David A. Liberles, Ph.D. - Publications

molecular evolution, comparative genomics, bioinformatics

106 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Ritchie AM, Stark TL, Liberles DA. Inferring the number and position of changes in selective regime in a non-equilibrium mutation-selection framework. Bmc Ecology and Evolution. 21: 39. PMID 33691618 DOI: 10.1186/s12862-021-01770-4  0.36
2021 Selberg AGA, Gaucher EA, Liberles DA. Ancestral Sequence Reconstruction: From Chemical Paleogenetics to Maximum Likelihood Algorithms and Beyond. Journal of Molecular Evolution. PMID 33486547 DOI: 10.1007/s00239-021-09993-1  0.92
2020 Chi PB, Kosater WM, Liberles DA. Detecting Signatures of Positive Selection against a Backdrop of Compensatory Processes. Molecular Biology and Evolution. PMID 32895716 DOI: 10.1093/Molbev/Msaa161  0.8
2019 Yohe LR, Liu L, Dávalos LM, Liberles DA. Protocols for the Molecular Evolutionary Analysis of Membrane Protein Gene Duplicates. Methods in Molecular Biology (Clifton, N.J.). 1851: 49-62. PMID 30298391 DOI: 10.1007/978-1-4939-8736-8_3  0.72
2018 Liberles DA, Teufel AI. Evolution and Structure of Proteins and Proteomes. Genes. 9. PMID 30487453 DOI: 10.3390/Genes9120583  1
2018 Teufel AI, Ritchie AM, Wilke CO, Liberles DA. Using the Mutation-Selection Framework to Characterize Selection on Protein Sequences. Genes. 9. PMID 30104502 DOI: 10.3390/Genes9080409  1
2018 Platt A, Weber CC, Liberles DA. Protein evolution depends on multiple distinct population size parameters. Bmc Evolutionary Biology. 18: 17. PMID 29422024 DOI: 10.1186/S12862-017-1085-X  0.44
2017 Chi PB, Kim D, Lai JK, Bykova N, Weber CC, Kubelka J, Liberles DA. A new parameter-rich structure-aware mechanistic model for amino acid substitution during evolution. Proteins. PMID 29178386 DOI: 10.1002/Prot.25429  0.8
2017 Hermansen RA, Oswald BP, Knight S, Shank SD, Northover D, Korunes KL, Michel SN, Liberles DA. The Adaptive Evolution Database (TAED): A New Release of a Database of Phylogenetically Indexed Gene Families from Chordates. Journal of Molecular Evolution. PMID 28795237 DOI: 10.1007/S00239-017-9806-8  0.6
2017 Orlenko A, Chi PB, Liberles DA. Characterizing the roles of changing population size and selection on the evolution of flux control in metabolic pathways. Bmc Evolutionary Biology. 17: 117. PMID 28545395 DOI: 10.1186/S12862-017-0962-7  0.8
2017 Arenas M, Weber CC, Liberles DA, Bastolla U. ProtASR: An Evolutionary Framework for Ancestral Protein Reconstruction with Selection on Folding Stability. Systematic Biology. PMID 28057858 DOI: 10.1093/Sysbio/Syw121  0.44
2016 Orlenko A, Teufel AI, Chi PB, Liberles DA. Selection on metabolic pathway function in the presence of mutation-selection-drift balance leads to rate-limiting steps that are not evolutionarily stable. Biology Direct. 11: 31. PMID 27393343 DOI: 10.1186/S13062-016-0133-6  1
2016 Hermansen RA, Hvidsten TR, Sandve SR, Liberles DA. Extracting functional trends from whole genome duplication events using comparative genomics. Biological Procedures Online. 18: 11. PMID 27168732 DOI: 10.1186/S12575-016-0041-2  0.6
2016 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, ... ... Liberles DA, et al. The Atlantic salmon genome provides insights into rediploidization. Nature. PMID 27088604 DOI: 10.1038/Nature17164  1
