D. Liberles

发表

Functional inferences from reconstructed evolutionary biology involving rectified databases--an evolutionarily grounded approach to functional genomics.

S. Benner, S. Govindarajan, S. G. Chamberlin, 2000, Research in microbiology.

1 Understanding Gene Duplication Through Biochemistry and Population Genetics

D. Liberles, G. Kolesov, K. Dittmar, 2011 .

Detecting and understanding natural selection

D. Liberles, M. Anisimova, 2011 .

A generalized birth and death process for modeling the fates of gene duplication

Ashley I. Teufel, Jing Zhao, D. Liberles, 2015, BMC Evolutionary Biology.

Lineage-specific differences in the amino acid substitution process.

D. Liberles, G. Kolesov, S. Massey, 2010, Journal of molecular biology.

Subfunctionalization of duplicated genes as a transition state to neofunctionalization

D. Liberles, S. Rastogi, 2005, BMC Evolutionary Biology.

Evolution in the light of fitness landscape theory.

D. Liberles, C. Bank, I. Fragata, 2019, Trends in ecology & evolution.

Evolution after gene duplication

D. Liberles, K. Dittmar, 2010 .

A phylogenetic analysis of normal modes evolution in enzymes and its relationship to enzyme function.

D. Liberles, J. Kubelka, J. Lai, 2012, Journal of molecular biology.

The interface of protein structure, protein biophysics, and molecular evolution

Lucy J. Colwell, Johan A. Grahnen, Nimrod D. Rubinstein, 2012, Protein science : a publication of the Protein Society.

Ancestral sequence reconstruction

D. Liberles, 2007 .

The Atlantic salmon genome provides insights into rediploidization

Steven J. M. Jones, James A. Yorke, Torgeir R. Hvidsten, 2016, Nature.

Characterizing selective pressures on the pathway for de novo biosynthesis of pyrimidines in yeast

R. Gutenkunst, D. Liberles, B. Mannakee, 2015, BMC Evolutionary Biology.

Finding the balance between the mathematical and biological optima in multiple sequence alignment

Gina Cannarozzi, Maria Anisimova, David A. Liberles, 2010 .

Emerging Frontiers in the Study of Molecular Evolution

M. Meyer, D. Liberles, D. Posada, 2020, Journal of Molecular Evolution.

Genome-Wide Influence of Indel Substitutions on Evolution of Bacteria of the PVC Superphylum, Revealed Using a Novel Computational Method

Olga K. Kamneva, N. Ward, D. Liberles, 2010, Genome biology and evolution.

A systematic analysis of lineage-specific evolution in metabolic pathways.

D. Liberles, Himanshu Ardawatia, 2007, Gene.

The quest for natural selection in the age of comparative genomics

D. Liberles, M. Anisimova, D A Liberles, 2007, Heredity.

Optimal Gene Trees from Sequences and Species Trees Using a Soft Interpretation of Parsimony

Matthew J. Betts, David A. Liberles, Pär Steffansson, 2006, Journal of Molecular Evolution.

The power-law distribution of gene family size is driven by the pseudogenisation rate's heterogeneity between gene families.

David A. Liberles, D. Liberles, T. Hughes, 2008, Gene.

Reconciling Phylogenetic Trees

Oliver Eulenstein, Snehalata Huzurbazar, David A. Liberles, 2011 .

Toward a General Model for the Evolutionary Dynamics of Gene Duplicates

Johan A. Grahnen, David A. Liberles, Ashley I. Teufel, 2011, Genome biology and evolution.

Analysis of Genome Content Evolution in PVC Bacterial Super-Phylum: Assessment of Candidate Genes Associated with Cellular Organization and Lifestyle

Olga K. Kamneva, David A. Liberles, N. Ward, 2012, Genome biology and evolution.

The Adaptive Evolution Database (TAED)

David A Liberles, Steven A Benner, S. Benner, 2001, Genome Biology.

Fast Side Chain Replacement in Proteins Using a Coarse-Grained Approach for Evaluating the Effects of Mutation During Evolution

Johan A. Grahnen, D. Liberles, J. Kubelka, 2011, Journal of Molecular Evolution.

