of new binding capabilities by an SH2 domain is demonstrated...
  22. ncbi Phylogenetic relationships of the Fox (Forkhead) gene family in the Bilateria
    Francoise Mazet
    School of Animal and Microbial Sciences, The University of Reading, P O Box 228 Whiteknights, RG6 6AJ Reading, UK
    Gene 316:79-89. 2003
    ..Our analyses suggest that the common ancestor of protostomes and deuterostomes had a minimum complement of 14 Fox genes...
  23. ncbi Visualising very large phylogenetic trees in three dimensional hyperbolic space
    Timothy Hughes
    Computational Biology Unit Bergen Centre for Computational Science University of Bergen, 5020 Bergen, Norway
    BMC Bioinformatics 5:48. 2004
    ..Common existing phylogenetic tree visualisation tools are not able to display readable trees with more than a few thousand nodes. These existing methodologies are based in two dimensional space...
  24. ncbi Characterization of hARD2, a processed hARD1 gene duplicate, encoding a human protein N-alpha-acetyltransferase
    Thomas Arnesen
    Department of Molecular Biology, University of Bergen, N 5020 Bergen, Norway
    BMC Biochem 7:13. 2006
    ..We recently described the human protein acetyltransferase hARD1 (human Arrest Defective 1). hARD1 interacts with NATH (N-Acetyl Transferase Human) forming a complex expressing protein N-terminal alpha-acetylation activity...
  25. ncbi The planetary biology of cytochrome P450 aromatases
    Eric A Gaucher
    Foundation for Applied Molecular Evolution, 1115 NW 4th Street, Gainesville FL 32601 4256, USA
    BMC Biol 2:19. 2004
    ..This strategy expands systems biology to a planetary context, necessary for a notion of fitness to underlie (as it must) any discussion of function within a biomolecular system...
  26. ncbi Datasets for evolutionary comparative genomics
    David A Liberles
    Computational Biology Unit, Bergen Centre for Computational Science, University of Bergen, 5020 Bergen, Norway
    Genome Biol 6:117. 2005
    ..One such rationale for whole-genome sequencing is discussed here, along with other important strategies for understanding the phenotypic divergence of species...
  27. ncbi Myostatin rapid sequence evolution in ruminants predates domestication
    Asa Tellgren
    Computational Biology Unit, Bergen Centre for Computational Science, University of Bergen, 5020 Bergen, Norway
    Mol Phylogenet Evol 33:782-90. 2004
    ..These periods of positive selective pressure on myostatin may correlate with changes in skeletal muscle mass during the same period...
  28. ncbi Characterizing positive and negative selection and their phylogenetic effects
    Steven E Massey
    Department of Molecular Biology, University of Wyoming, Laramie, WY 82071, USA
    Gene 418:22-6. 2008
    ..In this case, sequence convergence is promoted by functional convergence...