2016 Orlenko A, Hermansen RA, Liberles DA. Flux Control in Glycolysis Varies Across the Tree of Life. Journal of Molecular Evolution. PMID 26920685 DOI: 10.1007/S00239-016-9731-2  0.8
2016 Teufel AI, Liu L, Liberles DA. Models for gene duplication when dosage balance works as a transition state to subsequent neo-or sub-functionalization. Bmc Evolutionary Biology. 16: 45. PMID 26897341 DOI: 10.1186/S12862-016-0616-1  1
2016 Chi PB, Liberles DA. Selection on protein structure, interaction, and sequence. Protein Science : a Publication of the Protein Society. PMID 26808055 DOI: 10.1002/Pro.2886  1
2015 Zhao J, Teufel AI, Liberles DA, Liu L. A generalized birth and death process for modeling the fates of gene duplication. Bmc Evolutionary Biology. 15: 275. PMID 26643106 DOI: 10.1186/S12862-015-0539-2  1
2015 Hermansen RA, Mannakee BK, Knecht W, Liberles DA, Gutenkunst RN. Characterizing selective pressures on the pathway for de novo biosynthesis of pyrimidines in yeast. Bmc Evolutionary Biology. 15: 232. PMID 26511837 DOI: 10.1186/S12862-015-0515-X  1
2015 Teufel AI, Masel J, Liberles DA. What Fraction of Duplicates Observed in Recently Sequenced Genomes Is Segregating and Destined to Fail to Fix? Genome Biology and Evolution. PMID 26220936 DOI: 10.1093/Gbe/Evv139  1
2015 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, et al. Genetic simulation tools for post-genome wide association studies of complex diseases. Genetic Epidemiology. 39: 11-9. PMID 25371374 DOI: 10.1002/Gepi.21870  1
2014 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, ... ... Liberles DA, et al. Molecular traces of alternative social organization in a termite genome. Nature Communications. 5: 3636. PMID 24845553 DOI: 10.1038/Ncomms4636  1
2014 Konrad A, Lai J, Mutahir Z, Piškur J, Liberles DA. The phylogenetic distribution and evolution of enzymes within the thymidine kinase 2-like gene family in metazoa. Journal of Molecular Evolution. 78: 202-16. PMID 24500774 DOI: 10.1007/S00239-014-9611-6  1
2014 Ma Q, Reeves JH, Liberles DA, Yu L, Chang Z, Zhao J, Cui J, Xu Y, Liu L. A phylogenetic model for understanding the effect of gene duplication on cancer progression. Nucleic Acids Research. 42: 2870-8. PMID 24371277 DOI: 10.1093/nar/gkt1320  1
2014 Kamneva OK, Haft DH, Knight SJ, Liberles DA, Ward NL. Genomics and bioinformatics of the PVC superphylum Planctomycetes: Cell Structure, Origins and Biology. 165-193. DOI: 10.1007/978-1-62703-502-6_7  1
2013 Liberles DA, Teufel AI, Liu L, Stadler T. On the need for mechanistic models in computational genomics and metagenomics. Genome Biology and Evolution. 5: 2008-18. PMID 24115604 DOI: 10.1093/Gbe/Evt151  1
2013 Anisimova M, Liberles DA, Philippe H, Provan J, Pupko T, von Haeseler A. State-of the art methodologies dictate new standards for phylogenetic analysis. Bmc Evolutionary Biology. 13: 161. PMID 23914788 DOI: 10.1186/1471-2148-13-161  1
2012 Kamneva OK, Knight SJ, Liberles DA, Ward NL. Analysis of genome content evolution in pvc bacterial super-phylum: assessment of candidate genes associated with cellular organization and lifestyle. Genome Biology and Evolution. 4: 1375-90. PMID 23221607 DOI: 10.1093/Gbe/Evs113  1
2012 Lawson CB, Niino T, Hermansen RA, Brok-Volchanskaya V, Jackson MF, Garikipati DK, Liberles DA, Rodgers BD. The salmonid myostatin gene family: a novel model for investigating mechanisms that influence duplicate gene fate. Bmc Evolutionary Biology. 12: 202. PMID 23043301 DOI: 10.1186/1471-2148-12-202  1