Catalysis, subcellular localization, expression and evolution of the targeting peptides degrading protease, AtPreP2.

K. Shinozaki, D. Liberles, M. Seki, 2005, Plant & cell physiology.

The Adaptive Evolution Database (TAED): a phylogeny based tool for comparative genomics

Matthew J. Betts, Christian Roth, Gisle Sælensminde, 2004, Nucleic Acids Res..

Characterizing lineage-specific evolution and the processes driving genomic diversification in chordates

D. Liberles, S. D. Shank, David E. Northover, 2020, BMC Evolutionary Biology.

The Adaptive Evolution Database (TAED): A New Release of a Database of Phylogenetically Indexed Gene Families from Chordates

Katharine L Korunes, D. Liberles, Russell A. Hermansen, 2017, Journal of Molecular Evolution.

Extracting functional trends from whole genome duplication events using comparative genomics

D. Liberles, T. R. Hvidsten, S. Sandve, 2016, Biological Procedures Online.

Molecular Characterization of a isoenzyme of the targeting peptide degrading protease , PreP 2-catalysis , subcellular localization , expression and evolution

K. Shinozaki, D. Liberles, M. Seki, 2015 .

Binding constraints on the evolution of enzymes and signalling proteins: the important role of negative pleiotropy

Johan A. Grahnen, D. Liberles, Makayla D M Tisdell, 2011, Proceedings of the Royal Society B: Biological Sciences.

Whole-Genome Duplications in the Ancestral Vertebrate Are Detectable in the Distribution of Gene Family Sizes of Tetrapod Species

D. Liberles, T. Hughes, 2008, Journal of Molecular Evolution.

A systematic search for positive selection in higher plants (Embryophytes)

D. Liberles, C. Roth, 2006, BMC Plant Biology.

Characterization of hARD2, a processed hARD1 gene duplicate, encoding a human protein N-α-acetyltransferase

D. Liberles, J. Lillehaug, T. Arnesen, 2006, BMC Biochemistry.

Analysis of transitions at two-fold redundant sites in mammalian genomes. Transition redundant approach-to-equilibrium (TREx) distance metrics

S. Benner, S. G. Chamberlin, D. Liberles, 2006, BMC Evolutionary Biology.

A phylogenetic model for understanding the effect of gene duplication on cancer progression

Jing Zhao, J. Reeves, D. Liberles, 2013, Nucleic acids research.

Flux Control in Glycolysis Varies Across the Tree of Life

D. Liberles, Russell A. Hermansen, A. Orlenko, 2016, Journal of Molecular Evolution.

Protein evolution depends on multiple distinct population size parameters

Alexander Platt, D. Liberles, Claudia C. Weber, 2017, bioRxiv.

ProtASR: An Evolutionary Framework for Ancestral Protein Reconstruction with Selection on Folding Stability.

U. Bastolla, D. Liberles, M. Arenas, 2017, Systematic biology.

Repeat-Modulated Population Genetic Effects in Fungal Proteins

F. N. Braun, D. Liberles, 2004, Journal of Molecular Evolution.

Evaluating dosage compensation as a cause of duplicate gene retention in Paramecium tetraurelia

Arne Elofsson, David A Liberles, Timothy Hughes, 2007, Genome Biology.

Models for gene duplication when dosage balance works as a transition state to subsequent neo-or sub-functionalization

Ashley I. Teufel, D. Liberles, Liang Liu, 2016, BMC Evolutionary Biology.

Towards a general model for the evolutionary dynamics of gene duplicates Research Article

Johan A. Grahnen, Ashley I. Teufel, D. Liberles, 2011 .

Phylogenetic Analysis of the NEEP21/Calcyon/P19 Family of Endocytic Proteins: Evidence for Functional Evolution in the Vertebrate CNS

D. Liberles, C. Bergson, B. Rana, 2009, Journal of Molecular Evolution.

Level-dependent QBD models for the evolution of a family of gene duplicates

D. Liberles, B. Holland, M. O’Reilly, 2020, Stochastic Models.

What Fraction of Duplicates Observed in Recently Sequenced Genomes Is Segregating and Destined to Fail to Fix?

Ashley I. Teufel, J. Masel, D. Liberles, 2015, Genome biology and evolution.