2012 Konrad A, Piškur J, Liberles DA. The evolution of catalytic residues and enzyme mechanism within the bacterial nucleoside phosphorylase superfamily 1. Gene. 510: 154-61. PMID 22967797 DOI: 10.1016/J.Gene.2012.08.046  1
2012 Lai J, Jin J, Kubelka J, Liberles DA. A phylogenetic analysis of normal modes evolution in enzymes and its relationship to enzyme function. Journal of Molecular Biology. 422: 442-59. PMID 22651983 DOI: 10.1016/J.Bpj.2011.11.2468  1
2012 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, et al. The interface of protein structure, protein biophysics, and molecular evolution. Protein Science : a Publication of the Protein Society. 21: 769-85. PMID 22528593 DOI: 10.1002/Pro.2071  1
2012 Tinta T, Christiansen LS, Konrad A, Liberles DA, Turk V, Munch-Petersen B, Piškur J, Clausen AR. Deoxyribonucleoside kinases in two aquatic bacteria with high specificity for thymidine and deoxyadenosine. Fems Microbiology Letters. 331: 120-7. PMID 22462611 DOI: 10.1111/J.1574-6968.2012.02565.X  1
2012 Konrad A, Yarunova E, Tinta T, Piškur J, Liberles DA. The global distribution and evolution of deoxyribonucleoside kinases in bacteria. Gene. 492: 117-20. PMID 22057012 DOI: 10.1016/J.Gene.2011.10.039  1
2012 Grahnen JA, Liberles DA. CASS: Protein sequence simulation with explicit genotype-phenotype mapping Trends in Evolutionary Biology. 4: 47-49. DOI: 10.4081/Eb.2012.E9  1
2012 Anisimova M, Liberles DA. Detecting and understanding natural selection Codon Evolution: Mechanisms and Models. DOI: 10.1093/acprof:osobl/9780199601165.003.0006  1
2011 Siltberg-Liberles J, Grahnen JA, Liberles DA. The evolution of protein structures and structural ensembles under functional constraint. Genes. 2: 748-62. PMID 24710290 DOI: 10.3390/Genes2040748  1
2011 Grahnen JA, Nandakumar P, Kubelka J, Liberles DA. Biophysical and structural considerations for protein sequence evolution. Bmc Evolutionary Biology. 11: 361. PMID 22171550 DOI: 10.1186/1471-2148-11-361  1
2011 Konrad A, Teufel AI, Grahnen JA, Liberles DA. Toward a general model for the evolutionary dynamics of gene duplicates. Genome Biology and Evolution. 3: 1197-209. PMID 21920903 DOI: 10.1093/Gbe/Evr093  1
2011 Grahnen JA, Kubelka J, Liberles DA. 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. PMID 21800121 DOI: 10.1007/S00239-011-9454-3  1
2011 Liberles DA, Tisdell MD, Grahnen JA. Binding constraints on the evolution of enzymes and signalling proteins: the important role of negative pleiotropy. Proceedings. Biological Sciences / the Royal Society. 278: 1930-5. PMID 21490020 DOI: 10.1098/Rspb.2010.2637  1
2011 Eulenstein O, Huzurbazar S, Liberles DA. Reconciling Phylogenetic Trees Evolution After Gene Duplication. 185-206. DOI: 10.1002/9780470619902.ch10  1
2011 Liberles DA, Kolesov G, Dittmar K. Understanding Gene Duplication Through Biochemistry and Population Genetics Evolution After Gene Duplication. 1-21. DOI: 10.1002/9780470619902.ch1  1
2011 Liberles D, Dittmar K. Preface Evolution After Gene Duplication. xi. DOI: 10.1002/9780470619902  1
2010 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, ... ... Liberles DA, et al. Plasticity of animal genome architecture unmasked by rapid evolution of a pelagic tunicate. Science (New York, N.Y.). 330: 1381-5. PMID 21097902 DOI: 10.1126/Science.1194167  1
2010 Kamneva OK, Liberles DA, Ward NL. Genome-wide influence of indel Substitutions on evolution of bacteria of the PVC superphylum, revealed using a novel computational method. Genome Biology and Evolution. 2: 870-86. PMID 21048002 DOI: 10.1093/Gbe/Evq071  1
2010 Huzurbazar S, Kolesov G, Massey SE, Harris KC, Churbanov A, Liberles DA. Lineage-specific differences in the amino acid substitution process. Journal of Molecular Biology. 396: 1410-21. PMID 20004669 DOI: 10.1016/J.Jmb.2009.11.075  1
2010 Anisimova M, Cannarozzi GM, Liberles DA. Finding the balance between the mathematical and biological optima in multiple sequence alignment Trends in Evolutionary Biology. 2: 39-48. DOI: 10.4081/Eb.2010.E7  1
2009 Muthusamy N, Ahmed SA, Rana BK, Navarre S, Kozlowski DJ, Liberles DA, Bergson C. Phylogenetic analysis of the NEEP21/calcyon/P19 family of endocytic proteins: evidence for functional evolution in the vertebrate CNS. Journal of Molecular Evolution. 69: 319-32. PMID 19760447 DOI: 10.1007/S00239-009-9273-Y  1
2009 Liberles SD, Horowitz LF, Kuang D, Contos JJ, Wilson KL, Siltberg-Liberles J, Liberles DA, Buck LB. Formyl peptide receptors are candidate chemosensory receptors in the vomeronasal organ. Proceedings of the National Academy of Sciences of the United States of America. 106: 9842-7. PMID 19497865 DOI: 10.1073/Pnas.0904464106  1
2009 Tellgren-Roth A, Dittmar K, Massey SE, Kemi C, Tellgren-Roth C, Savolainen P, Lyons LA, Liberles DA. Keeping the blood flowing-plasminogen activator genes and feeding behavior in vampire bats. Die Naturwissenschaften. 96: 39-47. PMID 18791694 DOI: 10.1007/S00114-008-0446-0  1
2008 Liberles DA, Dittmar K. Characterizing gene family evolution. Biological Procedures Online. 10: 66-73. PMID 19461954 DOI: 10.1251/Bpo144  1
2008 Hughes T, Liberles DA. Whole-genome duplications in the ancestral vertebrate are detectable in the distribution of gene family sizes of tetrapod species. Journal of Molecular Evolution. 67: 343-57. PMID 18815825 DOI: 10.1007/S00239-008-9145-X  1
2008 Liberles DA. Gene duplication: red queens, linkage, redundancy and synfunctionalization. Heredity. 101: 299-300. PMID 18698335 DOI: 10.1038/hdy.2008.81  1
2008 Massey SE, Churbanov A, Rastogi S, Liberles DA. Characterizing positive and negative selection and their phylogenetic effects. Gene. 418: 22-6. PMID 18486364 DOI: 10.1016/J.Gene.2008.03.017  1
2008 Hughes T, Liberles DA. The power-law distribution of gene family size is driven by the pseudogenisation rate's heterogeneity between gene families. Gene. 414: 85-94. PMID 18378100 DOI: 10.1016/J.Gene.2008.02.014  1
2008 Tellgren-Roth A, Kolesov G, Sifuentes-Rincón AM, Liberles DA. Complex microsatellite dynamics in the myostatin gene within ruminants. Journal of Molecular Evolution. 66: 258-65. PMID 18320259 DOI: 10.1007/S00239-008-9080-X  1
2008 Liberles DA. Conclusion and a way forward Ancestral Sequence Reconstruction. DOI: 10.1093/acprof:oso/9780199299188.003.0020  1
2008 Pupko T, Doron-Faigenboim A, Liberles DA, Cannarozzi GM. Probabilistic models and their impact on the accuracy of reconstructed ancestral protein sequences Ancestral Sequence Reconstruction. DOI: 10.1093/acprof:oso/9780199299188.003.0004  1
2008 Kodra JT, Skovgaard M, Madsen D, Liberles DA. Linking sequence to function in drug design with ancestral sequence reconstruction Ancestral Sequence Reconstruction. DOI: 10.1093/acprof:oso/9780199299188.003.0003  1