Identification of a 350-kDa ClpP Protease Complex with 10 Different Clp Isoforms in Chloroplasts of Arabidopsis thaliana *

K. V. van Wijk, D. Liberles, P. Roepstorff, 2001, The Journal of Biological Chemistry.

Reading the Story in DNA: A Beginner's Guide to Molecular Evolution

D. Liberles, 2009 .

Detecting Signatures of Positive Selection against a Backdrop of Compensatory Processes.

D. Liberles, Peter B. Chi, Westin M. Kosater, 2020, Molecular biology and evolution.

The salmonid myostatin gene family: a novel model for investigating mechanisms that influence duplicate gene fate

D. Liberles, Melissa F. Jackson, Russell A. Hermansen, 2012, BMC Evolutionary Biology.

Genomics and Bioinformatics of the PVC Superphylum

Olga K. Kamneva, D. Haft, N. Ward, 2013 .

The Use of Phylogenetic Profiles for Gene Predictions

Arne Elofsson, Gunnar von Heijne, David A. Liberles, 2002 .

Characterizing the roles of changing population size and selection on the evolution of flux control in metabolic pathways

D. Liberles, Peter B. Chi, A. Orlenko, 2017, BMC Evolutionary Biology.

Analysis of a mechanistic Markov model for gene duplicates evolving under subfunctionalization

D. Liberles, B. Holland, M. O’Reilly, 2017, BMC Evolutionary Biology.

Characterizing gene family evolution

D. Liberles, K. Dittmar, 2008, Biological Procedures Online.

Evolution after Gene Duplication: Dittmar/Evolution After Gene Duplication

D. Liberles, K. Dittmar, 2010 .

Protocols for the Molecular Evolutionary Analysis of Membrane Protein Gene Duplicates.

D. Liberles, Liang Liu, L. Dávalos, 2018, Methods in molecular biology.

Modeling Proteins at the Interface of Structure, Evolution, and Population Genetics

Johan A. Grahnen, Ashley I. Teufel, D. Liberles, 2012 .

Detecting Selection on Segregating Gene Duplicates in a Population

D. Liberles, R. Kaufman, Peter B. Chi, 2020, Journal of Molecular Evolution.

WGDTree: a phylogenetic software tool to examine conditional probabilities of retention following whole genome duplication events

D. Liberles, Amanda E. Wilson, C. N. Henry, 2022, BMC Bioinformatics.

The Phylogenetic Distribution and Evolution of Enzymes Within the Thymidine Kinase 2-like Gene Family in Metazoa

D. Liberles, J. Piškur, J. Lai, 2014, Journal of Molecular Evolution.

A New Editorial Beginning at Journal of Molecular Evolution

D. Liberles, 2019, Journal of Molecular Evolution.

Central Functions of the Lumenal and Peripheral Thylakoid Proteome of Arabidopsis Determined by Experimentation and Genome-Wide Prediction Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.010304.

Peter Roepstorff, David A. Liberles, Gunnar von Heijne, 2002, The Plant Cell Online.

Triple-Helix Formation by Pyrimidine Oligonucleotides Containing Nonnatural Nucleosides with Extended Aromatic Nucleobases: Intercalation from the major groove as a method for recognizing C·G and T·A base pairs

D. Liberles, P. Dervan, C. K. Wada, 1997 .

Selection on metabolic pathway function in the presence of mutation-selection-drift balance leads to rate-limiting steps that are not evolutionarily stable

Ashley I. Teufel, D. Liberles, Peter B. Chi, 2016, Biology Direct.

Flux Control in Glycolysis Varies Across the Tree of Life

D. Liberles, Russell A. Hermansen, A. Orlenko, 2016, Journal of Molecular Evolution.

The planetary biology of cytochrome P450 aromatases

S. Benner, D. Liberles, E. Gaucher, 2004, BMC Biology.

Formyl peptide receptors are candidate chemosensory receptors in the vomeronasal organ

S. Liberles, D. Liberles, L. Buck, 2009, Proceedings of the National Academy of Sciences.

Design of artificial sequence-specific DNA bending ligands.

D. Liberles, P. Dervan, D A Liberles, 1996, Proceedings of the National Academy of Sciences of the United States of America.

The evolution of catalytic residues and enzyme mechanism within the bacterial nucleoside phosphorylase superfamily 1.

D. Liberles, J. Piškur, A. Konrad, 2012, Gene.

Characterizing selective pressures on the pathway for de novo biosynthesis of pyrimidines in yeast

R. Gutenkunst, D. Liberles, B. Mannakee, 2015, BMC Evolutionary Biology.

Deoxyribonucleoside kinases in two aquatic bacteria with high specificity for thymidine and deoxyadenosine.

D. Liberles, J. Piškur, V. Turk, 2012, FEMS microbiology letters.

The global distribution and evolution of deoxyribonucleoside kinases in bacteria.

D. Liberles, J. Piškur, T. Tinta, 2012, Gene.

Evolution after gene duplication: models, mechanisms, sequences, systems, and organisms.

Lars Arvestad, Katharina Dittmar, Sara Light, 2007, Journal of experimental zoology. Part B, Molecular and developmental evolution.

Inferring the number and position of changes in selective regime in a non-equilibrium mutation-selection framework

D. Liberles, Andrew M. Ritchie, Tristan L. Stark, 2021, BMC Ecology and Evolution.

Protein evolution depends on multiple distinct population size parameters

Alexander Platt, D. Liberles, Claudia C. Weber, 2017, BMC Evolutionary Biology.

Plasticity of Animal Genome Architecture Unmasked by Rapid Evolution of a Pelagic Tunicate

Frédéric Delsuc, Boris Lenhard, Hans Lehrach, 2010, Science.

Molecular traces of alternative social organization in a termite genome

Jun Wang, W. Gronenberg, E. Bornberg-Bauer, 2014, Nature Communications.

Positive Selection Scanning Reveals Decoupling of Enzymatic Activities of Carbamoyl Phosphate Synthetase in Helicobacter pylori

Winston A Hide, D. Liberles, J. Gamieldien, 2002, Journal of Molecular Evolution.

Phylogenetic relationships of the Fox (Forkhead) gene family in the Bilateria.

D. Liberles, L. Holland, Jr-Kai Yu, 2003, Gene.

Evolutionary history of the uterine serpins.

S. Benner, D. Liberles, P. Hansen, 2000, The Journal of experimental zoology.

Characterizing Amino Acid Substitution with Complete Linkage of Sites on a Lineage

D. Liberles, Tristan L. Stark, 2021, Genome biology and evolution.

Tracking adaptive evolutionary events in genomic sequences

D. Liberles, M. Wayne, 2002, Genome Biology.

Myostatin and its implications on animal breeding: a review.

D. Liberles, G. Tay, S. Iaschi, 2005, Animal genetics.

Complex Microsatellite Dynamics in the Myostatin Gene Within Ruminants

D. Liberles, G. Kolesov, A. M. Sifuentes-Rincón, 2008, Journal of Molecular Evolution.

Myostatin rapid sequence evolution in ruminants predates domestication.

D. Liberles, P. Savolainen, C. Janis, 2004, Molecular phylogenetics and evolution.

A simple covarion‐based approach to analyse nucleotide substitution rates

D. Liberles, J. Siltberg, J. Siltberg, 2002 .

The Adaptive Evolution Database (TAED)

David A Liberles, Steven A Benner, S. Benner, 2001, Genome Biology.

MYOSTATIN AND ITS IMPLICATIONS ON ANIMAL BREEDING

D. Liberles, S. Laschi, R. Belling, 2005 .

Genetic Simulation Tools for Post‐Genome Wide Association Studies of Complex Diseases

Bo Peng, Vineet Bafna, Chun Li, 2015, Genetic epidemiology.

Biophysical and structural considerations for protein sequence evolution

Johan A. Grahnen, Jan Kubelka, David A Liberles, 2011, BMC Evolutionary Biology.

A new parameter‐rich structure‐aware mechanistic model for amino acid substitution during evolution

Claudia C Weber, Peter B Chi, Dohyup Kim, 2018, Proteins.

Selection on metabolic pathway function in the presence of mutation-selection-drift balance leads to rate-limiting steps that are not evolutionarily stable

Ashley I. Teufel, D. Liberles, Peter B. Chi, 2016, Biology Direct.