2008 Liberles DA. Foreword and introduction Ancestral Sequence Reconstruction. DOI: 10.1093/acprof:oso/9780199299188.002.0005  1
2008 Liberles DA. Ancestral Sequence Reconstruction Ancestral Sequence Reconstruction. 1-272. DOI: 10.1093/acprof:oso/9780199299188.001.0001  1
2007 Hughes T, Liberles DA. The pattern of evolution of smaller-scale gene duplicates in mammalian genomes is more consistent with neo- than subfunctionalisation. Journal of Molecular Evolution. 65: 574-88. PMID 17957399 DOI: 10.1007/S00239-007-9041-9  1
2007 Anisimova M, Liberles DA. The quest for natural selection in the age of comparative genomics. Heredity. 99: 567-79. PMID 17848974 DOI: 10.1038/Sj.Hdy.6801052  1
2007 Hughes T, Ekman D, Ardawatia H, Elofsson A, Liberles DA. Evaluating dosage compensation as a cause of duplicate gene retention in Paramecium tetraurelia. Genome Biology. 8: 213. PMID 17521457 DOI: 10.1186/Gb-2007-8-5-213  1
2007 Ardawatia H, Liberles DA. A systematic analysis of lineage-specific evolution in metabolic pathways. Gene. 387: 67-74. PMID 17034962 DOI: 10.1016/J.Gene.2006.08.013  1
2007 Roth C, Rastogi S, Arvestad L, Dittmar K, Light S, Ekman D, Liberles DA. Evolution after gene duplication: models, mechanisms, sequences, systems, and organisms. Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution. 308: 58-73. PMID 16838295 DOI: 10.1002/Jez.B.21124  1
2007 Liberles DA. Using phylogeny to understand genomic evolution Parsimony, Phylogeny, and Genomics. DOI: 10.1093/acprof:oso/9780199297306.003.0010  1
2006 Skovgaard M, Kodra JT, Gram DX, Knudsen SM, Madsen D, Liberles DA. Using evolutionary information and ancestral sequences to understand the sequence-function relationship in GLP-1 agonists. Journal of Molecular Biology. 363: 977-88. PMID 16989858 DOI: 10.1016/J.Jmb.2006.08.066  1
2006 Rastogi S, Reuter N, Liberles DA. Evaluation of models for the evolution of protein sequences and functions under structural constraint. Biophysical Chemistry. 124: 134-44. PMID 16837122 DOI: 10.1016/J.Bpc.2006.06.008  1
2006 Berglund-Sonnhammer AC, Steffansson P, Betts MJ, Liberles DA. Optimal gene trees from sequences and species trees using a soft interpretation of parsimony. Journal of Molecular Evolution. 63: 240-50. PMID 16830091 DOI: 10.1007/S00239-005-0096-1  1
2006 Roth C, Liberles DA. A systematic search for positive selection in higher plants (Embryophytes). Bmc Plant Biology. 6: 12. PMID 16784532 DOI: 10.1186/1471-2229-6-12  1
2006 Arnesen T, Betts MJ, Pendino F, Liberles DA, Anderson D, Caro J, Kong X, Varhaug JE, Lillehaug JR. Characterization of hARD2, a processed hARD1 gene duplicate, encoding a human protein N-alpha-acetyltransferase. Bmc Biochemistry. 7: 13. PMID 16638120 DOI: 10.1186/1471-2091-7-13  1
2006 Li T, Chamberlin SG, Caraco MD, Liberles DA, Gaucher EA, Benner SA. Analysis of transitions at two-fold redundant sites in mammalian genomes. Transition redundant approach-to-equilibrium (TREx) distance metrics. Bmc Evolutionary Biology. 6: 25. PMID 16545144 DOI: 10.1186/1471-2148-6-25  1
2005 Liberles DA. Datasets for evolutionary comparative genomics. Genome Biology. 6: 117. PMID 16086856 DOI: 10.1186/Gb-2005-6-8-117  1
2005 Rossnes R, Eidhammer I, Liberles DA. Phylogenetic reconstruction of ancestral character states for gene expression and mRNA splicing data. Bmc Bioinformatics. 6: 127. PMID 15921519 DOI: 10.1186/1471-2105-6-127  1