Selection on protein structure, interaction, and sequence

Peter B Chi, David A Liberles, D. Liberles, 2016, Protein science : a publication of the Protein Society.

The Pattern of Evolution of Smaller-Scale Gene Duplicates in Mammalian Genomes is More Consistent with Neo- than Subfunctionalisation

Timothy Hughes, David A. Liberles, D. Liberles, 2007, Journal of Molecular Evolution.

The Memory Problem for Neutral Mutational Models of Evolution

D. Liberles, 2022, Journal of Molecular Evolution.

Using the Mutation-Selection Framework to Characterize Selection on Protein Sequences

David A Liberles, Claus O Wilke, Ashley I. Teufel, 2018, Genes.

On the Need for Mechanistic Models in Computational Genomics and Metagenomics

Tanja Stadler, Liang Liu, David A. Liberles, 2013, Genome biology and evolution.

The Adaptive Evolution Database (TAED): A New Release of a Database of Phylogenetically Indexed Gene Families from Chordates

Katharine L Korunes, D. Liberles, Russell A. Hermansen, 2017, Journal of Molecular Evolution.

Tertiary Windowing to Detect Positive Diversifying Selection

Arne Elofsson, Björn Wallner, David A. Liberles, 2005, Journal of Molecular Evolution.

On Mechanistic Modeling of Gene Content Evolution: Birth-Death Models and Mechanisms of Gene Birth and Gene Retention

Jing Zhao, Liang Liu, Malgorzata M. O'Reilly, 2014, Comput..

The salmonid myostatin gene family: a novel model for investigating mechanisms that influence duplicate gene fate

D. Liberles, Melissa F. Jackson, Russell A. Hermansen, 2012, BMC Evolutionary Biology.

Evaluation of models for the evolution of protein sequences and functions under structural constraint.

N. Reuter, D. Liberles, S. Rastogi, 2006, Biophysical chemistry.

Ancestral Sequence Reconstruction: From Chemical Paleogenetics to Maximum Likelihood Algorithms and Beyond

D. Liberles, E. Gaucher, Avery G A Selberg, 2021, Journal of Molecular Evolution.

Evaluation of methods for determination of a reconstructed history of gene sequence evolution.

D. Liberles, D A Liberles, 2001, Molecular biology and evolution.

Datasets for evolutionary comparative genomics

David A Liberles, D. Liberles, 2005, Genome Biology.

The Evolution of Protein Structures and Structural Ensembles Under Functional Constraint

Johan A. Grahnen, David A. Liberles, D. Liberles, 2011, Genes.

CASS: Protein sequence simulation with explicit genotype-phenotype mapping

Johan A. Grahnen, David A. Liberles, D. Liberles, 2012 .

Characterizing positive and negative selection and their phylogenetic effects.

Steven E Massey, Shruti Rastogi, David A Liberles, 2008, Gene.

Using evolutionary information and ancestral sequences to understand the sequence-function relationship in GLP-1 agonists.

David A Liberles, Dennis Madsen, Marie Skovgaard, 2006, Journal of molecular biology.

Evolutionary Models

Barbara R. Holland, David A. Liberles, D. Liberles, 2020, Encyclopedia of Bioinformatics and Computational Biology.

Linking sequence to function in drug design with ancestral sequence reconstruction

D. Liberles, M. Skovgaard, D. Madsen, 2007 .

A New Editorial Beginning at Journal of Molecular Evolution

D. Liberles, 2019, Journal of Molecular Evolution.

Exploring the consequences of lack of closure in codon models

D. Liberles, B. Holland, M. Charleston, 2017, 1709.05079.

Keeping the blood flowing—plasminogen activator genes and feeding behavior in vampire bats

D. Liberles, P. Savolainen, S. Massey, 2008, Naturwissenschaften.

Probabilistic models and their impact on the accuracy of reconstructed ancestral protein sequences

T. Pupko, D. Liberles, G. Cannarozzi, 2007 .

Retention of enzyme gene duplicates by subfunctionalization.