2005 Berglund AC, Wallner B, Elofsson A, Liberles DA. Tertiary windowing to detect positive diversifying selection. Journal of Molecular Evolution. 60: 499-504. PMID 15883884 DOI: 10.1007/S00239-004-0223-4  1
2005 Rastogi S, Liberles DA. Subfunctionalization of duplicated genes as a transition state to neofunctionalization. Bmc Evolutionary Biology. 5: 28. PMID 15831095 DOI: 10.1186/1471-2148-5-28  1
2005 Bhushan S, Ståhl A, Nilsson S, Lefebvre B, Seki M, Roth C, McWilliam D, Wright SJ, Liberles DA, Shinozaki K, Bruce BD, Boutry M, Glaser E. Catalysis, subcellular localization, expression and evolution of the targeting peptides degrading protease, AtPreP2. Plant & Cell Physiology. 46: 985-96. PMID 15827031 DOI: 10.1093/Pcp/Pci107  1
2005 Bellinge RH, Liberles DA, Iaschi SP, O'brien PA, Tay GK. Myostatin and its implications on animal breeding: a review. Animal Genetics. 36: 1-6. PMID 15670124 DOI: 10.1111/J.1365-2052.2004.01229.X  1
2005 Roth C, Betts MJ, Steffansson P, Saelensminde G, Liberles DA. The Adaptive Evolution Database (TAED): a phylogeny based tool for comparative genomics. Nucleic Acids Research. 33: D495-7. PMID 15608245 DOI: 10.1093/Nar/Gki090  1
2004 Tellgren A, Berglund AC, Savolainen P, Janis CM, Liberles DA. Myostatin rapid sequence evolution in ruminants predates domestication. Molecular Phylogenetics and Evolution. 33: 782-90. PMID 15522803 DOI: 10.1016/J.Ympev.2004.07.004  1
2004 Braun FN, Liberles DA. Repeat-modulated population genetic effects in fungal proteins. Journal of Molecular Evolution. 59: 97-102. PMID 15383912 DOI: 10.1007/S00239-004-2608-9  1
2004 Gaucher EA, Graddy LG, Li T, Simmen RC, Simmen FA, Schreiber DR, Liberles DA, Janis CM, Benner SA. The planetary biology of cytochrome P450 aromatases. Bmc Biology. 2: 19. PMID 15315709 DOI: 10.1186/1741-7007-2-19  1
2004 Hughes T, Hyun Y, Liberles DA. Visualising very large phylogenetic trees in three dimensional hyperbolic space. Bmc Bioinformatics. 5: 48. PMID 15117420 DOI: 10.1186/1471-2105-5-48  1
2003 Braun FN, Liberles DA. Retention of enzyme gene duplicates by subfunctionalization. International Journal of Biological Macromolecules. 33: 19-22. PMID 14599579 DOI: 10.1016/S0141-8130(03)00059-X  1
2003 Mazet F, Yu JK, Liberles DA, Holland LZ, Shimeld SM. Phylogenetic relationships of the Fox (Forkhead) gene family in the Bilateria. Gene. 316: 79-89. PMID 14563554 DOI: 10.1016/S0378-1119(03)00741-8  1
2002 Zhao Y, Kacskovics I, Pan Q, Liberles DA, Geli J, Davis SK, Rabbani H, Hammarstrom L. Artiodactyl IgD: the missing link. Journal of Immunology (Baltimore, Md. : 1950). 169: 4408-16. PMID 12370374 DOI: 10.4049/Jimmunol.169.8.4408  1
2002 Milchert LE, Liberles DA, Elofsson A. The salmon genome (and other issues in bioinformatics). Genome Biology. 3: REPORTS4022. PMID 12184805 DOI: 10.1186/Gb-2002-3-7-Reports4022  1
2002 Liberles DA, Wayne ML. Tracking adaptive evolutionary events in genomic sequences. Genome Biology. 3: REVIEWS1018. PMID 12093382 DOI: 10.1186/Gb-2002-3-6-Reviews1018  1
2002 Davids W, Gamieldien J, Liberles DA, Hide W. Positive selection scanning reveals decoupling of enzymatic activities of carbamoyl phosphate synthetase in Helicobacter pylori. Journal of Molecular Evolution. 54: 458-64. PMID 11956684 DOI: 10.1007/S00239-001-0029-6  1
2002 Peltier JB, Emanuelsson O, Kalume DE, Ytterberg J, Friso G, Rudella A, Liberles DA, Söderberg L, Roepstorff P, von Heijne G, van Wijk KJ. Central functions of the lumenal and peripheral thylakoid proteome of Arabidopsis determined by experimentation and genome-wide prediction. The Plant Cell. 14: 211-36. PMID 11826309 DOI: 10.1105/Tpc.010304  1
2002 Liberles DA, Thorén A, von Heijne G, Elofsson A. The use of phylogenetic profiles for gene predictions Current Genomics. 3: 131-137. DOI: 10.2174/1389202023350499  1
2002 Liberles DA, Thorén A, von Heijne G, Elofsson A. The use of phylogenetic profiles for gene predictions Current Genomics. 3: 131-137. DOI: 10.2174/1389202023350499  0.32
2002 Liberles DA. SNPing variation from genomes Genome Biology. 3: 4001.1-4001.4. DOI: 10.1186/Gb-2001-3-1-Reports4001  1
2002 Siltberg J, Liberles DA. A simple covarion-based approach to analyse nucleotide substitution rates Journal of Evolutionary Biology. 15: 588-594. DOI: 10.1046/j.1420-9101.2002.00416.x  1
2001 Liberles DA. Evolution enters the genomic era. Genome Biology. 2: REPORTS4026. PMID 11737940 DOI: 10.1186/Gb-2001-2-11-Reports4026  1
2001 Liberles DA. Evaluation of methods for determination of a reconstructed history of gene sequence evolution. Molecular Biology and Evolution. 18: 2040-7. PMID 11606700 DOI: 10.1093/Oxfordjournals.Molbev.A003745  1
2001 Liberles DA, Schreiber DR, Govindarajan S, Chamberlin SG, Benner SA. The adaptive evolution database (TAED). Genome Biology. 2: RESEARCH0028. PMID 11532212 DOI: 10.1186/Gb-2001-2-8-Research0028  1
2001 Liberles DA, Schreiber DR, Govindarajan S, Chamberlin SG, Benner SA. The Adaptive Evolution Database (TAED). Genome Biology. 2: PREPRINT0003. PMID 11305934  1
2001 Peltier JB, Ytterberg J, Liberles DA, Roepstorff P, van Wijk KJ. Identification of a 350-kDa ClpP protease complex with 10 different Clp isoforms in chloroplasts of Arabidopsis thaliana. The Journal of Biological Chemistry. 276: 16318-27. PMID 11278690 DOI: 10.1074/Jbc.M010503200  1
2000 Peltier MR, Raley LC, Liberles DA, Benner SA, Hansen PJ. Evolutionary history of the uterine serpins. The Journal of Experimental Zoology. 288: 165-74. PMID 10931499 DOI: 10.1002/1097-010X(20000815)288:2<165::Aid-Jez7>3.0.Co;2-R  1
2000 Benner SA, Chamberlin SG, Liberles DA, Govindarajan S, Knecht L. Functional inferences from reconstructed evolutionary biology involving rectified databases--an evolutionarily grounded approach to functional genomics. Research in Microbiology. 151: 97-106. PMID 10865954 DOI: 10.1016/S0923-2508(00)00123-6  1
1997 Polaczek P, Kwan K, Liberles DA, Campbell JL. Role of architectural elements in combinatorial regulation of initiation of DNA replication in Escherichia coli Molecular Microbiology. 26: 261-275. PMID 9383152 DOI: 10.1046/J.1365-2958.1997.5701931.X  1
1997 Lehmann TE, Greenberg WA, Liberies DA, Wada CK, Dervan PB. Triple-helix formation by pyrimidine oligonucleotide containing nonnatural nucleosides with extended aromatic nucleobases: Intercalation from the major groove as a method for recognizing C·G and T·A base pairs Helvetica Chimica Acta. 80: 2002-2022. DOI: 10.1002/Hlca.19970800618  0.36
1996 Liberles DA, Dervan PB. Design of artificial sequence-specific DNA bending ligands. Proceedings of the National Academy of Sciences of the United States of America. 93: 9510-4. PMID 8790361 DOI: 10.1073/Pnas.93.18.9510  1
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