F. N. Braun, D. Liberles, 2003, International journal of biological macromolecules.

The Journal of Molecular Evolution Turns 50

D. Liberles, A. Goldman, 2021, Journal of Molecular Evolution.

State-of the art methodologies dictate new standards for phylogenetic analysis

A. von Haeseler, T. Pupko, D. Liberles, 2013, BMC Evolutionary Biology.

Evolutionary Processes and Biophysical Mechanisms: Revisiting Why Evolved Proteins Are Marginally Stable

D. Liberles, Amanda E. Wilson, Westin M. Kosater, 2020, Journal of Molecular Evolution.

Evolution and Structure of Proteins and Proteomes

Ashley I. Teufel, D. Liberles, 2018, Genes.

Role of architectural elements in combinatorial regulation of initiation of DNA replication in Escherichia coli

D. Liberles, P. Polaczek, K. Kwan, 1997, Molecular microbiology.

Artiodactyl IgD: The Missing Link1 2

D. Liberles, Yaofeng Zhao, Lennart Hammarstrom, 2002, The Journal of Immunology.

Gene duplication: Red queens, linkage, redundancy and synfunctionalization

D. Liberles, 2008, Heredity.

A Phylogenetic Analysis of Normal Modes Evolution in Enzymes and its Relationship to Enzyme Function

Jan Kubelka, David A. Liberles, D. Liberles, 2012 .

Protein evolution depends on multiple distinct population size parameters

Alexander Platt, D. Liberles, Claudia C. Weber, 2017, bioRxiv.

Nucleobases in Meteorites to Nucleobases in RNA and DNA?

D. Liberles, K. Rogers, A. Goldman, 2022, Journal of Molecular Evolution.

Characterizing the roles of changing population size and selection on the evolution of flux control in metabolic pathways

D. Liberles, Peter B. Chi, A. Orlenko, 2017, BMC Evolutionary Biology.

Bayesian Analysis of High-Throughput Quantitative Measurement of Protein-DNA Interactions

D. Liberles, D. Pollock, M. Churchill, 2011, PloS one.

2020 Zuckerkandl Prize

D. Liberles, 2021, Journal of Molecular Evolution.

Faculty Opinions recommendation of Somatic evolution and global expansion of an ancient transmissible cancer lineage.

D. Liberles, 2019, Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature.

Dosage balance acts as a time-dependent selective barrier to subfunctionalization

D. Liberles, Amanda E. Wilson, 2023, BMC Ecology and Evolution.

Highly Abundant Proteins Are Highly Thermostable

D. Liberles, David Alvarez-Ponce, Andrew M. Ritchie, 2023, Genome biology and evolution.

Convergent evolution: limited forms most beautiful

D. Liberles, 2012 .

Visualising very large phylogenetic trees in three dimensional hyperbolic space

Young Hyun, Timothy Hughes, David A. Liberles, 2004, BMC Bioinformatics.

A systematic search for positive selection in higher plants (Embryophytes)

D. Liberles, C. Roth, 2006, BMC Plant Biology.

ProtASR: An Evolutionary Framework for Ancestral Protein Reconstruction with Selection on Folding Stability.

U. Bastolla, D. Liberles, M. Arenas, 2017, Systematic biology.

Evaluation of methods for determination of a reconstructed history of gene sequence evolution.

D. Liberles, 2001, Molecular biology and evolution.

Expectations of duplicate gene retention under the gene duplicability hypothesis

D. Liberles, Amanda E. Wilson, 2023, BMC ecology and evolution.

Models for the retention of duplicate genes and their biological underpinnings

D. Liberles, Gavin Conant, Amanda E. Wilson, 2023, F1000Research.

Datasets for evolutionary comparative genomics

D. Liberles, 2005, Genome Biology.

2023 Zuckerkandl Prize.

D. Liberles, Caroline M. Weisman, B. Q. Minh, 2024, Journal of molecular evolution.

PEMPS: a phylogenetic software tool to model the evolution of metabolic pathways

D. Liberles, Nicholas S. McCloskey, Ayna Mammedova, 2024, bioRxiv.

Corrigendum to “A Phylogenetic Analysis of Normal Modes Evolution in Enzymes and Its Relationship to Enzyme Function” [J. Mol. Biol. 422 (2012) 442–459]

D. Liberles, J. Kubelka, J. Lai, 2013 .